Call tree LLVMFuzzerTestOneInput /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=-1 abort linenumber=176 hopen /src/htslib/hfile.c linenumber=180 find_scheme_handler /src/htslib/hfile.c linenumber=1319 isalnum_c /src/htslib/./textutils_internal.h linenumber=1185 __ctype_b_loc linenumber=169 tolower_c /src/htslib/./textutils_internal.h linenumber=1186 tolower linenumber=179 pthread_mutex_lock linenumber=1194 load_hfile_plugins /src/htslib/hfile.c linenumber=1195 kh_init_scheme_string /src/htslib/hfile.c linenumber=1118 calloc linenumber=972 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1122 hts_log /src/htslib/hts.c linenumber=1059 __errno_location linenumber=5192 get_severity_tag /src/htslib/hts.c linenumber=5196 fprintf linenumber=5196 vfprintf linenumber=5199 fprintf linenumber=5202 __errno_location linenumber=5204 try_exe_add_scheme_handler /src/htslib/hfile.c linenumber=1063 hts_log /src/htslib/hts.c linenumber=1064 kh_put_scheme_string /src/htslib/hfile.c linenumber=1068 kh_resize_scheme_string /src/htslib/hfile.c linenumber=972 realloc linenumber=972 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=972 strcmp linenumber=972 __errno_location linenumber=1070 strerror linenumber=1070 hts_log /src/htslib/hts.c linenumber=1070 priority /src/htslib/hfile.c linenumber=1074 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1123 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1124 init_add_plugin /src/htslib/hfile.c linenumber=1125 hts_log /src/htslib/hts.c linenumber=1084 hts_log /src/htslib/hts.c linenumber=1096 hts_log /src/htslib/hts.c linenumber=1101 hfile_plugin_init_mem /src/htslib/hfile.c linenumber=1125 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=926 init_add_plugin /src/htslib/hfile.c linenumber=1126 hfile_plugin_init_crypt4gh_needed /src/htslib/hfile.c linenumber=1126 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=961 init_add_plugin /src/htslib/hfile.c linenumber=1145 hfile_plugin_init_libcurl /src/htslib/hfile_libcurl.c linenumber=1145 hts_version /src/htslib/hts.c linenumber=1692 curl_global_init linenumber=1700 easy_errno /src/htslib/hfile_libcurl.c linenumber=1701 curl_easy_getinfo linenumber=178 curl_easy_getinfo linenumber=192 http_status_errno /src/htslib/hfile_libcurl.c linenumber=193 curl_easy_strerror linenumber=227 hts_log /src/htslib/hts.c linenumber=227 __errno_location linenumber=1701 curl_share_init linenumber=1703 curl_global_cleanup linenumber=1704 __errno_location linenumber=1704 curl_share_setopt linenumber=1705 share_lock /src/htslib/hfile_libcurl.c linenumber=1705 pthread_mutex_lock linenumber=311 curl_share_setopt linenumber=1706 share_unlock /src/htslib/hfile_libcurl.c linenumber=1706 pthread_mutex_unlock linenumber=315 curl_share_setopt linenumber=1707 curl_share_cleanup linenumber=1709 curl_global_cleanup linenumber=1710 __errno_location linenumber=1711 getenv linenumber=1715 strdup linenumber=1716 kh_init_auth_map /src/htslib/hfile_libcurl.c linenumber=1717 calloc linenumber=69 __errno_location linenumber=1719 kh_destroy_auth_map /src/htslib/hfile_libcurl.c linenumber=1721 curl_share_cleanup linenumber=1722 curl_global_cleanup linenumber=1723 __errno_location linenumber=1724 getenv linenumber=1728 strcmp linenumber=1729 getenv linenumber=1735 atoi linenumber=1736 getenv linenumber=1737 atol linenumber=1738 getenv linenumber=1739 atol linenumber=1740 getenv linenumber=1741 atol linenumber=1742 getenv linenumber=1743 atol linenumber=1744 curl_version_info linenumber=1747 ksprintf /src/htslib/kstring.c linenumber=1748 kvsprintf /src/htslib/kstring.c linenumber=182 kputd /src/htslib/kstring.c linenumber=150 kputsn /src/htslib/./htslib/kstring.h linenumber=43 __errno_location linenumber=245 ks_resize /src/htslib/./htslib/kstring.h linenumber=246 realloc linenumber=169 kputsn /src/htslib/./htslib/kstring.h linenumber=46 kputc /src/htslib/./htslib/kstring.h linenumber=52 ks_resize /src/htslib/./htslib/kstring.h linenumber=261 ks_resize /src/htslib/./htslib/kstring.h linenumber=57 snprintf linenumber=60 kputsn /src/htslib/./htslib/kstring.h linenumber=138 vsnprintf linenumber=164 ks_resize /src/htslib/./htslib/kstring.h linenumber=167 vsnprintf linenumber=170 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1754 init_add_plugin /src/htslib/hfile.c linenumber=1148 hfile_plugin_init_gcs /src/htslib/hfile_gcs.c linenumber=1148 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=156 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=157 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=158 init_add_plugin /src/htslib/hfile.c linenumber=1151 hfile_plugin_init_s3 /src/htslib/hfile_s3.c linenumber=1151 hts_version /src/htslib/hts.c linenumber=2453 curl_global_init linenumber=2460 curl_share_init linenumber=2467 curl_global_cleanup linenumber=2470 __errno_location linenumber=2471 curl_share_setopt linenumber=2475 share_lock /src/htslib/hfile_s3.c linenumber=2475 pthread_mutex_lock linenumber=1135 curl_share_setopt linenumber=2476 share_unlock /src/htslib/hfile_s3.c linenumber=2476 pthread_mutex_unlock linenumber=1139 curl_share_setopt linenumber=2477 curl_share_cleanup linenumber=2480 curl_global_cleanup linenumber=2481 __errno_location linenumber=2482 curl_version_info linenumber=2486 ksprintf /src/htslib/kstring.c linenumber=2487 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2492 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2493 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2494 atexit linenumber=1159 hfile_exit /src/htslib/hfile.c linenumber=1159 hfile_shutdown /src/htslib/hfile.c linenumber=1007 pthread_mutex_lock linenumber=985 kh_destroy_scheme_string /src/htslib/hfile.c linenumber=988 pthread_mutex_unlock linenumber=1002 pthread_mutex_destroy linenumber=1008 pthread_mutex_unlock linenumber=1196 pthread_mutex_unlock linenumber=1199 kh_get_scheme_string /src/htslib/hfile.c linenumber=1201 strchr linenumber=1321 strcmp linenumber=1335 hopen_fd_stdinout /src/htslib/hfile.c linenumber=1335 strchr linenumber=763 snprintf linenumber=765 hdopen /src/htslib/hfile.c linenumber=769 blksize /src/htslib/hfile.c linenumber=737 fstat linenumber=652 hfile_init /src/htslib/hfile.c linenumber=737 strchr linenumber=114 posix_memalign linenumber=118 strchr linenumber=131 hfile_destroy /src/htslib/hfile.c linenumber=137 __errno_location linenumber=165 __errno_location linenumber=168 strchr linenumber=741 strchr linenumber=742 hopen_fd /src/htslib/hfile.c linenumber=1336 hfile_oflags /src/htslib/hfile.c linenumber=667 open linenumber=667 blksize /src/htslib/hfile.c linenumber=670 hfile_init /src/htslib/hfile.c linenumber=670 __errno_location linenumber=680 close linenumber=680 hfile_destroy /src/htslib/hfile.c linenumber=681 hts_hopen /src/htslib/hts.c linenumber=186 calloc linenumber=1467 strdup linenumber=1473 ed_is_big /src/htslib/./htslib/hts.h linenumber=1474 strchr linenumber=1477 strncpy linenumber=1478 strncpy linenumber=1482 strchr linenumber=1486 hts_detect_format2 /src/htslib/hts.c linenumber=1489 hpeek /src/htslib/hfile.c linenumber=561 refill_buffer /src/htslib/hfile.c linenumber=317 __errno_location linenumber=195 memcmp linenumber=576 memcmp linenumber=578 decompress_peek_gz /src/htslib/hts.c linenumber=584 hpeek /src/htslib/hfile.c linenumber=318 inflateInit2_ linenumber=328 inflate linenumber=333 inflateReset linenumber=339 inflateEnd linenumber=348 memcmp linenumber=586 memcmp linenumber=587 memcmp linenumber=588 memcmp linenumber=598 decompress_peek_xz /src/htslib/hts.c linenumber=601 hpeek /src/htslib/hfile.c linenumber=360 lzma_easy_decoder_memusage linenumber=364 lzma_stream_decoder linenumber=364 lzma_code linenumber=372 lzma_end linenumber=374 lzma_end linenumber=379 memcmp linenumber=607 hpeek /src/htslib/hfile.c linenumber=612 strcmp linenumber=626 find_file_extension /src/htslib/./hts_internal.h linenumber=628 strstr linenumber=142 strlen linenumber=144 tolower_c /src/htslib/./textutils_internal.h linenumber=629 memcmp linenumber=633 memcmp linenumber=641 memcmp linenumber=648 memcmp linenumber=654 memcmp linenumber=660 memcmp linenumber=667 memcmp linenumber=673 strcmp linenumber=680 memcmp linenumber=686 parse_version /src/htslib/hts.c linenumber=690 isdigit_c /src/htslib/./textutils_internal.h linenumber=397 __ctype_b_loc linenumber=171 isdigit_c /src/htslib/./textutils_internal.h linenumber=404 memcmp linenumber=694 memcmp linenumber=695 memcmp linenumber=696 memcmp linenumber=701 parse_version /src/htslib/hts.c linenumber=702 memcmp linenumber=707 cmp_nonblank /src/htslib/hts.c linenumber=714 isspace_c /src/htslib/./textutils_internal.h linenumber=421 __ctype_b_loc linenumber=176 memcmp linenumber=719 is_fastaq /src/htslib/hts.c linenumber=724 memchr linenumber=460 is_text_only /src/htslib/hts.c linenumber=463 toupper linenumber=471 is_fastaq /src/htslib/hts.c linenumber=729 parse_tabbed_text /src/htslib/hts.c linenumber=734 isdigit_c /src/htslib/./textutils_internal.h linenumber=499 strchr linenumber=503 isdigit_c /src/htslib/./textutils_internal.h linenumber=503 colmatch /src/htslib/hts.c linenumber=739 colmatch /src/htslib/hts.c linenumber=746 strstr linenumber=751 colmatch /src/htslib/hts.c linenumber=751 strstr linenumber=756 colmatch /src/htslib/hts.c linenumber=756 colmatch /src/htslib/hts.c linenumber=761 is_text_only /src/htslib/hts.c linenumber=769 __errno_location linenumber=1499 hopen_htsget_redirect /src/htslib/multipart.c linenumber=1504 hfile_init /src/htslib/hfile.c linenumber=247 parse_ga4gh_redirect_json /src/htslib/multipart.c linenumber=253 hts_json_fnext /src/htslib/textutils.c linenumber=225 hgetc /src/htslib/./htslib/hfile.h linenumber=298 hgetc2 /src/htslib/hfile.c linenumber=167 refill_buffer /src/htslib/hfile.c linenumber=238 fscan_string /src/htslib/textutils.c linenumber=318 hgetc /src/htslib/./htslib/hfile.h linenumber=169 hgetc /src/htslib/./htslib/hfile.h linenumber=171 kputc /src/htslib/./htslib/kstring.h linenumber=173 kputc /src/htslib/./htslib/kstring.h linenumber=174 kputc /src/htslib/./htslib/kstring.h linenumber=175 kputc /src/htslib/./htslib/kstring.h linenumber=176 kputc /src/htslib/./htslib/kstring.h linenumber=177 kputc /src/htslib/./htslib/kstring.h linenumber=178 hgetc /src/htslib/./htslib/hfile.h linenumber=180 dehex /src/htslib/textutils.c linenumber=180 hgetc /src/htslib/./htslib/hfile.h linenumber=181 dehex /src/htslib/textutils.c linenumber=181 hgetc /src/htslib/./htslib/hfile.h linenumber=182 dehex /src/htslib/textutils.c linenumber=182 hgetc /src/htslib/./htslib/hfile.h linenumber=183 dehex /src/htslib/textutils.c linenumber=183 encode_utf8 /src/htslib/textutils.c linenumber=185 kputsn /src/htslib/./htslib/kstring.h linenumber=186 kputc /src/htslib/./htslib/kstring.h linenumber=196 kputsn /src/htslib/./htslib/kstring.h linenumber=319 kputc /src/htslib/./htslib/kstring.h linenumber=325 hpeek /src/htslib/hfile.c linenumber=326 strchr linenumber=326 hgetc /src/htslib/./htslib/hfile.h linenumber=327 kputc /src/htslib/./htslib/kstring.h linenumber=328 token_type /src/htslib/textutils.c linenumber=331 strcmp linenumber=208 strcmp linenumber=210 strcmp linenumber=212 hts_json_fnext /src/htslib/textutils.c linenumber=226 strcmp linenumber=229 parse_ga4gh_body_json /src/htslib/multipart.c linenumber=230 hts_json_fnext /src/htslib/textutils.c linenumber=155 hts_json_fnext /src/htslib/textutils.c linenumber=156 strcmp linenumber=159 hts_json_fnext /src/htslib/textutils.c linenumber=160 hts_json_fnext /src/htslib/textutils.c linenumber=162 hts_realloc_or_die /src/htslib/hts.c linenumber=166 __errno_location linenumber=5055 realloc linenumber=5059 __errno_location linenumber=5073 strerror linenumber=5073 hts_log /src/htslib/hts.c linenumber=5073 exit linenumber=5074 hts_json_fnext /src/htslib/textutils.c linenumber=172 strcmp linenumber=175 hts_json_fnext /src/htslib/textutils.c linenumber=176 ks_release /src/htslib/./htslib/kstring.h linenumber=177 strcmp linenumber=179 hts_json_fnext /src/htslib/textutils.c linenumber=180 hts_json_fnext /src/htslib/textutils.c linenumber=182 hts_json_fnext /src/htslib/textutils.c linenumber=185 kputs /src/htslib/./htslib/kstring.h linenumber=188 __errno_location linenumber=255 strlen linenumber=256 kputsn /src/htslib/./htslib/kstring.h linenumber=256 kputs /src/htslib/./htslib/kstring.h linenumber=189 hts_realloc_or_die /src/htslib/hts.c linenumber=191 ks_release /src/htslib/./htslib/kstring.h linenumber=192 hts_json_fskip_value /src/htslib/textutils.c linenumber=196 skip_value /src/htslib/textutils.c linenumber=406 fnext /src/htslib/textutils.c linenumber=406 hts_json_fnext /src/htslib/textutils.c linenumber=399 strcmp linenumber=203 hts_json_fnext /src/htslib/textutils.c linenumber=204 hts_log /src/htslib/hts.c linenumber=206 hts_json_fskip_value /src/htslib/textutils.c linenumber=208 hts_json_fnext /src/htslib/textutils.c linenumber=236 free_all_parts /src/htslib/multipart.c linenumber=257 free_part /src/htslib/multipart.c linenumber=69 hfile_destroy /src/htslib/hfile.c linenumber=258 __errno_location linenumber=259 hclose_abruptly /src/htslib/hfile.c linenumber=1509 __errno_location linenumber=522 hfile_destroy /src/htslib/hfile.c linenumber=526 __errno_location linenumber=527 hts_crypt4gh_redirect /src/htslib/hts.c linenumber=1517 strlen linenumber=1437 snprintf linenumber=1448 strchr linenumber=1449 snprintf linenumber=1449 hopen /src/htslib/hfile.c linenumber=1450 hts_detect_format2 /src/htslib/hts.c linenumber=1534 strchr linenumber=1537 strchr linenumber=1541 strchr linenumber=1542 strchr linenumber=1543 strchr linenumber=1544 strchr linenumber=1547 strchr linenumber=1548 strchr linenumber=1549 abort linenumber=1558 format_category /src/htslib/hts.c linenumber=1563 __errno_location linenumber=1569 bgzf_hopen /src/htslib/bgzf.c linenumber=1575 strchr linenumber=542 bgzf_read_init /src/htslib/bgzf.c linenumber=543 hpeek /src/htslib/hfile.c linenumber=387 calloc linenumber=390 memcmp linenumber=398 memcmp linenumber=399 hts_log /src/htslib/hts.c linenumber=400 razf_info /src/htslib/bgzf.c linenumber=401 strcmp linenumber=320 hseek /src/htslib/hfile.c linenumber=323 writebuffer_is_nonempty /src/htslib/hfile.c linenumber=450 flush_buffer /src/htslib/hfile.c linenumber=451 __errno_location linenumber=381 htell /src/htslib/./htslib/hfile.h linenumber=455 __errno_location linenumber=464 __errno_location linenumber=476 __errno_location linenumber=493 hread /src/htslib/./htslib/hfile.h linenumber=324 hread2 /src/htslib/hfile.c linenumber=257 __errno_location linenumber=341 refill_buffer /src/htslib/hfile.c linenumber=360 ed_is_big /src/htslib/./htslib/hts.h linenumber=325 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=325 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=1599 hts_log /src/htslib/hts.c linenumber=328 hts_log /src/htslib/hts.c linenumber=339 __errno_location linenumber=404 kh_init_bgzf_cache /src/htslib/bgzf.c linenumber=413 calloc linenumber=86 strchr linenumber=545 bgzf_write_init /src/htslib/bgzf.c linenumber=546 calloc linenumber=438 mode2level /src/htslib/bgzf.c linenumber=450 strchr linenumber=432 strchr linenumber=464 calloc linenumber=468 deflateInit2_ linenumber=474 bgzf_zerr /src/htslib/bgzf.c linenumber=476 __errno_location linenumber=363 strerror linenumber=363 snprintf linenumber=378 hts_log /src/htslib/hts.c linenumber=476 __errno_location linenumber=483 strerror linenumber=483 hts_log /src/htslib/hts.c linenumber=483 __errno_location linenumber=549 ed_is_big /src/htslib/./htslib/hts.h linenumber=552 cram_dopen /src/htslib/cram/cram_io.c linenumber=1581 calloc linenumber=5290 cram_read_file_def /src/htslib/cram/cram_io.c linenumber=5310 hread /src/htslib/cram/../htslib/hfile.h linenumber=4665 memcmp linenumber=4670 hts_log /src/htslib/hts.c linenumber=4676 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5316 cram_init_varint /src/htslib/cram/cram_io.c linenumber=5248 cram_read_SAM_hdr /src/htslib/cram/cram_io.c linenumber=5318 int32_decode /src/htslib/cram/cram_io.c linenumber=4723 hread /src/htslib/cram/../htslib/hfile.h linenumber=1007 hread /src/htslib/cram/../htslib/hfile.h linenumber=4735 cram_read_container /src/htslib/cram/cram_io.c linenumber=4743 int32_decode /src/htslib/cram/cram_io.c linenumber=3805 crc32 linenumber=3816 calloc linenumber=3876 __errno_location linenumber=3882 cram_free_container /src/htslib/cram/cram_io.c linenumber=3883 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=3717 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=4363 cram_free_block /src/htslib/cram/cram_io.c linenumber=4393 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4395 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4397 cram_free_block /src/htslib/cram/cram_io.c linenumber=3720 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3726 cram_free_block /src/htslib/cram/cram_io.c linenumber=4424 cram_free_block /src/htslib/cram/cram_io.c linenumber=4433 cram_free_block /src/htslib/cram/cram_io.c linenumber=4444 cram_free_slice_header /src/htslib/cram/cram_io.c linenumber=4451 cram_free_block /src/htslib/cram/cram_io.c linenumber=4454 cram_free_block /src/htslib/cram/cram_io.c linenumber=4457 cram_free_block /src/htslib/cram/cram_io.c linenumber=4460 cram_free_block /src/htslib/cram/cram_io.c linenumber=4463 cram_free_block /src/htslib/cram/cram_io.c linenumber=4466 cram_free_block /src/htslib/cram/cram_io.c linenumber=4469 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4484 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4487 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4489 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3735 cram_stats_free /src/htslib/cram/cram_stats.c linenumber=3740 kh_destroy_m_i2i /src/htslib/cram/cram_structs.h linenumber=225 cram_free_block /src/htslib/cram/cram_io.c linenumber=3762 cram_free_block /src/htslib/cram/cram_io.c linenumber=3763 kh_destroy_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3768 free_bam_list /src/htslib/cram/cram_io.c linenumber=3775 bam_destroy1 /src/htslib/sam.c linenumber=3698 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=472 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=474 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=482 __errno_location linenumber=3888 cram_free_container /src/htslib/cram/cram_io.c linenumber=3889 cram_free_container /src/htslib/cram/cram_io.c linenumber=3894 int32_decode /src/htslib/cram/cram_io.c linenumber=3902 cram_free_container /src/htslib/cram/cram_io.c linenumber=3903 hts_log /src/htslib/hts.c linenumber=3915 cram_free_container /src/htslib/cram/cram_io.c linenumber=3916 cram_free_container /src/htslib/cram/cram_io.c linenumber=4755 cram_read_block /src/htslib/cram/cram_io.c linenumber=4759 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1423 hts_log /src/htslib/hts.c linenumber=1425 crc32 linenumber=1428 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1429 crc32 linenumber=1430 hread /src/htslib/cram/../htslib/hfile.h linenumber=1445 hread /src/htslib/cram/../htslib/hfile.h linenumber=1457 int32_decode /src/htslib/cram/cram_io.c linenumber=1465 cram_free_container /src/htslib/cram/cram_io.c linenumber=4760 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=4763 crc32 linenumber=1586 hts_log /src/htslib/hts.c linenumber=1589 __assert_fail linenumber=1599 zlib_mem_inflate /src/htslib/cram/cram_io.c linenumber=1607 inflateInit2_ linenumber=1180 hts_log /src/htslib/hts.c linenumber=1182 inflate linenumber=1193 hts_log /src/htslib/hts.c linenumber=1198 inflateEnd linenumber=1200 realloc linenumber=1206 inflateEnd linenumber=1209 inflateEnd linenumber=1214 BZ2_bzBuffToBuffDecompress linenumber=1626 lzma_mem_inflate /src/htslib/cram/cram_io.c linenumber=1647 lzma_easy_decoder_memusage linenumber=1320 lzma_stream_decoder linenumber=1320 realloc linenumber=1330 lzma_code linenumber=1338 hts_log /src/htslib/hts.c linenumber=1340 lzma_code linenumber=1351 hts_log /src/htslib/hts.c linenumber=1353 realloc linenumber=1357 lzma_end linenumber=1362 lzma_end linenumber=1367 rans_uncompress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1668 rans_uncompress_O1 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=848 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=635 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=177 pthread_once linenumber=122 htscodecs_tls_init /src/htslib/htscodecs/htscodecs/utils.c linenumber=122 pthread_key_create linenumber=104 htscodecs_tls_free_all /src/htslib/htscodecs/htscodecs/utils.c linenumber=104 fprintf linenumber=95 strerror linenumber=125 fprintf linenumber=124 pthread_getspecific linenumber=130 calloc linenumber=132 pthread_setspecific linenumber=134 fprintf linenumber=156 calloc linenumber=162 RansDecSymbolInit32 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=683 __assert_fail linenumber=558 __assert_fail linenumber=559 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=730 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=731 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=732 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=733 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=779 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=780 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=781 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=782 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=787 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=788 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=790 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=791 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=792 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=793 RansDecGet /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=809 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=814 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=821 pthread_getspecific linenumber=187 fprintf linenumber=199 fprintf linenumber=204 rans_uncompress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=849 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=314 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=315 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=316 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=317 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=348 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=349 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=351 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=352 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=353 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=354 fqz_decompress /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1686 uncompress_block_fqz2f /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1628 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1470 fqz_read_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1483 read_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1343 fqz_read_parameters1 /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1360 read_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1286 read_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1297 read_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1307 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1375 fqz_create_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1500 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=323 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=327 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=330 SIMPLE_MODEL2_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=332 SIMPLE_MODEL2_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=333 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=335 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1503 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1504 realloc linenumber=1536 realloc linenumber=1537 decompress_new_read /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1543 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1395 RC_GetFreq /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=142 RC_Decode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=155 SIMPLE_MODEL256_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=160 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1409 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1410 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1411 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1412 SIMPLE_MODEL2_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1423 SIMPLE_MODEL2_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=160 SIMPLE_MODEL2_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1429 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1556 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1559 realloc linenumber=1567 realloc linenumber=1568 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1591 fqz_destroy_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1594 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=341 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1597 fqz_destroy_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1606 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1609 rans_uncompress_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1699 rans_uncompress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1877 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1600 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1627 rans_uncompress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1659 unstripe /src/htslib/htscodecs/htscodecs/utils.h linenumber=1668 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1686 hts_unpack_meta /src/htslib/htscodecs/htscodecs/pack.c linenumber=1768 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1779 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1792 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1793 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1801 rans_dec_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1804 pthread_once linenumber=1025 htscodecs_tls_cpu_init /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1025 __get_cpuid_max /usr/local/lib/clang/22/include/cpuid.h linenumber=878 not_ancient_darwin /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=926 strerror linenumber=1028 fprintf linenumber=1027 fprintf linenumber=1029 rans_dec_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1826 hts_rle_decode /src/htslib/htscodecs/htscodecs/rle.c linenumber=1843 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=169 hts_unpack /src/htslib/htscodecs/htscodecs/pack.c linenumber=1857 arith_uncompress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1718 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1048 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1071 arith_uncompress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1103 unstripe /src/htslib/htscodecs/htscodecs/utils.h linenumber=1112 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1130 hts_unpack_meta /src/htslib/htscodecs/htscodecs/pack.c linenumber=1190 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1201 BZ2_bzBuffToBuffDecompress linenumber=1227 arith_uncompress_O1_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1238 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=673 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=679 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=682 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=684 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=689 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=691 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=692 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=696 SIMPLE_MODEL258_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=702 SIMPLE_MODEL258_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=160 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=713 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=714 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=715 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=720 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=721 arith_uncompress_O0_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1239 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=531 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=534 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=541 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=543 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=544 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=548 SIMPLE_MODEL258_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=552 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=564 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=565 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=570 arith_uncompress_O1 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1245 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=239 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=247 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=249 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=250 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=254 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=258 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=259 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=264 arith_uncompress_O0 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1246 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=147 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=155 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=156 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=159 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=161 hts_unpack /src/htslib/htscodecs/htscodecs/pack.c linenumber=1261 tok3_decode_names /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1737 create_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1698 fprintf linenumber=185 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=189 uncompressed_size /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1773 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1421 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1424 uncompress /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1790 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1432 arith_decode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1434 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1230 arith_uncompress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1232 rans_decode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1435 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1257 rans_uncompress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1259 decode_name /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1816 decode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1022 decode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1032 strlen linenumber=1042 strcpy linenumber=1043 strlen linenumber=1055 decode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1067 decode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1075 decode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1082 decode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1092 decode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1093 append_uint32_fixed /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1095 decode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1104 append_uint32_fixed /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1107 decode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1115 append_uint32_var /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1117 decode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1125 append_uint32_var /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1128 append_uint32_var /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1164 append_uint32_fixed /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1172 realloc linenumber=1194 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1824 pool_destroy /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=218 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=227 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1830 cram_free_container /src/htslib/cram/cram_io.c linenumber=4764 cram_free_block /src/htslib/cram/cram_io.c linenumber=4765 int32_get_blk /src/htslib/cram/cram_io.c linenumber=4775 cram_free_container /src/htslib/cram/cram_io.c linenumber=4778 cram_free_block /src/htslib/cram/cram_io.c linenumber=4779 cram_free_container /src/htslib/cram/cram_io.c linenumber=4783 cram_free_block /src/htslib/cram/cram_io.c linenumber=4784 cram_free_block /src/htslib/cram/cram_io.c linenumber=4789 cram_read_block /src/htslib/cram/cram_io.c linenumber=4793 cram_free_container /src/htslib/cram/cram_io.c linenumber=4794 cram_free_block /src/htslib/cram/cram_io.c linenumber=4802 cram_free_container /src/htslib/cram/cram_io.c linenumber=4809 hread /src/htslib/cram/../htslib/hfile.h linenumber=4814 cram_free_container /src/htslib/cram/cram_io.c linenumber=4815 cram_free_container /src/htslib/cram/cram_io.c linenumber=4823 sam_hdr_init /src/htslib/sam.c linenumber=4827 calloc linenumber=110 sam_hdr_add_lines /src/htslib/header.c linenumber=4833 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1667 sam_hrecs_new /src/htslib/header.c linenumber=1290 calloc linenumber=2733 kh_init_sam_hrecs_t /src/htslib/./header.h linenumber=2738 calloc linenumber=168 kh_init_m_s2i /src/htslib/./header.h linenumber=2747 calloc linenumber=169 kh_init_m_s2i /src/htslib/./header.h linenumber=2754 kh_init_m_s2i /src/htslib/./header.h linenumber=2762 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2765 next_power_2 /src/htslib/cram/pooled_alloc.c linenumber=75 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2768 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2771 sam_hrecs_init_type_order /src/htslib/header.c linenumber=2774 calloc linenumber=75 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2781 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2784 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2787 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2790 sam_hrecs_refs_from_targets_array /src/htslib/header.c linenumber=1296 hts_log /src/htslib/hts.c linenumber=1192 realloc linenumber=1197 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1206 kh_resize_m_s2i /src/htslib/./header.h linenumber=169 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=169 string_dup /src/htslib/cram/string_alloc.c linenumber=1212 strlen linenumber=150 string_ndup /src/htslib/cram/string_alloc.c linenumber=150 string_alloc /src/htslib/cram/string_alloc.c linenumber=154 new_string_pool /src/htslib/cram/string_alloc.c linenumber=138 realloc linenumber=80 kh_get_s2i /src/htslib/hts.c linenumber=1218 __ac_FNV1a_hash_string /src/htslib/./cram/../htslib/khash.h linenumber=79 strcmp linenumber=79 kh_put_m_s2i /src/htslib/./header.h linenumber=1226 strcmp linenumber=169 hts_log /src/htslib/hts.c linenumber=1229 __errno_location linenumber=1241 strerror linenumber=1241 hts_log /src/htslib/hts.c linenumber=1241 kh_get_m_s2i /src/htslib/./header.h linenumber=1245 kh_del_m_s2i /src/htslib/./header.h linenumber=1246 sam_hrecs_free /src/htslib/header.c linenumber=1297 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2817 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2820 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2826 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2832 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2841 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2844 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2847 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1304 strlen linenumber=1002 sam_hrecs_error /src/htslib/header.c linenumber=1006 hts_log /src/htslib/hts.c linenumber=64 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1017 sam_hrecs_error /src/htslib/header.c linenumber=919 isalpha_c /src/htslib/./textutils_internal.h linenumber=924 __ctype_b_loc linenumber=170 sam_hrecs_error /src/htslib/header.c linenumber=925 TYPEKEY /src/htslib/./header.h linenumber=929 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=935 new_pool /src/htslib/cram/pooled_alloc.c linenumber=137 realloc linenumber=100 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=940 kh_resize_sam_hrecs_t /src/htslib/./header.h linenumber=168 realloc linenumber=168 TYPEKEY /src/htslib/./header.h linenumber=947 parse_comment_line /src/htslib/header.c linenumber=949 sam_hrecs_error /src/htslib/header.c linenumber=806 warn_if_known_stderr /src/htslib/header.c linenumber=807 kmemmem /src/htslib/kstring.c linenumber=790 boyer_moore /src/htslib/kstring.c linenumber=498 memchr linenumber=467 ksBM_prep /src/htslib/kstring.c linenumber=472 calloc linenumber=410 calloc linenumber=417 karp_rabin /src/htslib/kstring.c linenumber=473 fast_exp /src/htslib/kstring.c linenumber=372 memcmp linenumber=392 known_stderr /src/htslib/header.c linenumber=791 hts_log /src/htslib/hts.c linenumber=781 hts_log /src/htslib/hts.c linenumber=782 kmemmem /src/htslib/kstring.c linenumber=792 known_stderr /src/htslib/header.c linenumber=793 kmemmem /src/htslib/kstring.c linenumber=794 known_stderr /src/htslib/header.c linenumber=795 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=814 string_ndup /src/htslib/cram/string_alloc.c linenumber=816 parse_noncomment_line /src/htslib/header.c linenumber=956 TYPEKEY /src/htslib/./header.h linenumber=831 sam_hrecs_error /src/htslib/header.c linenumber=841 warn_if_known_stderr /src/htslib/header.c linenumber=842 sam_hrecs_error /src/htslib/header.c linenumber=852 warn_if_known_stderr /src/htslib/header.c linenumber=853 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=865 string_ndup /src/htslib/cram/string_alloc.c linenumber=867 sam_hrecs_global_list_add /src/htslib/header.c linenumber=964 TYPEKEY /src/htslib/./header.h linenumber=503 __assert_fail linenumber=971 sam_hrecs_free_tags /src/htslib/header.c linenumber=988 sam_hrecs_free_tags /src/htslib/header.c linenumber=698 pool_free /src/htslib/cram/pooled_alloc.c linenumber=700 pool_free /src/htslib/cram/pooled_alloc.c linenumber=989 TYPEKEY /src/htslib/./header.h linenumber=1029 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1044 realloc linenumber=1048 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1062 TYPEKEY /src/htslib/./header.h linenumber=145 __assert_fail linenumber=156 __assert_fail linenumber=159 strtoll linenumber=161 __assert_fail linenumber=166 hts_log /src/htslib/hts.c linenumber=173 hts_log /src/htslib/hts.c linenumber=178 hts_log /src/htslib/hts.c linenumber=184 kh_get_m_s2i /src/htslib/./header.h linenumber=190 snprintf linenumber=202 sam_hrecs_update /src/htslib/header.c linenumber=204 sam_hrecs_vupdate /src/htslib/header.c linenumber=2994 sam_hrecs_find_key /src/htslib/header.c linenumber=2952 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=2954 strlen linenumber=2964 string_alloc /src/htslib/cram/string_alloc.c linenumber=2965 snprintf linenumber=2969 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=208 kstrtok /src/htslib/kstring.c linenumber=95 strchr linenumber=215 strlen linenumber=216 string_ndup /src/htslib/cram/string_alloc.c linenumber=99 kh_put_m_s2i /src/htslib/./header.h linenumber=103 hts_log /src/htslib/hts.c linenumber=109 strcmp linenumber=222 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=226 strcmp linenumber=236 hts_log /src/htslib/hts.c linenumber=237 hts_log /src/htslib/hts.c linenumber=245 realloc linenumber=251 kh_put_m_s2i /src/htslib/./header.h linenumber=262 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=266 TYPEKEY /src/htslib/./header.h linenumber=275 sam_hrecs_find_key /src/htslib/header.c linenumber=276 hts_log /src/htslib/hts.c linenumber=281 __assert_fail linenumber=284 kh_get_m_s2i /src/htslib/./header.h linenumber=287 __assert_fail linenumber=290 hts_log /src/htslib/hts.c linenumber=292 realloc linenumber=303 kh_put_m_s2i /src/htslib/./header.h linenumber=315 TYPEKEY /src/htslib/./header.h linenumber=323 realloc linenumber=330 __assert_fail linenumber=348 hts_log /src/htslib/hts.c linenumber=352 kh_get_m_s2i /src/htslib/./header.h linenumber=357 kh_put_m_s2i /src/htslib/./header.h linenumber=387 realloc linenumber=399 sam_hrecs_free /src/htslib/header.c linenumber=1305 add_stub_ref_sq_lines /src/htslib/header.c linenumber=1310 snprintf linenumber=1272 sam_hrecs_add /src/htslib/header.c linenumber=1273 sam_hrecs_vadd /src/htslib/header.c linenumber=685 TYPEKEY /src/htslib/./header.h linenumber=557 strncmp linenumber=559 sam_hrecs_find_type_id /src/htslib/header.c linenumber=559 kh_get_m_s2i /src/htslib/./header.h linenumber=2879 kh_get_m_s2i /src/htslib/./header.h linenumber=2887 kh_get_m_s2i /src/htslib/./header.h linenumber=2895 TYPEKEY /src/htslib/./header.h linenumber=2902 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=2902 sam_hrecs_vupdate /src/htslib/header.c linenumber=560 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=562 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=564 __assert_fail linenumber=575 sam_hrecs_global_list_add /src/htslib/header.c linenumber=589 __assert_fail linenumber=592 __assert_fail linenumber=593 __assert_fail linenumber=594 __assert_fail linenumber=595 strncmp linenumber=604 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=609 strncmp linenumber=612 strlen linenumber=613 string_alloc /src/htslib/cram/string_alloc.c linenumber=614 snprintf linenumber=615 strlen linenumber=619 string_ndup /src/htslib/cram/string_alloc.c linenumber=620 strncmp linenumber=641 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=644 strncmp linenumber=647 strlen linenumber=648 string_alloc /src/htslib/cram/string_alloc.c linenumber=649 snprintf linenumber=650 strlen linenumber=654 string_ndup /src/htslib/cram/string_alloc.c linenumber=655 TYPEKEY /src/htslib/./header.h linenumber=669 sam_hrecs_update_hashes /src/htslib/header.c linenumber=669 strncmp linenumber=672 hts_log /src/htslib/hts.c linenumber=1280 sam_hrecs_free /src/htslib/header.c linenumber=1311 rebuild_target_arrays /src/htslib/header.c linenumber=1317 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1161 realloc linenumber=1083 realloc linenumber=1088 strcmp linenumber=1103 strdup linenumber=1106 kh_get_s2i /src/htslib/hts.c linenumber=1117 kh_del_s2i /src/htslib/hts.c linenumber=1119 kh_init_s2i /src/htslib/hts.c linenumber=1125 calloc linenumber=79 kh_put_s2i /src/htslib/hts.c linenumber=1131 kh_resize_s2i /src/htslib/hts.c linenumber=79 realloc linenumber=79 kh_get_s2i /src/htslib/hts.c linenumber=1142 kh_del_s2i /src/htslib/hts.c linenumber=1144 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1672 rebuild_target_arrays /src/htslib/header.c linenumber=1675 redact_header_text /src/htslib/header.c linenumber=1679 __assert_fail linenumber=1531 sam_hdr_destroy /src/htslib/sam.c linenumber=4835 sam_hrecs_free /src/htslib/header.c linenumber=136 kh_destroy_s2i /src/htslib/hts.c linenumber=138 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5319 calloc linenumber=5325 strncpy linenumber=5338 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5341 strrchr linenumber=5346 strdup linenumber=5346 refs_create /src/htslib/cram/cram_io.c linenumber=5354 calloc linenumber=2468 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2475 kh_init_refs /src/htslib/cram/cram_structs.h linenumber=2483 calloc linenumber=686 pthread_mutex_init linenumber=2486 refs_free /src/htslib/cram/cram_io.c linenumber=2491 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2437 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2449 mfclose /src/htslib/cram/mFILE.c linenumber=2419 mfflush /src/htslib/cram/mFILE.c linenumber=365 fwrite linenumber=615 fflush linenumber=617 fseek linenumber=630 fwrite linenumber=632 fflush linenumber=634 ftell linenumber=637 fileno linenumber=638 ftell linenumber=638 ftruncate linenumber=638 munmap linenumber=370 fclose linenumber=376 mfdestroy /src/htslib/cram/mFILE.c linenumber=378 kh_destroy_refs /src/htslib/cram/cram_structs.h linenumber=2453 bgzf_close /src/htslib/bgzf.c linenumber=2460 bgzf_flush /src/htslib/bgzf.c linenumber=2085 mt_queue /src/htslib/bgzf.c linenumber=1955 pthread_mutex_lock linenumber=1859 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=1860 pthread_mutex_unlock linenumber=1862 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=1871 pthread_mutex_lock linenumber=853 pthread_mutex_unlock linenumber=859 __errno_location linenumber=860 pthread_mutex_unlock linenumber=865 pthread_cond_wait linenumber=880 pthread_mutex_unlock linenumber=884 wake_next_worker /src/htslib/thread_pool.c linenumber=912 pthread_mutex_lock linenumber=658 __assert_fail linenumber=662 __assert_fail linenumber=676 pthread_cond_signal linenumber=713 pthread_mutex_unlock linenumber=716 pthread_mutex_unlock linenumber=914 bgzf_encode_level0_func /src/htslib/bgzf.c linenumber=1871 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1355 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1359 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1360 hts_crc32 /src/htslib/bgzf.c linenumber=1363 crc32 linenumber=621 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1364 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1365 job_cleanup /src/htslib/bgzf.c linenumber=1871 pthread_mutex_lock linenumber=1325 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1326 pthread_mutex_unlock linenumber=1327 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=1880 bgzf_encode_func /src/htslib/bgzf.c linenumber=1880 bgzf_compress /src/htslib/bgzf.c linenumber=1334 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=635 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=636 deflateInit2_ linenumber=647 bgzf_zerr /src/htslib/bgzf.c linenumber=649 hts_log /src/htslib/hts.c linenumber=649 deflate linenumber=652 deflateEnd linenumber=654 bgzf_zerr /src/htslib/bgzf.c linenumber=657 hts_log /src/htslib/hts.c linenumber=657 deflateEnd linenumber=665 deflateEnd linenumber=668 bgzf_zerr /src/htslib/bgzf.c linenumber=669 hts_log /src/htslib/hts.c linenumber=669 packInt16 /src/htslib/bgzf.c linenumber=677 crc32 linenumber=679 packInt32 /src/htslib/bgzf.c linenumber=680 packInt32 /src/htslib/bgzf.c linenumber=681 job_cleanup /src/htslib/bgzf.c linenumber=1880 job_cleanup /src/htslib/bgzf.c linenumber=1890 pthread_mutex_lock linenumber=1891 pthread_mutex_unlock linenumber=1893 mt_flush_queue /src/htslib/bgzf.c linenumber=1956 pthread_mutex_lock linenumber=1906 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=1909 pthread_mutex_lock linenumber=334 pthread_mutex_unlock linenumber=336 pthread_mutex_unlock linenumber=1911 hts_usleep /src/htslib/./hts_internal.h linenumber=1912 nanosleep linenumber=162 pthread_mutex_lock linenumber=1913 pthread_mutex_unlock linenumber=1915 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=1921 pthread_mutex_lock linenumber=948 pthread_cond_signal linenumber=953 pthread_cond_wait linenumber=966 gettimeofday linenumber=975 pthread_cond_timedwait linenumber=978 gettimeofday linenumber=985 pthread_cond_timedwait linenumber=988 pthread_mutex_unlock linenumber=994 pthread_mutex_lock linenumber=1962 pthread_mutex_unlock linenumber=1964 hflush /src/htslib/hfile.c linenumber=1971 flush_buffer /src/htslib/hfile.c linenumber=392 __errno_location linenumber=394 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1978 realloc linenumber=2361 deflate_block /src/htslib/bgzf.c linenumber=1981 bgzf_compress /src/htslib/bgzf.c linenumber=714 bgzf_gzip_compress /src/htslib/bgzf.c linenumber=716 deflate linenumber=695 bgzf_zerr /src/htslib/bgzf.c linenumber=697 hts_log /src/htslib/hts.c linenumber=697 hts_log /src/htslib/hts.c linenumber=701 hts_log /src/htslib/hts.c linenumber=720 bgzf_zerr /src/htslib/bgzf.c linenumber=1983 hts_log /src/htslib/hts.c linenumber=1983 hwrite /src/htslib/./htslib/hfile.h linenumber=1986 hfile_set_blksize /src/htslib/hfile.c linenumber=303 realloc linenumber=224 hwrite2 /src/htslib/hfile.c linenumber=312 flush_buffer /src/htslib/hfile.c linenumber=421 __errno_location linenumber=427 hwrite2 /src/htslib/hfile.c linenumber=318 hts_log /src/htslib/hts.c linenumber=1987 bgzf_close_mt /src/htslib/bgzf.c linenumber=2086 mt_destroy /src/htslib/bgzf.c linenumber=2075 pthread_mutex_lock linenumber=1810 pthread_cond_signal linenumber=1812 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=1813 pthread_mutex_lock linenumber=924 pthread_cond_signal linenumber=926 pthread_mutex_unlock linenumber=927 pthread_mutex_unlock linenumber=1814 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=1819 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=1823 pthread_mutex_lock linenumber=420 pthread_mutex_unlock linenumber=422 hts_tpool_process_reset /src/htslib/thread_pool.c linenumber=425 pthread_mutex_lock linenumber=1017 pthread_mutex_unlock linenumber=1030 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1046 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=1052 pthread_mutex_lock linenumber=1056 pthread_cond_signal linenumber=1063 pthread_mutex_unlock linenumber=1064 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1074 pthread_mutex_lock linenumber=426 hts_tpool_process_detach_locked /src/htslib/thread_pool.c linenumber=427 hts_tpool_process_shutdown_locked /src/htslib/thread_pool.c linenumber=428 pthread_cond_broadcast linenumber=321 pthread_cond_broadcast linenumber=322 pthread_cond_broadcast linenumber=323 pthread_cond_broadcast linenumber=324 pthread_mutex_unlock linenumber=432 pthread_cond_destroy linenumber=436 pthread_cond_destroy linenumber=437 pthread_cond_destroy linenumber=438 pthread_cond_destroy linenumber=439 pthread_mutex_unlock linenumber=440 pthread_join linenumber=1828 pthread_mutex_destroy linenumber=1831 pthread_mutex_destroy linenumber=1832 pthread_mutex_destroy linenumber=1833 pthread_cond_destroy linenumber=1834 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1836 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=1839 pthread_mutex_lock linenumber=1095 pthread_cond_signal linenumber=1101 pthread_mutex_unlock linenumber=1103 pthread_join linenumber=1108 pthread_mutex_destroy linenumber=1110 pthread_cond_destroy linenumber=1112 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=1841 fflush linenumber=1847 deflate_block /src/htslib/bgzf.c linenumber=2090 bgzf_zerr /src/htslib/bgzf.c linenumber=2092 hts_log /src/htslib/hts.c linenumber=2092 bgzf_close_mt /src/htslib/bgzf.c linenumber=2093 hwrite /src/htslib/./htslib/hfile.h linenumber=2096 hflush /src/htslib/hfile.c linenumber=2097 hts_log /src/htslib/hts.c linenumber=2098 bgzf_close_mt /src/htslib/bgzf.c linenumber=2104 inflateEnd linenumber=2109 deflateEnd linenumber=2110 bgzf_zerr /src/htslib/bgzf.c linenumber=2112 hts_log /src/htslib/hts.c linenumber=2112 hclose /src/htslib/hfile.c linenumber=2116 writebuffer_is_nonempty /src/htslib/hfile.c linenumber=507 hflush /src/htslib/hfile.c linenumber=507 __errno_location linenumber=509 hfile_destroy /src/htslib/hfile.c linenumber=510 __errno_location linenumber=514 bgzf_index_destroy /src/htslib/bgzf.c linenumber=2118 free_cache /src/htslib/bgzf.c linenumber=2120 kh_destroy_bgzf_cache /src/htslib/bgzf.c linenumber=912 bgzf_clear_private_data /src/htslib/./bgzf_internal.h linenumber=914 __assert_fail linenumber=59 pthread_mutex_destroy linenumber=2462 pthread_mutex_init linenumber=5390 pthread_mutex_init linenumber=5391 pthread_mutex_init linenumber=5392 pthread_mutex_init linenumber=5393 cram_new_metrics /src/htslib/cram/cram_io.c linenumber=5396 calloc linenumber=2328 kh_init_m_metrics /src/htslib/cram/cram_structs.h linenumber=5401 calloc linenumber=308 refs_from_header /src/htslib/cram/cram_io.c linenumber=5411 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2781 realloc linenumber=2791 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2804 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=686 strcmp linenumber=686 calloc linenumber=2809 string_dup /src/htslib/cram/string_alloc.c linenumber=2815 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2820 sam_hrecs_find_key /src/htslib/header.c linenumber=2821 string_dup /src/htslib/cram/string_alloc.c linenumber=2822 sam_hrecs_find_key /src/htslib/header.c linenumber=2824 strtoll linenumber=2826 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2833 kh_resize_refs /src/htslib/cram/cram_structs.h linenumber=686 realloc linenumber=686 cram_set_option /src/htslib/cram/cram_io.c linenumber=1584 cram_set_voption /src/htslib/cram/cram_io.c linenumber=5679 __errno_location linenumber=5696 strdup linenumber=5708 refs_free /src/htslib/cram/cram_io.c linenumber=5784 cram_seek_to_refpos /src/htslib/cram/cram_index.c linenumber=5791 cram_index_query /src/htslib/cram/cram_index.c linenumber=581 cram_seek /src/htslib/cram/cram_io.c linenumber=582 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5432 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3639 pthread_mutex_lock linenumber=261 pthread_mutex_unlock linenumber=263 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3640 pthread_mutex_lock linenumber=227 hts_tpool_next_result_locked /src/htslib/thread_pool.c linenumber=228 pthread_cond_signal linenumber=181 wake_next_worker /src/htslib/thread_pool.c linenumber=183 gettimeofday linenumber=233 pthread_mutex_unlock linenumber=240 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=242 pthread_cond_timedwait linenumber=245 pthread_mutex_unlock linenumber=249 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3643 cram_free_container /src/htslib/cram/cram_io.c linenumber=3652 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3656 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3657 cram_free_container /src/htslib/cram/cram_io.c linenumber=3672 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3676 cram_free_container /src/htslib/cram/cram_io.c linenumber=3686 hseek /src/htslib/hfile.c linenumber=5434 pthread_mutex_lock linenumber=590 pthread_mutex_unlock linenumber=598 cram_free_container /src/htslib/cram/cram_io.c linenumber=601 cram_free_container /src/htslib/cram/cram_io.c linenumber=603 pthread_mutex_lock linenumber=615 pthread_mutex_unlock linenumber=617 pthread_mutex_lock linenumber=5792 pthread_mutex_unlock linenumber=5797 pthread_mutex_lock linenumber=5803 pthread_mutex_unlock linenumber=5816 cram_load_reference /src/htslib/cram/cram_io.c linenumber=5821 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3601 strlen linenumber=2546 refs_create /src/htslib/cram/cram_io.c linenumber=2552 bgzf_close /src/htslib/bgzf.c linenumber=2556 strstr linenumber=2561 string_ndup /src/htslib/cram/string_alloc.c linenumber=2563 snprintf linenumber=2566 strcmp linenumber=2569 string_ndup /src/htslib/cram/string_alloc.c linenumber=2571 snprintf linenumber=2574 string_dup /src/htslib/cram/string_alloc.c linenumber=2577 snprintf linenumber=2579 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=2583 strncmp linenumber=2506 hisremote /src/htslib/hfile.c linenumber=2509 find_scheme_handler /src/htslib/hfile.c linenumber=1347 snprintf linenumber=2512 access linenumber=2513 fai_build /src/htslib/faidx.c linenumber=2514 fai_build3 /src/htslib/faidx.c linenumber=563 fai_build3_core /src/htslib/faidx.c linenumber=558 bgzf_open /src/htslib/bgzf.c linenumber=470 strchr linenumber=498 hopen /src/htslib/hfile.c linenumber=500 bgzf_read_init /src/htslib/bgzf.c linenumber=501 hclose_abruptly /src/htslib/hfile.c linenumber=502 strchr linenumber=504 hopen /src/htslib/hfile.c linenumber=506 bgzf_write_init /src/htslib/bgzf.c linenumber=507 __errno_location linenumber=511 ed_is_big /src/htslib/./htslib/hts.h linenumber=513 __errno_location linenumber=473 strerror linenumber=473 hts_log /src/htslib/hts.c linenumber=473 bgzf_index_build_init /src/htslib/bgzf.c linenumber=478 bgzf_index_destroy /src/htslib/bgzf.c linenumber=2347 calloc linenumber=2348 hts_log /src/htslib/hts.c linenumber=479 fai_build_core /src/htslib/faidx.c linenumber=484 calloc linenumber=141 kh_init_s /src/htslib/faidx.c linenumber=142 calloc linenumber=76 bgzf_getc_ /src/htslib/faidx.c linenumber=148 bgzf_getc /src/htslib/bgzf.c linenumber=65 bgzf_read_block /src/htslib/bgzf.c linenumber=2286 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=1017 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=1018 mt_destroy /src/htslib/bgzf.c linenumber=1026 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1030 hts_log /src/htslib/hts.c linenumber=1039 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1042 hts_log /src/htslib/hts.c linenumber=1049 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1059 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1073 pthread_mutex_lock linenumber=1080 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1081 pthread_mutex_unlock linenumber=1082 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1091 bgzf_htell /src/htslib/bgzf.c linenumber=1102 pthread_mutex_lock linenumber=995 pthread_mutex_unlock linenumber=997 htell /src/htslib/./htslib/hfile.h linenumber=1000 hread /src/htslib/./htslib/hfile.h linenumber=1107 __errno_location linenumber=1110 strerror linenumber=1110 hts_log /src/htslib/hts.c linenumber=1110 inflate_gzip_block /src/htslib/bgzf.c linenumber=1130 hread /src/htslib/./htslib/hfile.h linenumber=844 inflate linenumber=858 bgzf_zerr /src/htslib/bgzf.c linenumber=862 hts_log /src/htslib/hts.c linenumber=862 hpeek /src/htslib/hfile.c linenumber=870 inflateReset linenumber=872 bgzf_zerr /src/htslib/bgzf.c linenumber=874 hts_log /src/htslib/hts.c linenumber=874 hts_log /src/htslib/hts.c linenumber=885 hts_log /src/htslib/hts.c linenumber=1133 load_block_from_cache /src/htslib/bgzf.c linenumber=1142 kh_get_bgzf_cache /src/htslib/bgzf.c linenumber=924 hseek /src/htslib/hfile.c linenumber=931 hts_log /src/htslib/hts.c linenumber=934 exit linenumber=935 hread /src/htslib/./htslib/hfile.h linenumber=1147 hts_log /src/htslib/hts.c linenumber=1151 check_header /src/htslib/bgzf.c linenumber=1157 unpackInt16 /src/htslib/bgzf.c linenumber=900 unpackInt16 /src/htslib/bgzf.c linenumber=902 hts_log /src/htslib/hts.c linenumber=1160 hread /src/htslib/./htslib/hfile.h linenumber=1170 calloc linenumber=1173 inflateInit2_ linenumber=1175 bgzf_zerr /src/htslib/bgzf.c linenumber=1178 hts_log /src/htslib/hts.c linenumber=1178 inflate_gzip_block /src/htslib/bgzf.c linenumber=1184 hts_log /src/htslib/hts.c linenumber=1187 unpackInt16 /src/htslib/bgzf.c linenumber=1198 hts_log /src/htslib/hts.c linenumber=1201 hread /src/htslib/./htslib/hfile.h linenumber=1209 hts_log /src/htslib/hts.c linenumber=1211 inflate_block /src/htslib/bgzf.c linenumber=1218 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=811 bgzf_uncompress /src/htslib/bgzf.c linenumber=812 inflateInit2_ linenumber=775 bgzf_zerr /src/htslib/bgzf.c linenumber=777 hts_log /src/htslib/hts.c linenumber=777 inflate linenumber=780 bgzf_zerr /src/htslib/bgzf.c linenumber=781 inflateEnd linenumber=782 bgzf_zerr /src/htslib/bgzf.c linenumber=783 hts_log /src/htslib/hts.c linenumber=783 inflateEnd linenumber=787 bgzf_zerr /src/htslib/bgzf.c linenumber=788 hts_log /src/htslib/hts.c linenumber=788 crc32 linenumber=793 hts_log /src/htslib/hts.c linenumber=799 bgzf_zerr /src/htslib/bgzf.c linenumber=1219 hts_log /src/htslib/hts.c linenumber=1219 bgzf_htell /src/htslib/bgzf.c linenumber=1227 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1234 cache_block /src/htslib/bgzf.c linenumber=1237 kh_del_bgzf_cache /src/htslib/bgzf.c linenumber=969 kh_put_bgzf_cache /src/htslib/bgzf.c linenumber=975 kh_resize_bgzf_cache /src/htslib/bgzf.c linenumber=86 realloc linenumber=86 bgzf_htell /src/htslib/bgzf.c linenumber=2291 hts_log /src/htslib/hts.c linenumber=154 hts_log /src/htslib/hts.c linenumber=164 bgzf_getc_ /src/htslib/faidx.c linenumber=174 hts_log /src/htslib/hts.c linenumber=177 __ctype_b_loc linenumber=189 hts_log /src/htslib/hts.c linenumber=189 fai_insert_index /src/htslib/faidx.c linenumber=197 hts_log /src/htslib/hts.c linenumber=96 strdup linenumber=100 kh_put_s /src/htslib/faidx.c linenumber=102 kh_resize_s /src/htslib/faidx.c linenumber=76 realloc linenumber=76 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=76 strcmp linenumber=76 hts_log /src/htslib/hts.c linenumber=106 realloc linenumber=114 hts_log /src/htslib/hts.c linenumber=115 __ctype_b_loc linenumber=206 kputc /src/htslib/./htslib/kstring.h linenumber=207 bgzf_getc_ /src/htslib/faidx.c linenumber=211 kputsn /src/htslib/./htslib/kstring.h linenumber=213 hts_log /src/htslib/hts.c linenumber=216 bgzf_getc_ /src/htslib/faidx.c linenumber=221 bgzf_utell /src/htslib/bgzf.c linenumber=224 bgzf_getc_ /src/htslib/faidx.c linenumber=241 bgzf_utell /src/htslib/bgzf.c linenumber=242 hts_log /src/htslib/hts.c linenumber=246 isgraph_ /src/htslib/faidx.c linenumber=257 bgzf_getc_ /src/htslib/faidx.c linenumber=258 hts_log /src/htslib/hts.c linenumber=273 bgzf_getc_ /src/htslib/faidx.c linenumber=283 bgzf_utell /src/htslib/bgzf.c linenumber=284 hts_log /src/htslib/hts.c linenumber=287 hts_log /src/htslib/hts.c linenumber=295 isgraph_ /src/htslib/faidx.c linenumber=311 bgzf_getc_ /src/htslib/faidx.c linenumber=312 hts_log /src/htslib/hts.c linenumber=317 hts_log /src/htslib/hts.c linenumber=322 hts_log /src/htslib/hts.c linenumber=325 fai_insert_index /src/htslib/faidx.c linenumber=335 hts_log /src/htslib/hts.c linenumber=338 fai_destroy /src/htslib/faidx.c linenumber=347 kh_destroy_s /src/htslib/faidx.c linenumber=454 bgzf_close /src/htslib/bgzf.c linenumber=455 hts_log /src/htslib/hts.c linenumber=488 ksprintf /src/htslib/kstring.c linenumber=500 ksprintf /src/htslib/kstring.c linenumber=505 bgzf_index_dump /src/htslib/bgzf.c linenumber=510 hts_log /src/htslib/hts.c linenumber=2426 __errno_location linenumber=2427 get_name_suffix /src/htslib/bgzf.c linenumber=2433 strlen linenumber=2378 snprintf linenumber=2381 hopen /src/htslib/hfile.c linenumber=2438 bgzf_index_dump_hfile /src/htslib/bgzf.c linenumber=2444 hts_log /src/htslib/hts.c linenumber=2394 __errno_location linenumber=2395 bgzf_flush /src/htslib/bgzf.c linenumber=2399 hwrite_uint64 /src/htslib/bgzf.c linenumber=2405 ed_is_big /src/htslib/./htslib/hts.h linenumber=2371 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2371 hwrite /src/htslib/./htslib/hfile.h linenumber=2372 hwrite_uint64 /src/htslib/bgzf.c linenumber=2409 hwrite_uint64 /src/htslib/bgzf.c linenumber=2410 __errno_location linenumber=2415 strerror linenumber=2415 hts_log /src/htslib/hts.c linenumber=2415 hclose /src/htslib/hfile.c linenumber=2446 __errno_location linenumber=2458 strerror linenumber=2458 hts_log /src/htslib/hts.c linenumber=2458 hclose_abruptly /src/htslib/hfile.c linenumber=2460 hts_log /src/htslib/hts.c linenumber=511 bgzf_close /src/htslib/bgzf.c linenumber=516 __errno_location linenumber=520 strerror linenumber=520 hts_log /src/htslib/hts.c linenumber=520 hopen /src/htslib/hfile.c linenumber=524 strerror linenumber=527 hts_log /src/htslib/hts.c linenumber=527 fai_save /src/htslib/faidx.c linenumber=531 kh_get_s /src/htslib/faidx.c linenumber=359 __assert_fail linenumber=360 snprintf linenumber=364 snprintf linenumber=368 hputs /src/htslib/./htslib/hfile.h linenumber=373 strlen linenumber=280 hputs2 /src/htslib/hfile.c linenumber=284 hwrite2 /src/htslib/hfile.c linenumber=443 hputs /src/htslib/./htslib/hfile.h linenumber=374 __errno_location linenumber=532 strerror linenumber=532 hts_log /src/htslib/hts.c linenumber=532 hclose /src/htslib/hfile.c linenumber=536 __errno_location linenumber=537 strerror linenumber=537 hts_log /src/htslib/hts.c linenumber=537 fai_destroy /src/htslib/faidx.c linenumber=543 __errno_location linenumber=547 bgzf_close /src/htslib/bgzf.c linenumber=550 fai_destroy /src/htslib/faidx.c linenumber=551 __errno_location linenumber=552 bgzf_open /src/htslib/bgzf.c linenumber=2518 perror linenumber=2519 bgzf_index_load /src/htslib/bgzf.c linenumber=2523 get_name_suffix /src/htslib/bgzf.c linenumber=2513 hopen /src/htslib/hfile.c linenumber=2518 bgzf_index_load_hfile /src/htslib/bgzf.c linenumber=2524 calloc linenumber=2474 hread_uint64 /src/htslib/bgzf.c linenumber=2477 hread /src/htslib/./htslib/hfile.h linenumber=2467 ed_is_big /src/htslib/./htslib/hts.h linenumber=2468 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2468 hread_uint64 /src/htslib/bgzf.c linenumber=2490 hread_uint64 /src/htslib/bgzf.c linenumber=2491 __errno_location linenumber=2497 strerror linenumber=2497 hts_log /src/htslib/hts.c linenumber=2497 hclose /src/htslib/hfile.c linenumber=2526 __errno_location linenumber=2537 strerror linenumber=2537 hts_log /src/htslib/hts.c linenumber=2537 hclose_abruptly /src/htslib/hfile.c linenumber=2539 hts_log /src/htslib/hts.c linenumber=2524 bgzf_close /src/htslib/bgzf.c linenumber=2525 hts_log /src/htslib/hts.c linenumber=2584 hopen /src/htslib/hfile.c linenumber=2588 hts_log /src/htslib/hts.c linenumber=2589 perror linenumber=2591 hgets /src/htslib/hfile.c linenumber=2594 __errno_location linenumber=294 hgetln /src/htslib/./htslib/hfile.h linenumber=297 hgetdelim /src/htslib/hfile.c linenumber=198 __errno_location linenumber=248 writebuffer_is_nonempty /src/htslib/hfile.c linenumber=251 __errno_location linenumber=252 memchr linenumber=263 refill_buffer /src/htslib/hfile.c linenumber=282 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2604 string_dup /src/htslib/cram/string_alloc.c linenumber=2607 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2610 strtoll linenumber=2612 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2615 strtoll linenumber=2617 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2620 strtol linenumber=2622 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2625 strtol linenumber=2627 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2638 realloc linenumber=2664 hclose /src/htslib/hfile.c linenumber=2676 hclose_abruptly /src/htslib/hfile.c linenumber=2682 refs_free /src/htslib/cram/cram_io.c linenumber=2685 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3606 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2704 strcmp linenumber=2716 __assert_fail linenumber=2716 hts_log /src/htslib/hts.c linenumber=2720 refs_free /src/htslib/cram/cram_io.c linenumber=3612 refs_create /src/htslib/cram/cram_io.c linenumber=3613 refs_from_header /src/htslib/cram/cram_io.c linenumber=3615 refs2id /src/htslib/cram/cram_io.c linenumber=3620 calloc linenumber=2746 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2752 hts_log /src/htslib/hts.c linenumber=2756 __isoc99_sscanf linenumber=5826 hts_log /src/htslib/hts.c linenumber=5827 hts_log /src/htslib/hts.c linenumber=5834 __errno_location linenumber=5835 hts_log /src/htslib/hts.c linenumber=5840 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5853 hts_tpool_init /src/htslib/thread_pool.c linenumber=5867 pthread_mutexattr_init linenumber=755 pthread_mutexattr_settype linenumber=756 pthread_mutex_init linenumber=757 pthread_mutexattr_destroy linenumber=758 pthread_mutex_lock linenumber=760 pthread_attr_init linenumber=766 pthread_attr_getstacksize linenumber=769 pthread_attr_setstacksize linenumber=772 pthread_cond_init linenumber=781 pthread_create linenumber=782 tpool_worker /src/htslib/thread_pool.c linenumber=782 pthread_mutex_lock linenumber=523 __assert_fail linenumber=527 pthread_cond_wait linenumber=557 __assert_fail linenumber=587 pthread_cond_broadcast linenumber=600 pthread_cond_signal linenumber=603 pthread_mutex_unlock linenumber=607 hts_tpool_add_result /src/htslib/thread_pool.c linenumber=612 pthread_mutex_lock linenumber=99 pthread_cond_signal linenumber=105 pthread_mutex_unlock linenumber=109 pthread_mutex_unlock linenumber=114 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=115 pthread_mutex_lock linenumber=328 hts_tpool_process_shutdown_locked /src/htslib/thread_pool.c linenumber=329 pthread_mutex_unlock linenumber=330 __assert_fail linenumber=132 pthread_cond_broadcast linenumber=137 pthread_mutex_unlock linenumber=141 pthread_mutex_lock linenumber=617 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=620 pthread_mutex_unlock linenumber=630 pthread_mutex_lock linenumber=641 hts_tpool_process_shutdown_locked /src/htslib/thread_pool.c linenumber=645 pthread_mutex_unlock linenumber=650 pthread_mutex_unlock linenumber=786 pthread_attr_destroy linenumber=787 __errno_location linenumber=796 __errno_location linenumber=797 strerror linenumber=797 hts_log /src/htslib/hts.c linenumber=797 pthread_mutex_unlock linenumber=800 pthread_join linenumber=802 pthread_cond_destroy linenumber=803 pthread_mutex_destroy linenumber=805 pthread_attr_destroy linenumber=807 __errno_location linenumber=811 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5870 pthread_cond_init linenumber=377 pthread_cond_init linenumber=378 pthread_cond_init linenumber=379 pthread_cond_init linenumber=380 hts_tpool_process_attach /src/htslib/thread_pool.c linenumber=402 pthread_mutex_lock linenumber=457 __assert_fail linenumber=468 pthread_mutex_unlock linenumber=469 hts_tpool_size /src/htslib/thread_pool.c linenumber=5884 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5883 hts_log /src/htslib/hts.c linenumber=5950 __errno_location linenumber=5951 bgzf_hopen /src/htslib/bgzf.c linenumber=1596 __errno_location linenumber=1605 hts_process_opts /src/htslib/hts.c linenumber=1610 hts_parse_opt_list /src/htslib/hts.c linenumber=1417 strncpy linenumber=1313 hts_opt_add /src/htslib/hts.c linenumber=1316 strdup linenumber=1037 strchr linenumber=1042 strcmp linenumber=1047 strcmp linenumber=1048 atoi linenumber=1049 strcmp linenumber=1051 strcmp linenumber=1052 atoi linenumber=1053 strcmp linenumber=1055 strcmp linenumber=1056 atoi linenumber=1057 strcmp linenumber=1059 strcmp linenumber=1060 atoi linenumber=1061 strcmp linenumber=1063 strcmp linenumber=1064 atoi linenumber=1065 strcmp linenumber=1067 strcmp linenumber=1068 atoi linenumber=1069 strcmp linenumber=1071 strcmp linenumber=1072 atoi linenumber=1073 strcmp linenumber=1075 strcmp linenumber=1076 atoi linenumber=1077 strcmp linenumber=1079 strcmp linenumber=1080 atoi linenumber=1081 strcmp linenumber=1083 strcmp linenumber=1084 atoi linenumber=1085 strcmp linenumber=1087 strcmp linenumber=1088 atoi linenumber=1089 strcmp linenumber=1091 strcmp linenumber=1092 atoi linenumber=1093 strcmp linenumber=1095 strcmp linenumber=1096 atoi linenumber=1097 strcmp linenumber=1099 strcmp linenumber=1100 atoi linenumber=1101 strcmp linenumber=1104 atoi linenumber=1105 strcmp linenumber=1107 strcmp linenumber=1108 strcmp linenumber=1111 strcmp linenumber=1112 strcmp linenumber=1115 strcmp linenumber=1116 strcmp linenumber=1119 strcmp linenumber=1120 strcmp linenumber=1123 strcmp linenumber=1124 strcmp linenumber=1127 strcmp linenumber=1128 strcmp linenumber=1131 strcmp linenumber=1132 atoi linenumber=1133 strcmp linenumber=1135 strcmp linenumber=1136 atoi linenumber=1137 strcmp linenumber=1139 strcmp linenumber=1140 strtol linenumber=1143 hts_log /src/htslib/hts.c linenumber=1152 strcmp linenumber=1159 strcmp linenumber=1160 strtol linenumber=1161 strcmp linenumber=1163 strcmp linenumber=1164 strtol linenumber=1165 strcmp linenumber=1167 strcmp linenumber=1168 strcmp linenumber=1171 strcmp linenumber=1172 atoi linenumber=1173 strcmp linenumber=1175 strcmp linenumber=1176 atoi linenumber=1177 strcmp linenumber=1179 strcmp linenumber=1180 strtol linenumber=1181 strcmp linenumber=1183 strcmp linenumber=1184 strtol linenumber=1185 strcmp linenumber=1187 strcmp linenumber=1188 strcmp linenumber=1191 strcmp linenumber=1192 strcmp linenumber=1195 strcmp linenumber=1196 strcmp linenumber=1199 strcmp linenumber=1200 strcmp linenumber=1203 strcmp linenumber=1204 strcmp linenumber=1207 strcmp linenumber=1208 strcmp linenumber=1211 strcmp linenumber=1212 strcmp linenumber=1215 strcmp linenumber=1216 hts_log /src/htslib/hts.c linenumber=1220 hts_opt_apply /src/htslib/hts.c linenumber=1420 strdup linenumber=1253 hts_set_opt /src/htslib/hts.c linenumber=1263 hts_set_threads /src/htslib/hts.c linenumber=1800 sam_set_threads /src/htslib/sam.c linenumber=1925 hts_tpool_init /src/htslib/thread_pool.c linenumber=3751 sam_set_thread_pool /src/htslib/sam.c linenumber=3754 sam_state_create /src/htslib/sam.c linenumber=3723 calloc linenumber=3056 pthread_mutex_init linenumber=3727 pthread_mutex_init linenumber=3728 pthread_cond_init linenumber=3729 hts_tpool_size /src/htslib/thread_pool.c linenumber=3733 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=3734 sam_state_destroy /src/htslib/sam.c linenumber=3736 pthread_mutex_lock linenumber=3102 pthread_cond_signal linenumber=3105 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3108 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3115 pthread_mutex_unlock linenumber=3116 hts_usleep /src/htslib/./hts_internal.h linenumber=3117 pthread_mutex_lock linenumber=3118 pthread_mutex_unlock linenumber=3121 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3127 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=831 sam_format_worker /src/htslib/sam.c linenumber=3127 pthread_mutex_lock linenumber=3660 pthread_mutex_unlock linenumber=3665 calloc linenumber=3668 sam_state_err /src/htslib/sam.c linenumber=3670 pthread_mutex_lock linenumber=3070 pthread_mutex_unlock linenumber=3073 sam_format1_append /src/htslib/sam.c linenumber=3682 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4332 __errno_location linenumber=279 ks_resize /src/htslib/./htslib/kstring.h linenumber=280 kputc_ /src/htslib/./htslib/kstring.h linenumber=4333 ks_resize /src/htslib/./htslib/kstring.h linenumber=270 kputw /src/htslib/./htslib/kstring.h linenumber=4334 ks_resize /src/htslib/./htslib/kstring.h linenumber=376 kputuw /src/htslib/./htslib/kstring.h linenumber=381 ks_resize /src/htslib/./htslib/kstring.h linenumber=320 ks_resize /src/htslib/./htslib/kstring.h linenumber=350 kputc_ /src/htslib/./htslib/kstring.h linenumber=4334 kputs /src/htslib/./htslib/kstring.h linenumber=4336 kputc_ /src/htslib/./htslib/kstring.h linenumber=4337 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4338 kputll /src/htslib/./htslib/kstring.h linenumber=4339 ks_resize /src/htslib/./htslib/kstring.h linenumber=388 kputuw /src/htslib/./htslib/kstring.h linenumber=398 kputc_ /src/htslib/./htslib/kstring.h linenumber=4339 kputw /src/htslib/./htslib/kstring.h linenumber=4340 kputc_ /src/htslib/./htslib/kstring.h linenumber=4340 kputw /src/htslib/./htslib/kstring.h linenumber=4344 kputc_ /src/htslib/./htslib/kstring.h linenumber=4345 kputc_ /src/htslib/./htslib/kstring.h linenumber=4347 kputc_ /src/htslib/./htslib/kstring.h linenumber=4348 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4349 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4350 kputs /src/htslib/./htslib/kstring.h linenumber=4352 kputc_ /src/htslib/./htslib/kstring.h linenumber=4353 kputll /src/htslib/./htslib/kstring.h linenumber=4355 kputc_ /src/htslib/./htslib/kstring.h linenumber=4355 kputll /src/htslib/./htslib/kstring.h linenumber=4356 kputc_ /src/htslib/./htslib/kstring.h linenumber=4356 ks_resize /src/htslib/./htslib/kstring.h linenumber=4359 nibble2base /src/htslib/./sam_internal.h linenumber=4363 add33 /src/htslib/sam.c linenumber=4373 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4379 kputc_ /src/htslib/./htslib/kstring.h linenumber=4385 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4386 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1470 kputc_ /src/htslib/./htslib/kstring.h linenumber=1471 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1473 kputw /src/htslib/./htslib/kstring.h linenumber=1474 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1477 kputw /src/htslib/./htslib/kstring.h linenumber=1478 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1482 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1483 kputuw /src/htslib/./htslib/kstring.h linenumber=1483 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1488 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1489 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=241 kputw /src/htslib/./htslib/kstring.h linenumber=1489 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1494 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1495 kputuw /src/htslib/./htslib/kstring.h linenumber=1495 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1500 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1501 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=252 kputw /src/htslib/./htslib/kstring.h linenumber=1501 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1505 kputc_ /src/htslib/./htslib/kstring.h linenumber=1506 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1511 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=314 ksprintf /src/htslib/kstring.c linenumber=1511 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=1521 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=330 ksprintf /src/htslib/kstring.c linenumber=1521 kputc_ /src/htslib/./htslib/kstring.h linenumber=1525 kputc_ /src/htslib/./htslib/kstring.h linenumber=1526 kputc_ /src/htslib/./htslib/kstring.h linenumber=1527 kputsn /src/htslib/./htslib/kstring.h linenumber=1528 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1555 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1559 kputc /src/htslib/./htslib/kstring.h linenumber=1560 ks_expand /src/htslib/./htslib/kstring.h linenumber=1563 __errno_location linenumber=183 ks_resize /src/htslib/./htslib/kstring.h linenumber=184 kputw /src/htslib/./htslib/kstring.h linenumber=1566 ks_expand /src/htslib/./htslib/kstring.h linenumber=1571 kputuw /src/htslib/./htslib/kstring.h linenumber=1574 ks_expand /src/htslib/./htslib/kstring.h linenumber=1579 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1582 kputw /src/htslib/./htslib/kstring.h linenumber=1582 ks_expand /src/htslib/./htslib/kstring.h linenumber=1587 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1590 kputuw /src/htslib/./htslib/kstring.h linenumber=1590 ks_expand /src/htslib/./htslib/kstring.h linenumber=1595 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1598 kputw /src/htslib/./htslib/kstring.h linenumber=1598 ks_expand /src/htslib/./htslib/kstring.h linenumber=1603 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1606 kputuw /src/htslib/./htslib/kstring.h linenumber=1606 ks_expand /src/htslib/./htslib/kstring.h linenumber=1611 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1615 kputd /src/htslib/kstring.c linenumber=1615 __errno_location linenumber=1628 hts_log /src/htslib/hts.c linenumber=1632 __errno_location linenumber=1633 kputsn /src/htslib/./htslib/kstring.h linenumber=4389 hts_log /src/htslib/hts.c linenumber=4395 __errno_location linenumber=4397 hts_log /src/htslib/hts.c linenumber=4401 __errno_location linenumber=4402 __errno_location linenumber=3683 sam_state_err /src/htslib/sam.c linenumber=3683 kputc /src/htslib/./htslib/kstring.h linenumber=3686 pthread_mutex_lock linenumber=3689 pthread_mutex_unlock linenumber=3703 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3131 pthread_mutex_lock linenumber=3132 pthread_mutex_unlock linenumber=3134 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3136 hts_usleep /src/htslib/./hts_internal.h linenumber=3137 pthread_mutex_lock linenumber=3138 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=3141 pthread_mutex_unlock linenumber=3143 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3146 pthread_join linenumber=3151 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=3157 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3160 pthread_mutex_destroy linenumber=3163 pthread_mutex_destroy linenumber=3164 pthread_cond_destroy linenumber=3165 sam_free_sp_bams /src/htslib/sam.c linenumber=3180 sam_free_sp_bams /src/htslib/sam.c linenumber=3185 bam_hdr_destroy /src/htslib/./htslib/sam.h linenumber=3191 sam_hdr_destroy /src/htslib/sam.c linenumber=401 bgzf_thread_pool /src/htslib/bgzf.c linenumber=3741 calloc linenumber=1748 hts_tpool_size /src/htslib/thread_pool.c linenumber=1753 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=1756 hts_tpool_process_ref_incr /src/htslib/thread_pool.c linenumber=1758 pthread_mutex_lock linenumber=269 pthread_mutex_unlock linenumber=271 pool_create /src/htslib/cram/pooled_alloc.c linenumber=1760 pthread_mutex_init linenumber=1764 pthread_mutex_init linenumber=1765 pthread_mutex_init linenumber=1766 pthread_cond_init linenumber=1767 pthread_create linenumber=1772 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3757 hts_get_bgzfp /src/htslib/hts.c linenumber=1927 bgzf_mt /src/htslib/bgzf.c linenumber=1927 hts_tpool_init /src/htslib/thread_pool.c linenumber=1790 bgzf_thread_pool /src/htslib/bgzf.c linenumber=1795 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=1796 hts_set_opt /src/htslib/hts.c linenumber=1929 hts_hfile /src/htslib/hts.c linenumber=1804 bgzf_hfile /src/htslib/bgzf.c linenumber=1778 cram_hfile /src/htslib/./cram/cram_io.h linenumber=1779 bgzf_hfile /src/htslib/bgzf.c linenumber=1785 hfile_set_blksize /src/htslib/hfile.c linenumber=1808 hts_log /src/htslib/hts.c linenumber=1809 hts_log /src/htslib/hts.c linenumber=1814 hts_set_thread_pool /src/htslib/hts.c linenumber=1824 sam_set_thread_pool /src/htslib/sam.c linenumber=1936 hts_get_bgzfp /src/htslib/hts.c linenumber=1938 bgzf_thread_pool /src/htslib/bgzf.c linenumber=1938 hts_set_opt /src/htslib/hts.c linenumber=1940 hts_set_cache_size /src/htslib/hts.c linenumber=1831 hts_get_bgzfp /src/htslib/hts.c linenumber=1948 bgzf_set_cache_size /src/htslib/bgzf.c linenumber=1948 fastq_state_set /src/htslib/sam.c linenumber=1840 fastq_state_init /src/htslib/sam.c linenumber=3821 calloc linenumber=3787 strcpy linenumber=3790 regcomp linenumber=3794 strcmp linenumber=3841 kh_init_tag /src/htslib/sam.c linenumber=3843 calloc linenumber=62 strlen linenumber=3846 hts_log /src/htslib/hts.c linenumber=3850 kh_put_tag /src/htslib/sam.c linenumber=3854 kh_resize_tag /src/htslib/sam.c linenumber=62 realloc linenumber=62 strncpy linenumber=3866 strcmp linenumber=3876 __ctype_b_loc linenumber=3880 isalnum_c /src/htslib/./textutils_internal.h linenumber=3880 strncpy linenumber=3885 hts_log /src/htslib/hts.c linenumber=3899 regfree linenumber=3909 regcomp linenumber=3910 hts_log /src/htslib/hts.c linenumber=3911 fastq_state_set /src/htslib/sam.c linenumber=1849 fastq_state_set /src/htslib/sam.c linenumber=1861 cram_set_option /src/htslib/cram/cram_io.c linenumber=1873 hts_set_filter_expression /src/htslib/hts.c linenumber=1881 hts_filter_free /src/htslib/hts_expr.c linenumber=1970 regfree linenumber=869 hts_filter_init /src/htslib/hts_expr.c linenumber=1975 calloc linenumber=850 strlen linenumber=854 strcpy linenumber=859 cram_set_voption /src/htslib/cram/cram_io.c linenumber=1914 hts_set_opt /src/htslib/hts.c linenumber=1267 hts_opt_free /src/htslib/hts.c linenumber=1421 hts_opt_free /src/htslib/hts.c linenumber=1425 hclose_abruptly /src/htslib/hfile.c linenumber=1618 hts_log /src/htslib/hts.c linenumber=1623 hclose_abruptly /src/htslib/hfile.c linenumber=1626 hclose /src/htslib/hfile.c linenumber=188 abort linenumber=189 hts_close /src/htslib/hts.c linenumber=194 __errno_location linenumber=1643 bgzf_close /src/htslib/bgzf.c linenumber=1651 cram_eof /src/htslib/cram/cram_io.c linenumber=1656 hts_log /src/htslib/hts.c linenumber=1658 cram_close /src/htslib/cram/cram_io.c linenumber=1665 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=5565 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=5567 pthread_mutex_lock linenumber=4286 reset_metrics /src/htslib/cram/cram_io.c linenumber=4289 pthread_mutex_unlock linenumber=4254 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=4255 pthread_mutex_lock linenumber=4256 pthread_mutex_unlock linenumber=4292 cram_flush_container /src/htslib/cram/cram_io.c linenumber=4295 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=4143 pthread_mutex_lock linenumber=1864 hts_log /src/htslib/hts.c linenumber=1867 hts_log /src/htslib/hts.c linenumber=1872 pthread_mutex_unlock linenumber=1875 pthread_mutex_lock linenumber=1879 pthread_mutex_unlock linenumber=1881 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1893 pthread_mutex_lock linenumber=3423 hts_log /src/htslib/hts.c linenumber=3438 pthread_mutex_unlock linenumber=3439 pthread_mutex_lock linenumber=3456 hts_log /src/htslib/hts.c linenumber=3459 cram_populate_ref /src/htslib/cram/cram_io.c linenumber=3461 getenv linenumber=2978 getenv linenumber=2983 hts_log /src/htslib/hts.c linenumber=2987 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2992 sam_hrecs_find_key /src/htslib/header.c linenumber=2995 hts_log /src/htslib/hts.c linenumber=2998 expand_cache_path /src/htslib/cram/cram_io.c linenumber=3003 strchr linenumber=2889 strncpy linenumber=2891 strlen linenumber=2896 strcpy linenumber=2898 strtol linenumber=2907 strlen linenumber=2908 strncpy linenumber=2911 strlen linenumber=2930 strcpy linenumber=2932 strlen linenumber=2936 strcpy linenumber=2940 stat linenumber=3004 stat linenumber=3025 bgzf_open /src/htslib/bgzf.c linenumber=3027 string_dup /src/htslib/cram/string_alloc.c linenumber=3031 bgzf_close /src/htslib/bgzf.c linenumber=3034 open_path_mfile /src/htslib/cram/open_trace_file.c linenumber=3050 getenv linenumber=363 tokenise_search_path /src/htslib/cram/open_trace_file.c linenumber=364 strlen linenumber=117 strncmp linenumber=132 strncmp linenumber=133 strncmp linenumber=134 strncmp linenumber=135 strncmp linenumber=136 strncmp linenumber=137 strncmp linenumber=138 strncmp linenumber=139 strncmp linenumber=140 strncmp linenumber=388 find_file_url /src/htslib/cram/open_trace_file.c linenumber=389 expand_path /src/htslib/cram/open_trace_file.c linenumber=191 strlen linenumber=232 strlen linenumber=233 hts_log /src/htslib/hts.c linenumber=239 strchr linenumber=256 strtol linenumber=259 hopen /src/htslib/hfile.c linenumber=195 __errno_location linenumber=196 __errno_location linenumber=197 strerror linenumber=197 hts_log /src/htslib/hts.c linenumber=197 mfcreate /src/htslib/cram/mFILE.c linenumber=201 hread /src/htslib/cram/../htslib/hfile.h linenumber=203 mfwrite /src/htslib/cram/mFILE.c linenumber=204 realloc linenumber=538 hclose_abruptly /src/htslib/hfile.c linenumber=205 hclose /src/htslib/hfile.c linenumber=209 __errno_location linenumber=210 strerror linenumber=210 hts_log /src/htslib/hts.c linenumber=210 mrewind /src/htslib/cram/mFILE.c linenumber=215 mfdestroy /src/htslib/cram/mFILE.c linenumber=219 strncmp linenumber=391 hisremote /src/htslib/hfile.c linenumber=395 find_file_url /src/htslib/cram/open_trace_file.c linenumber=396 find_file_dir /src/htslib/cram/open_trace_file.c linenumber=402 expand_path /src/htslib/cram/open_trace_file.c linenumber=318 is_file /src/htslib/cram/open_trace_file.c linenumber=322 stat linenumber=92 mfopen /src/htslib/cram/mFILE.c linenumber=323 fopen linenumber=350 mfreopen /src/htslib/cram/mFILE.c linenumber=352 strchr linenumber=276 strchr linenumber=278 strchr linenumber=280 strchr linenumber=282 strchr linenumber=284 strchr linenumber=286 strchr linenumber=292 mfcreate /src/htslib/cram/mFILE.c linenumber=297 mfmmap /src/htslib/cram/mFILE.c linenumber=302 stat linenumber=130 fileno linenumber=135 mmap linenumber=134 mfload /src/htslib/cram/mFILE.c linenumber=309 stat linenumber=88 realloc linenumber=101 fread linenumber=109 feof linenumber=112 fseek linenumber=316 mfcreate /src/htslib/cram/mFILE.c linenumber=321 hts_log /src/htslib/hts.c linenumber=324 fseek linenumber=336 strlen linenumber=372 strcpy linenumber=414 strrchr linenumber=415 find_file_dir /src/htslib/cram/open_trace_file.c linenumber=417 mfsteal /src/htslib/cram/mFILE.c linenumber=3052 mfdetach /src/htslib/cram/mFILE.c linenumber=437 mfflush /src/htslib/cram/mFILE.c linenumber=393 fclose linenumber=398 mfdestroy /src/htslib/cram/mFILE.c linenumber=441 sam_hrecs_find_key /src/htslib/header.c linenumber=3070 strstr linenumber=3073 strncmp linenumber=3074 hts_log /src/htslib/hts.c linenumber=3076 strncmp linenumber=3080 bgzf_close /src/htslib/bgzf.c linenumber=3085 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3089 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3091 bgzf_close /src/htslib/bgzf.c linenumber=3095 refs2id /src/htslib/cram/cram_io.c linenumber=3103 expand_cache_path /src/htslib/cram/cram_io.c linenumber=3116 hts_log /src/htslib/hts.c linenumber=3119 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=3120 strrchr linenumber=2948 is_directory /src/htslib/cram/cram_io.c linenumber=2953 stat linenumber=2875 mkdir linenumber=2958 chmod linenumber=2959 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2964 mkdir linenumber=2965 chmod linenumber=2966 hts_open_tmpfile /src/htslib/hts.c linenumber=3122 getpid linenumber=1981 time linenumber=1988 clock linenumber=1988 ks_clear /src/htslib/./htslib/kstring.h linenumber=1991 ksprintf /src/htslib/kstring.c linenumber=1992 hopen /src/htslib/hfile.c linenumber=1994 __errno_location linenumber=1995 perror linenumber=3124 hts_md5_init /src/htslib/md5.c linenumber=3136 hts_md5_reset /src/htslib/md5.c linenumber=329 hclose_abruptly /src/htslib/hfile.c linenumber=3137 unlink linenumber=3138 hts_md5_update /src/htslib/md5.c linenumber=3142 body /src/htslib/md5.c linenumber=260 body /src/htslib/md5.c linenumber=264 hts_md5_final /src/htslib/md5.c linenumber=3143 body /src/htslib/md5.c linenumber=283 body /src/htslib/md5.c linenumber=300 hts_md5_destroy /src/htslib/md5.c linenumber=3144 hts_md5_hex /src/htslib/md5.c linenumber=3145 strncmp linenumber=3147 hts_log /src/htslib/hts.c linenumber=3148 hclose_abruptly /src/htslib/hfile.c linenumber=3149 unlink linenumber=3150 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=3155 hclose /src/htslib/hfile.c linenumber=3156 chmod linenumber=3157 rename linenumber=3158 __errno_location linenumber=3159 strerror linenumber=3159 hts_log /src/htslib/hts.c linenumber=3159 unlink linenumber=3161 hts_log /src/htslib/hts.c linenumber=3462 hts_log /src/htslib/hts.c linenumber=3464 pthread_mutex_unlock linenumber=3465 pthread_mutex_unlock linenumber=3466 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3471 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3503 cram_ref_load /src/htslib/cram/cram_io.c linenumber=3506 __assert_fail linenumber=3332 __assert_fail linenumber=3342 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3346 strcmp linenumber=3354 bgzf_close /src/htslib/bgzf.c linenumber=3356 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3359 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3365 bgzf_useek /src/htslib/bgzf.c linenumber=3254 hseek /src/htslib/hfile.c linenumber=2559 bgzf_read_block /src/htslib/bgzf.c linenumber=2567 bgzf_seek_common /src/htslib/bgzf.c linenumber=2592 pthread_mutex_lock linenumber=2192 pthread_cond_signal linenumber=2199 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=2200 pthread_cond_wait linenumber=2202 pthread_cond_signal linenumber=2207 abort linenumber=2210 __errno_location linenumber=2218 pthread_mutex_unlock linenumber=2219 pthread_mutex_unlock linenumber=2227 hseek /src/htslib/hfile.c linenumber=2229 bgzf_read_block /src/htslib/bgzf.c linenumber=2595 __assert_fail linenumber=2607 perror linenumber=3255 bgzf_read /src/htslib/bgzf.c linenumber=3263 __assert_fail linenumber=1246 bgzf_read_block /src/htslib/bgzf.c linenumber=1251 hts_log /src/htslib/hts.c linenumber=1253 bgzf_htell /src/htslib/bgzf.c linenumber=1263 hts_log /src/htslib/hts.c linenumber=1268 bgzf_htell /src/htslib/bgzf.c linenumber=1283 perror linenumber=3264 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3281 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3286 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3295 hts_log /src/htslib/hts.c linenumber=3302 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=3309 toupper linenumber=180 pthread_mutex_unlock linenumber=3507 pthread_mutex_unlock linenumber=3508 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3516 pthread_mutex_unlock linenumber=3532 pthread_mutex_unlock linenumber=3533 pthread_mutex_unlock linenumber=3553 pthread_mutex_unlock linenumber=3554 strcmp linenumber=3559 bgzf_close /src/htslib/bgzf.c linenumber=3561 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3564 pthread_mutex_unlock linenumber=3565 pthread_mutex_unlock linenumber=3566 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3571 pthread_mutex_unlock linenumber=3572 pthread_mutex_unlock linenumber=3573 pthread_mutex_unlock linenumber=3586 pthread_mutex_unlock linenumber=3587 hts_log /src/htslib/hts.c linenumber=1897 hts_log /src/htslib/hts.c linenumber=1899 pthread_mutex_lock linenumber=1901 pthread_mutex_unlock linenumber=1904 hts_log /src/htslib/hts.c linenumber=1909 hts_log /src/htslib/hts.c linenumber=1912 hts_log /src/htslib/hts.c linenumber=1913 hts_log /src/htslib/hts.c linenumber=1916 pthread_mutex_lock linenumber=1918 pthread_mutex_unlock linenumber=1920 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1923 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1805 sam_hrecs_find_key /src/htslib/header.c linenumber=1810 hts_md5_init /src/htslib/md5.c linenumber=1821 hts_md5_update /src/htslib/md5.c linenumber=1823 hts_md5_final /src/htslib/md5.c linenumber=1824 hts_md5_destroy /src/htslib/md5.c linenumber=1825 hts_md5_hex /src/htslib/md5.c linenumber=1826 strcmp linenumber=1829 hts_log /src/htslib/hts.c linenumber=1830 hts_log /src/htslib/hts.c linenumber=1832 cram_ref_incr /src/htslib/cram/cram_io.c linenumber=1956 pthread_mutex_lock linenumber=3184 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3185 pthread_mutex_unlock linenumber=3186 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1963 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1964 hts_log /src/htslib/hts.c linenumber=1967 __assert_fail linenumber=1982 lossy_read_names /src/htslib/cram/cram_encode.c linenumber=1986 kh_init_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1351 calloc linenumber=54 expected_template_count /src/htslib/cram/cram_encode.c linenumber=1369 bam_aux_get /src/htslib/sam.c linenumber=1304 bam_aux_first /src/htslib/sam.c linenumber=4845 __errno_location linenumber=4823 skip_aux /src/htslib/sam.c linenumber=4848 aux_type2size /src/htslib/sam.c linenumber=4798 memchr linenumber=4802 aux_type2size /src/htslib/sam.c linenumber=4806 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=4807 bam_aux_next /src/htslib/sam.c linenumber=4845 skip_aux /src/htslib/sam.c linenumber=4830 __errno_location linenumber=4832 hts_log /src/htslib/hts.c linenumber=4836 __errno_location linenumber=4838 hts_log /src/htslib/hts.c linenumber=4859 __errno_location linenumber=4861 bam_data_end /src/htslib/cram/cram_encode.c linenumber=1306 bam_aux2i_end /src/htslib/cram/cram_encode.c linenumber=1306 __errno_location linenumber=1258 __errno_location linenumber=1264 __errno_location linenumber=1270 le_to_i16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1273 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=241 __errno_location linenumber=1276 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1279 __errno_location linenumber=1282 le_to_i32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1285 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=252 __errno_location linenumber=1288 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1291 __errno_location linenumber=1293 bam_aux_get /src/htslib/sam.c linenumber=1311 kh_put_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1372 kh_resize_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=54 realloc linenumber=54 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=54 strcmp linenumber=54 kh_get_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1404 kh_destroy_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1417 cram_generate_reference /src/htslib/cram/cram_encode.c linenumber=1997 extend_ref /src/htslib/cram/cram_encode.c linenumber=1744 realloc linenumber=1527 realloc linenumber=1532 hts_log /src/htslib/hts.c linenumber=1755 cram_add_to_ref /src/htslib/cram/cram_encode.c linenumber=1759 bam_aux_get /src/htslib/sam.c linenumber=1662 cram_add_to_ref_MD /src/htslib/cram/cram_encode.c linenumber=1666 bam_cigar2rlen /src/htslib/sam.c linenumber=1562 extend_ref /src/htslib/cram/cram_encode.c linenumber=1566 __ctype_b_loc linenumber=1576 hts_str2uint /src/htslib/cram/../textutils_internal.h linenumber=1579 extend_ref /src/htslib/cram/cram_encode.c linenumber=1581 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1586 hts_log /src/htslib/hts.c linenumber=1593 __ctype_b_loc linenumber=1612 extend_ref /src/htslib/cram/cram_encode.c linenumber=1613 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1616 hts_log /src/htslib/hts.c linenumber=1622 extend_ref /src/htslib/cram/cram_encode.c linenumber=1630 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1633 hts_log /src/htslib/hts.c linenumber=1639 extend_ref /src/htslib/cram/cram_encode.c linenumber=1694 hts_log /src/htslib/hts.c linenumber=2007 hts_log /src/htslib/hts.c linenumber=2011 pthread_mutex_lock linenumber=2014 pthread_mutex_unlock linenumber=2018 pthread_mutex_lock linenumber=2022 pthread_mutex_unlock linenumber=2024 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2043 pthread_mutex_lock linenumber=3214 cram_ref_decr_locked /src/htslib/cram/cram_io.c linenumber=3215 __assert_fail linenumber=3199 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3205 pthread_mutex_unlock linenumber=3216 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2045 hts_log /src/htslib/hts.c linenumber=2046 validate_md5 /src/htslib/cram/cram_encode.c linenumber=2050 process_one_read /src/htslib/cram/cram_encode.c linenumber=2062 bam_aux_get /src/htslib/sam.c linenumber=3406 bam_aux_get /src/htslib/sam.c linenumber=3415 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3422 kh_init_m_i2i /src/htslib/cram/cram_structs.h linenumber=64 calloc linenumber=64 kh_put_m_i2i /src/htslib/cram/cram_structs.h linenumber=69 kh_resize_m_i2i /src/htslib/cram/cram_structs.h linenumber=64 realloc linenumber=64 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3424 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3444 block_grow /src/htslib/cram/cram_io.h linenumber=3460 block_resize /src/htslib/cram/cram_io.h linenumber=244 block_resize_exact /src/htslib/cram/cram_io.h linenumber=233 realloc linenumber=217 block_grow /src/htslib/cram/cram_io.h linenumber=3461 nibble2base /src/htslib/cram/../sam_internal.h linenumber=3466 hts_log /src/htslib/hts.c linenumber=3479 realloc linenumber=3487 hts_log /src/htslib/hts.c linenumber=3521 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3534 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=320 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=350 kputc /src/htslib/cram/../htslib/kstring.h linenumber=3535 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=261 cram_add_substitution /src/htslib/cram/cram_encode.c linenumber=3598 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2611 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2618 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2619 block_append_char /src/htslib/cram/cram_io.h linenumber=2620 block_grow /src/htslib/cram/cram_io.h linenumber=262 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2622 realloc linenumber=2578 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2585 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2588 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2593 cram_add_bases /src/htslib/cram/cram_encode.c linenumber=3611 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2638 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3617 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2649 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2650 block_append_char /src/htslib/cram/cram_io.h linenumber=2651 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2652 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3626 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3642 kputc_ /src/htslib/cram/../htslib/kstring.h linenumber=3644 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=270 kputsn /src/htslib/cram/../htslib/kstring.h linenumber=3645 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=246 cram_add_deletion /src/htslib/cram/cram_encode.c linenumber=3651 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2679 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2680 cram_add_skip /src/htslib/cram/cram_encode.c linenumber=3658 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2735 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2736 cram_add_insertion /src/htslib/cram/cram_encode.c linenumber=3665 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2757 block_append /src/htslib/cram/cram_io.h linenumber=2763 block_grow /src/htslib/cram/cram_io.h linenumber=249 block_append_char /src/htslib/cram/cram_io.h linenumber=2767 block_append_char /src/htslib/cram/cram_io.h linenumber=2769 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2771 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3670 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2665 block_append_char /src/htslib/cram/cram_io.h linenumber=2666 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2667 cram_add_softclip /src/htslib/cram/cram_encode.c linenumber=3679 block_append /src/htslib/cram/cram_io.h linenumber=2692 block_append_char /src/htslib/cram/cram_io.h linenumber=2693 block_append /src/htslib/cram/cram_io.h linenumber=2700 block_append_char /src/htslib/cram/cram_io.h linenumber=2704 block_append_char /src/htslib/cram/cram_io.h linenumber=2706 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2713 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3688 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3692 cram_add_hardclip /src/htslib/cram/cram_encode.c linenumber=3701 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2725 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2726 cram_add_pad /src/htslib/cram/cram_encode.c linenumber=3706 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2745 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2746 hts_log /src/htslib/hts.c linenumber=3711 hts_log /src/htslib/hts.c linenumber=3716 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3722 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3726 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3735 cram_encode_aux /src/htslib/cram/cram_encode.c linenumber=3743 bam_data_end /src/htslib/cram/cram_encode.c linenumber=2793 hts_log /src/htslib/hts.c linenumber=2836 sam_hrecs_find_rg /src/htslib/header.c linenumber=2840 kh_get_m_s2i /src/htslib/./header.h linenumber=3069 block_append /src/htslib/cram/cram_io.h linenumber=2843 hts_log /src/htslib/hts.c linenumber=2847 strncasecmp linenumber=2855 hts_log /src/htslib/hts.c linenumber=2858 block_append /src/htslib/cram/cram_io.h linenumber=2863 bam_aux2i_end /src/htslib/cram/cram_encode.c linenumber=2872 hts_log /src/htslib/hts.c linenumber=2879 block_append /src/htslib/cram/cram_io.h linenumber=2883 block_append /src/htslib/cram/cram_io.h linenumber=2889 kh_put_m_tagmap /src/htslib/cram/cram_structs.h linenumber=2896 kh_resize_m_tagmap /src/htslib/cram/cram_structs.h linenumber=394 realloc linenumber=394 pthread_mutex_lock linenumber=2906 kh_put_m_metrics /src/htslib/cram/cram_structs.h linenumber=2907 kh_resize_m_metrics /src/htslib/cram/cram_structs.h linenumber=308 realloc linenumber=308 pthread_mutex_unlock linenumber=2909 cram_new_metrics /src/htslib/cram/cram_io.c linenumber=2913 kh_del_m_metrics /src/htslib/cram/cram_structs.h linenumber=2915 pthread_mutex_unlock linenumber=2916 pthread_mutex_unlock linenumber=2921 calloc linenumber=2925 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2937 cram_encoding2str /src/htslib/cram/cram_codecs.c linenumber=3952 hts_log /src/htslib/hts.c linenumber=3952 cram_encoding2str /src/htslib/cram/cram_codecs.c linenumber=3958 hts_log /src/htslib/hts.c linenumber=3958 abort linenumber=3959 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2955 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2956 realloc linenumber=149 realloc linenumber=150 realloc linenumber=176 realloc linenumber=177 __assert_fail linenumber=199 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2961 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2980 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2981 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2986 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3004 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=3005 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=3010 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=3032 hts_log /src/htslib/hts.c linenumber=3039 pthread_mutex_lock linenumber=3049 pthread_mutex_unlock linenumber=3051 cram_new_block /src/htslib/cram/cram_io.c linenumber=3065 block_append_char /src/htslib/cram/cram_io.h linenumber=3073 cram_new_block /src/htslib/cram/cram_io.c linenumber=3082 block_append /src/htslib/cram/cram_io.h linenumber=3089 cram_new_block /src/htslib/cram/cram_io.c linenumber=3098 block_append /src/htslib/cram/cram_io.h linenumber=3105 cram_new_block /src/htslib/cram/cram_io.c linenumber=3114 block_append /src/htslib/cram/cram_io.h linenumber=3121 cram_new_block /src/htslib/cram/cram_io.c linenumber=3130 hts_log /src/htslib/hts.c linenumber=3140 cram_new_block /src/htslib/cram/cram_io.c linenumber=3161 cram_new_block /src/htslib/cram/cram_io.c linenumber=3164 hts_log /src/htslib/hts.c linenumber=3189 hts_log /src/htslib/hts.c linenumber=3203 block_append_char /src/htslib/cram/cram_io.h linenumber=3212 kh_put_m_s2i /src/htslib/cram/../header.h linenumber=3215 kh_resize_m_s2i /src/htslib/cram/../header.h linenumber=169 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=169 string_ndup /src/htslib/cram/string_alloc.c linenumber=3223 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3234 sam_hrecs_find_rg /src/htslib/header.c linenumber=3752 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3758 block_grow /src/htslib/cram/cram_io.h linenumber=3770 block_grow /src/htslib/cram/cram_io.h linenumber=3774 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3799 kh_put_m_s2i /src/htslib/cram/../header.h linenumber=3811 string_ndup /src/htslib/cram/string_alloc.c linenumber=3817 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3933 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3935 cram_stats_del /src/htslib/cram/cram_stats.c linenumber=3942 __assert_fail linenumber=87 kh_get_m_i2i /src/htslib/cram/cram_structs.h linenumber=89 kh_del_m_i2i /src/htslib/cram/cram_structs.h linenumber=93 hts_log /src/htslib/hts.c linenumber=95 hts_log /src/htslib/hts.c linenumber=99 cram_stats_del /src/htslib/cram/cram_stats.c linenumber=3943 cram_stats_del /src/htslib/cram/cram_stats.c linenumber=3946 cram_stats_del /src/htslib/cram/cram_stats.c linenumber=3947 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3963 cram_stats_del /src/htslib/cram/cram_stats.c linenumber=3968 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3974 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3978 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3996 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=4000 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=4004 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=4008 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=4010 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=4018 add_read_names /src/htslib/cram/cram_encode.c linenumber=2082 block_append /src/htslib/cram/cram_io.h linenumber=1450 block_append /src/htslib/cram/cram_io.h linenumber=1453 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=1461 calloc linenumber=2106 __assert_fail linenumber=2126 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2132 pthread_mutex_lock linenumber=2138 pthread_mutex_unlock linenumber=2142 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2146 pthread_mutex_lock linenumber=2148 pthread_mutex_unlock linenumber=2150 hts_log /src/htslib/hts.c linenumber=2154 hts_md5_init /src/htslib/md5.c linenumber=2170 hts_md5_update /src/htslib/md5.c linenumber=2173 hts_md5_final /src/htslib/md5.c linenumber=2176 hts_md5_destroy /src/htslib/md5.c linenumber=2177 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2189 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2189 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2195 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2195 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2208 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2208 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2214 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2223 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2238 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2238 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2246 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2246 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2252 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2252 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2258 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2258 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2264 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2264 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2271 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2271 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2278 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2278 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2284 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2284 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2290 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2290 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2296 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2296 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2302 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2302 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2308 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2308 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2314 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2314 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2331 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2340 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2340 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2354 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2354 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2360 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2360 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2369 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2369 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2376 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2376 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2382 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2382 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2388 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2388 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2394 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2394 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2403 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2430 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2436 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2442 hts_log /src/htslib/hts.c linenumber=2451 cram_encode_slice /src/htslib/cram/cram_encode.c linenumber=2455 calloc linenumber=1122 cram_new_block /src/htslib/cram/cram_io.c linenumber=1129 cram_new_block /src/htslib/cram/cram_io.c linenumber=1135 cram_new_block /src/htslib/cram/cram_io.c linenumber=1144 block_append /src/htslib/cram/cram_io.h linenumber=1147 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1156 cram_new_block /src/htslib/cram/cram_io.c linenumber=1030 cram_new_block /src/htslib/cram/cram_io.c linenumber=1037 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1047 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1050 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1057 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1060 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1066 cram_new_block /src/htslib/cram/cram_io.c linenumber=1068 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1075 cram_new_block /src/htslib/cram/cram_io.c linenumber=1077 cram_encode_slice_read /src/htslib/cram/cram_encode.c linenumber=1176 hts_log /src/htslib/hts.c linenumber=779 cram_free_block /src/htslib/cram/cram_io.c linenumber=1184 cram_free_block /src/htslib/cram/cram_io.c linenumber=1186 cram_free_block /src/htslib/cram/cram_io.c linenumber=1188 cram_free_block /src/htslib/cram/cram_io.c linenumber=1190 cram_compress_slice /src/htslib/cram/cram_encode.c linenumber=1209 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=810 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2319 pthread_mutex_lock linenumber=1979 pthread_mutex_unlock linenumber=2056 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2074 zlib_mem_deflate /src/htslib/cram/cram_io.c linenumber=1778 deflateInit2_ linenumber=1247 hts_log /src/htslib/hts.c linenumber=1249 hts_log /src/htslib/hts.c linenumber=1258 deflate linenumber=1261 hts_log /src/htslib/hts.c linenumber=1264 deflate linenumber=1268 hts_log /src/htslib/hts.c linenumber=1269 deflateEnd linenumber=1273 hts_log /src/htslib/hts.c linenumber=1274 BZ2_bzBuffToBuffCompress linenumber=1788 fqz_compress /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1821 compress_block_fqz2f /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1622 fqz_pick_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1024 calloc linenumber=758 fqz_qual_stats /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=798 calloc linenumber=428 memcmp linenumber=443 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=564 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=565 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=566 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=567 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=568 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=569 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=570 log linenumber=573 log linenumber=574 log linenumber=575 log linenumber=633 log linenumber=635 log linenumber=637 log linenumber=640 log linenumber=641 log linenumber=815 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1060 var_put_u32_safe /src/htslib/htscodecs/htscodecs/varint.h linenumber=208 fqz_store_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1061 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=722 fqz_store_parameters1 /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=727 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=697 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=701 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=705 fqz_create_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1078 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1081 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1082 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1083 compress_new_read /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1126 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=945 RC_Encode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=125 RC_ShiftLowCheck /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=143 SIMPLE_MODEL256_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=954 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=955 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=956 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=957 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=965 SIMPLE_MODEL2_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=967 memcmp linenumber=985 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=986 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=992 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1153 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1155 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1157 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1159 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1161 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1163 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1165 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1167 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1169 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1170 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1171 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1172 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1177 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1179 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1180 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1186 RC_ShiftLowCheck /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=125 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1223 fqz_destroy_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1227 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1229 lzma_mem_deflate /src/htslib/cram/cram_io.c linenumber=1829 lzma_stream_buffer_bound linenumber=1298 lzma_easy_buffer_encode linenumber=1304 rans_compress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1838 rans_compress_O1 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=837 rans_compress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=394 hist8 /src/htslib/htscodecs/htscodecs/utils.h linenumber=95 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=148 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=178 __assert_fail linenumber=126 RansEncSymbolInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=154 __assert_fail linenumber=200 __assert_fail linenumber=201 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=163 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=164 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=165 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=166 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=169 __assert_fail linenumber=285 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=171 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=173 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=184 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=185 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=186 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=187 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=190 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=191 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=192 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=193 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=399 hist1_4 /src/htslib/htscodecs/htscodecs/utils.h linenumber=416 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=287 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=322 RansEncSymbolInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=506 __assert_fail linenumber=516 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=519 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=520 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=521 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=522 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=541 RansEncPutSymbol4 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=556 __assert_fail linenumber=333 __assert_fail linenumber=334 __assert_fail linenumber=335 __assert_fail linenumber=336 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=565 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=566 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=567 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=568 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=570 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=571 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=572 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=573 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=593 rans_compress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=838 rans_compress_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1859 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1583 rans_compress_bound_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1222 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1294 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1324 realloc linenumber=1332 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1363 var_put_u32 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linenumber=1500 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1501 rans_enc_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1531 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1879 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=742 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=755 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=799 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=870 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=885 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=895 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=912 hts_pack /src/htslib/htscodecs/htscodecs/pack.c linenumber=929 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=942 BZ2_bzBuffToBuffCompress linenumber=964 arith_compress_O0_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=985 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=443 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=461 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=464 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=471 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=474 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=475 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=476 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=481 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=490 SIMPLE_MODEL258_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=498 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=502 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=503 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=509 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=513 arith_compress_O1_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=987 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=577 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=595 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=601 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=604 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=606 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=611 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=614 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=615 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=616 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=621 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=630 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=638 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=642 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=643 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=644 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=650 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=654 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=655 arith_compress_O1 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=993 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=174 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=185 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=200 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=203 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=204 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=205 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=209 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=213 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=215 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=220 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=222 arith_compress_O0 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=995 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=100 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=118 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=121 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=122 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=123 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=126 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=128 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=134 tok3_encode_names /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1891 create_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1463 build_trie /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1477 calloc linenumber=482 pool_create /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=505 pool_alloc /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=506 new_pool /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=133 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1478 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1496 encode_name /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1502 search_trie /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=700 __ctype_b_loc linenumber=613 __ctype_b_loc linenumber=614 __ctype_b_loc linenumber=615 __ctype_b_loc linenumber=616 __ctype_b_loc linenumber=617 calloc linenumber=645 __ctype_b_loc linenumber=667 strlen linenumber=711 encode_token_dup /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=712 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=465 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=342 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=316 realloc linenumber=302 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=343 encode_token_diff /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=727 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=470 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=743 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=443 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=444 memcmp linenumber=758 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=759 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=324 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=761 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=415 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=416 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=764 __ctype_b_loc linenumber=785 __ctype_b_loc linenumber=791 __ctype_b_loc linenumber=792 memcmp linenumber=809 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=815 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=822 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=828 __ctype_b_loc linenumber=842 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=856 encode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=863 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=375 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=376 encode_token_int1_ /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=869 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=387 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=870 encode_token_int1_ /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=877 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=878 __ctype_b_loc linenumber=887 __ctype_b_loc linenumber=893 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=923 encode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=933 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=940 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=948 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=965 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=970 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=976 encode_token_end /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=998 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=328 realloc linenumber=1007 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1503 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1565 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1568 compress /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1572 arith_encode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1380 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1214 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1217 rans_encode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1383 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1241 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1244 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1574 memcmp linenumber=1592 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1618 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1659 pthread_mutex_lock linenumber=2101 pthread_mutex_unlock linenumber=2236 pthread_mutex_unlock linenumber=2248 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2249 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2257 hts_log /src/htslib/hts.c linenumber=2257 pthread_mutex_lock linenumber=2260 pthread_mutex_unlock linenumber=2264 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2265 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2283 hts_log /src/htslib/hts.c linenumber=2286 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2301 hts_log /src/htslib/hts.c linenumber=2301 pthread_mutex_lock linenumber=877 pthread_mutex_unlock linenumber=881 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=884 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=891 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=896 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=901 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=904 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=908 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=913 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=918 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=921 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=925 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=930 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=940 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=946 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=963 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=981 realloc linenumber=1216 cram_free_block /src/htslib/cram/cram_io.c linenumber=1225 cram_encode_slice_header /src/htslib/cram/cram_encode.c linenumber=1236 cram_new_block /src/htslib/cram/cram_io.c linenumber=514 cram_free_block /src/htslib/cram/cram_io.c linenumber=522 cram_free_block /src/htslib/cram/cram_io.c linenumber=533 __assert_fail linenumber=557 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=2470 cram_new_block /src/htslib/cram/cram_io.c linenumber=86 cram_new_block /src/htslib/cram/cram_io.c linenumber=87 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=106 itf8_put /src/htslib/cram/cram_io.c linenumber=624 block_append /src/htslib/cram/cram_io.h linenumber=625 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=107 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=108 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=109 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=110 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=112 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=117 kh_init_map /src/htslib/cram/cram_structs.h linenumber=127 calloc linenumber=83 kh_put_map /src/htslib/cram/cram_structs.h linenumber=130 kh_resize_map /src/htslib/cram/cram_structs.h linenumber=83 realloc linenumber=83 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=83 strcmp linenumber=83 kh_put_map /src/htslib/cram/cram_structs.h linenumber=135 kh_put_map /src/htslib/cram/cram_structs.h linenumber=139 kh_put_map /src/htslib/cram/cram_structs.h linenumber=143 kh_put_map /src/htslib/cram/cram_structs.h linenumber=149 kh_put_map /src/htslib/cram/cram_structs.h linenumber=153 kh_put_map /src/htslib/cram/cram_structs.h linenumber=157 kh_put_map /src/htslib/cram/cram_structs.h linenumber=162 kh_put_map /src/htslib/cram/cram_structs.h linenumber=169 block_append /src/htslib/cram/cram_io.h linenumber=193 block_append_char /src/htslib/cram/cram_io.h linenumber=203 sub_idx /src/htslib/cram/cram_encode.c linenumber=216 sub_idx /src/htslib/cram/cram_encode.c linenumber=217 sub_idx /src/htslib/cram/cram_encode.c linenumber=218 sub_idx /src/htslib/cram/cram_encode.c linenumber=219 sub_idx /src/htslib/cram/cram_encode.c linenumber=221 sub_idx /src/htslib/cram/cram_encode.c linenumber=222 sub_idx /src/htslib/cram/cram_encode.c linenumber=223 sub_idx /src/htslib/cram/cram_encode.c linenumber=224 sub_idx /src/htslib/cram/cram_encode.c linenumber=226 sub_idx /src/htslib/cram/cram_encode.c linenumber=227 sub_idx /src/htslib/cram/cram_encode.c linenumber=228 sub_idx /src/htslib/cram/cram_encode.c linenumber=229 sub_idx /src/htslib/cram/cram_encode.c linenumber=231 sub_idx /src/htslib/cram/cram_encode.c linenumber=232 sub_idx /src/htslib/cram/cram_encode.c linenumber=233 sub_idx /src/htslib/cram/cram_encode.c linenumber=234 sub_idx /src/htslib/cram/cram_encode.c linenumber=236 sub_idx /src/htslib/cram/cram_encode.c linenumber=237 sub_idx /src/htslib/cram/cram_encode.c linenumber=238 sub_idx /src/htslib/cram/cram_encode.c linenumber=239 block_append /src/htslib/cram/cram_io.h linenumber=240 block_append /src/htslib/cram/cram_io.h linenumber=246 hts_log /src/htslib/hts.c linenumber=253 block_append /src/htslib/cram/cram_io.h linenumber=262 block_append /src/htslib/cram/cram_io.h linenumber=463 block_append /src/htslib/cram/cram_io.h linenumber=489 hts_log /src/htslib/hts.c linenumber=491 cram_free_block /src/htslib/cram/cram_io.c linenumber=495 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2546 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2554 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=4146 htell /src/htslib/cram/../htslib/hfile.h linenumber=4095 cram_write_container /src/htslib/cram/cram_io.c linenumber=4098 itf8_put /src/htslib/cram/cram_io.c linenumber=4033 crc32 linenumber=4066 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4074 htell /src/htslib/cram/../htslib/hfile.h linenumber=4101 cram_write_block /src/htslib/cram/cram_io.c linenumber=4104 __assert_fail linenumber=1515 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1517 hputc2 /src/htslib/hfile.c linenumber=268 flush_buffer /src/htslib/hfile.c linenumber=403 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1518 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1522 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1527 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1530 __assert_fail linenumber=1535 crc32 linenumber=1547 crc32 linenumber=1550 crc32 linenumber=1552 int32_encode /src/htslib/cram/cram_io.c linenumber=1555 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1022 htell /src/htslib/cram/../htslib/hfile.h linenumber=4108 cram_write_block /src/htslib/cram/cram_io.c linenumber=4113 cram_write_block /src/htslib/cram/cram_io.c linenumber=4117 htell /src/htslib/cram/../htslib/hfile.h linenumber=4121 cram_index_slice /src/htslib/cram/cram_index.c linenumber=4125 hts_log /src/htslib/hts.c linenumber=706 cram_index_build_multiref /src/htslib/cram/cram_index.c linenumber=712 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=644 cram_dependent_data_series /src/htslib/cram/cram_decode.c linenumber=2360 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=619 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=625 calloc linenumber=632 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=693 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=3997 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=3998 hts_log /src/htslib/hts.c linenumber=4010 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=709 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=739 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=755 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=784 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=830 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2381 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2382 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2383 strcmp linenumber=2395 hts_log /src/htslib/hts.c linenumber=2416 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2421 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=2424 hts_log /src/htslib/hts.c linenumber=2430 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2441 hts_log /src/htslib/hts.c linenumber=2450 pthread_mutex_lock linenumber=2455 pthread_mutex_lock linenumber=2456 pthread_mutex_unlock linenumber=2462 pthread_mutex_unlock linenumber=2463 hts_log /src/htslib/hts.c linenumber=2469 memcmp linenumber=2482 hts_log /src/htslib/hts.c linenumber=2492 hts_log /src/htslib/hts.c linenumber=2500 hts_md5_init /src/htslib/md5.c linenumber=2505 hts_md5_update /src/htslib/md5.c linenumber=2510 hts_md5_final /src/htslib/md5.c linenumber=2511 hts_md5_destroy /src/htslib/md5.c linenumber=2512 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2514 hts_md5_init /src/htslib/md5.c linenumber=2516 hts_md5_update /src/htslib/md5.c linenumber=2518 hts_md5_final /src/htslib/md5.c linenumber=2519 hts_md5_destroy /src/htslib/md5.c linenumber=2520 memcmp linenumber=2526 sam_hdr_tid2name /src/htslib/header.c linenumber=2528 hts_log /src/htslib/hts.c linenumber=2530 md5_print /src/htslib/cram/cram_decode.c linenumber=2532 hts_log /src/htslib/hts.c linenumber=2532 md5_print /src/htslib/cram/cram_decode.c linenumber=2533 hts_log /src/htslib/hts.c linenumber=2533 sam_hdr_find_tag_id /src/htslib/header.c linenumber=2535 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2293 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2298 sam_hrecs_find_key /src/htslib/header.c linenumber=2302 kputsn /src/htslib/./htslib/kstring.h linenumber=2307 hts_log /src/htslib/hts.c linenumber=2536 ks_free /src/htslib/cram/../htslib/kstring.h linenumber=2538 ks_initialize /src/htslib/cram/../htslib/kstring.h linenumber=238 pthread_mutex_lock linenumber=2544 pthread_mutex_lock linenumber=2545 calloc linenumber=2546 pthread_mutex_unlock linenumber=2547 pthread_mutex_unlock linenumber=2548 hts_log /src/htslib/hts.c linenumber=2606 pthread_mutex_lock linenumber=2617 pthread_mutex_unlock linenumber=2619 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2622 pthread_mutex_lock linenumber=2631 pthread_mutex_unlock linenumber=2636 pthread_mutex_lock linenumber=2638 pthread_mutex_unlock linenumber=2640 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2643 pthread_mutex_lock linenumber=2648 pthread_mutex_lock linenumber=2649 pthread_mutex_unlock linenumber=2651 pthread_mutex_unlock linenumber=2652 hts_log /src/htslib/hts.c linenumber=2663 hts_log /src/htslib/hts.c linenumber=2674 pthread_mutex_lock linenumber=2697 pthread_mutex_unlock linenumber=2699 hts_log /src/htslib/hts.c linenumber=2792 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2822 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2850 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2859 cram_decode_aux_1_0 /src/htslib/cram/cram_decode.c linenumber=2885 map_find /src/htslib/cram/cram_decode.c linenumber=1971 block_append /src/htslib/cram/cram_io.h linenumber=1974 cram_decode_aux /src/htslib/cram/cram_decode.c linenumber=2887 strlen linenumber=2030 sam_hdr_line_name /src/htslib/header.c linenumber=2067 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2243 hts_log /src/htslib/hts.c linenumber=2254 hts_log /src/htslib/hts.c linenumber=2262 hts_log /src/htslib/hts.c linenumber=2270 hts_log /src/htslib/hts.c linenumber=2274 strlen linenumber=2071 block_append /src/htslib/cram/cram_io.h linenumber=2073 block_append /src/htslib/cram/cram_io.h linenumber=2074 block_append_char /src/htslib/cram/cram_io.h linenumber=2075 block_append /src/htslib/cram/cram_io.h linenumber=2084 map_find /src/htslib/cram/cram_decode.c linenumber=2089 block_append /src/htslib/cram/cram_io.h linenumber=2093 aux_ele_size /src/htslib/cram/cram_decode.c linenumber=2102 hts_log /src/htslib/hts.c linenumber=2128 block_resize /src/htslib/cram/cram_io.h linenumber=2893 block_resize /src/htslib/cram/cram_io.h linenumber=2901 hts_log /src/htslib/hts.c linenumber=2911 cram_decode_seq /src/htslib/cram/cram_decode.c linenumber=2918 block_append /src/htslib/cram/cram_io.h linenumber=1134 realloc linenumber=1165 hts_log /src/htslib/hts.c linenumber=1190 hts_log /src/htslib/hts.c linenumber=1204 hts_log /src/htslib/hts.c linenumber=1215 memchr linenumber=1245 add_md_char /src/htslib/cram/cram_decode.c linenumber=1251 block_append_uint /src/htslib/cram/cram_io.h linenumber=1082 block_grow /src/htslib/cram/cram_io.h linenumber=272 append_uint32 /src/htslib/cram/cram_io.h linenumber=276 block_append_char /src/htslib/cram/cram_io.h linenumber=1083 block_append_uint /src/htslib/cram/cram_io.h linenumber=1380 add_md_char /src/htslib/cram/cram_decode.c linenumber=1392 block_append_uint /src/htslib/cram/cram_io.h linenumber=1421 block_append_char /src/htslib/cram/cram_io.h linenumber=1424 block_append /src/htslib/cram/cram_io.h linenumber=1425 block_append_char /src/htslib/cram/cram_io.h linenumber=1435 block_append /src/htslib/cram/cram_io.h linenumber=1436 block_append_uint /src/htslib/cram/cram_io.h linenumber=1439 block_append_uint /src/htslib/cram/cram_io.h linenumber=1518 block_append_uint /src/htslib/cram/cram_io.h linenumber=1522 block_append_char /src/htslib/cram/cram_io.h linenumber=1531 block_append_uint /src/htslib/cram/cram_io.h linenumber=1596 block_append_char /src/htslib/cram/cram_io.h linenumber=1603 hts_log /src/htslib/hts.c linenumber=1702 hts_log /src/htslib/hts.c linenumber=1717 memchr linenumber=1746 add_md_char /src/htslib/cram/cram_decode.c linenumber=1757 realloc linenumber=1778 block_append_uint /src/htslib/cram/cram_io.h linenumber=1802 realloc linenumber=1808 block_append_char /src/htslib/cram/cram_io.h linenumber=1845 block_append /src/htslib/cram/cram_io.h linenumber=1897 pthread_mutex_lock linenumber=2970 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2975 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2980 pthread_mutex_unlock linenumber=2982 cram_decode_slice_xref /src/htslib/cram/cram_decode.c linenumber=2985 hts_log /src/htslib/hts.c linenumber=2275 cram_free_block /src/htslib/cram/cram_io.c linenumber=2992 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3006 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3007 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3008 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3009 pthread_mutex_lock linenumber=3016 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3019 pthread_mutex_unlock linenumber=3022 hts_log /src/htslib/hts.c linenumber=654 snprintf linenumber=667 strlen linenumber=671 bgzf_write /src/htslib/bgzf.c linenumber=671 hwrite /src/htslib/./htslib/hfile.h linenumber=2008 __assert_fail linenumber=2013 lazy_flush /src/htslib/bgzf.c linenumber=2023 mt_queue /src/htslib/bgzf.c linenumber=1930 bgzf_flush /src/htslib/bgzf.c linenumber=1932 snprintf linenumber=681 strlen linenumber=685 bgzf_write /src/htslib/bgzf.c linenumber=685 snprintf linenumber=714 strlen linenumber=718 bgzf_write /src/htslib/bgzf.c linenumber=718 __errno_location linenumber=4306 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=4307 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=843 cram_flush_thread /src/htslib/cram/cram_io.c linenumber=4307 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=4158 hts_log /src/htslib/hts.c linenumber=4159 __errno_location linenumber=4308 cram_flush_result /src/htslib/cram/cram_io.c linenumber=4309 hts_tpool_next_result /src/htslib/thread_pool.c linenumber=4174 pthread_mutex_lock linenumber=205 hts_tpool_next_result_locked /src/htslib/thread_pool.c linenumber=206 pthread_mutex_unlock linenumber=207 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4175 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4179 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=4187 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4194 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4203 cram_free_container /src/htslib/cram/cram_io.c linenumber=4216 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4221 cram_free_container /src/htslib/cram/cram_io.c linenumber=4228 hts_usleep /src/htslib/cram/../hts_internal.h linenumber=4314 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5572 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=5575 cram_flush_result /src/htslib/cram/cram_io.c linenumber=5577 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=5585 pthread_mutex_destroy linenumber=5588 pthread_mutex_destroy linenumber=5589 pthread_mutex_destroy linenumber=5590 pthread_mutex_destroy linenumber=5591 cram_write_eof_block /src/htslib/cram/cram_io.c linenumber=5595 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=5507 cram_write_container /src/htslib/cram/cram_io.c linenumber=5512 cram_write_block /src/htslib/cram/cram_io.c linenumber=5513 cram_close /src/htslib/cram/cram_io.c linenumber=5514 free_bam_list /src/htslib/cram/cram_io.c linenumber=5603 hclose /src/htslib/hfile.c linenumber=5607 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5611 sam_hdr_destroy /src/htslib/sam.c linenumber=5614 cram_free_container /src/htslib/cram/cram_io.c linenumber=5619 cram_free_container /src/htslib/cram/cram_io.c linenumber=5622 refs_free /src/htslib/cram/cram_io.c linenumber=5625 kh_destroy_m_metrics /src/htslib/cram/cram_structs.h linenumber=5641 cram_index_free /src/htslib/cram/cram_index.c linenumber=5645 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=380 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=367 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=5648 bgzf_close /src/htslib/bgzf.c linenumber=5651 cram_free_block /src/htslib/cram/cram_io.c linenumber=5515 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=5519 cram_free_block /src/htslib/cram/cram_io.c linenumber=5520 sam_state_destroy /src/htslib/sam.c linenumber=1676 fastq_state_destroy /src/htslib/sam.c linenumber=1679 kh_destroy_tag /src/htslib/sam.c linenumber=3806 ks_free /src/htslib/./htslib/kstring.h linenumber=3807 ks_initialize /src/htslib/./htslib/kstring.h linenumber=238 ks_free /src/htslib/./htslib/kstring.h linenumber=3808 ks_free /src/htslib/./htslib/kstring.h linenumber=3809 regfree linenumber=3810 bgzf_close /src/htslib/bgzf.c linenumber=1682 hclose /src/htslib/hfile.c linenumber=1684 hts_idx_close_otf_fp /src/htslib/hts.c linenumber=1697 need_idx_ugly_delay_hack /src/htslib/hts.c linenumber=2914 idx_write_uint64 /src/htslib/hts.c linenumber=2916 ed_is_big /src/htslib/./htslib/hts.h linenumber=2735 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2735 bgzf_write /src/htslib/bgzf.c linenumber=2736 bgzf_close /src/htslib/bgzf.c linenumber=2918 __errno_location linenumber=1700 sam_hdr_destroy /src/htslib/sam.c linenumber=1701 hts_idx_destroy /src/htslib/hts.c linenumber=1702 cram_index_free /src/htslib/cram/cram_index.c linenumber=2696 kh_destroy_bin /src/htslib/hts.c linenumber=2708 hts_filter_free /src/htslib/hts_expr.c linenumber=1703 __errno_location linenumber=1708 view_sam /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=201 abort linenumber=50 hopen /src/htslib/hfile.c linenumber=54 hts_hopen /src/htslib/hts.c linenumber=60 hclose /src/htslib/hfile.c linenumber=62 abort linenumber=63 hts_open /src/htslib/hts.c linenumber=67 hts_open_format /src/htslib/hts.c linenumber=992 strncpy linenumber=900 strchr linenumber=902 strchr linenumber=930 strchr linenumber=936 strstr linenumber=941 strdup linenumber=943 hopen /src/htslib/hfile.c linenumber=949 hts_hopen /src/htslib/hts.c linenumber=952 hts_opt_apply /src/htslib/hts.c linenumber=966 __errno_location linenumber=968 __errno_location linenumber=969 __errno_location linenumber=972 __errno_location linenumber=981 strerror linenumber=981 hts_log /src/htslib/hts.c linenumber=981 hclose_abruptly /src/htslib/hfile.c linenumber=986 abort linenumber=69 sam_hdr_read /src/htslib/sam.c linenumber=86 __errno_location linenumber=1929 bam_hdr_read /src/htslib/sam.c linenumber=1935 bgzf_check_EOF /src/htslib/bgzf.c linenumber=238 pthread_mutex_lock linenumber=2136 pthread_cond_signal linenumber=2142 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=2143 pthread_mutex_unlock linenumber=2147 pthread_cond_wait linenumber=2150 pthread_cond_signal linenumber=2155 abort linenumber=2160 pthread_mutex_unlock linenumber=2165 bgzf_check_EOF_common /src/htslib/bgzf.c linenumber=2167 htell /src/htslib/./htslib/hfile.h linenumber=1545 hseek /src/htslib/hfile.c linenumber=1546 __errno_location linenumber=1547 hclearerr /src/htslib/./htslib/hfile.h linenumber=1547 __errno_location linenumber=1554 hclearerr /src/htslib/./htslib/hfile.h linenumber=1554 hread /src/htslib/./htslib/hfile.h linenumber=1558 hseek /src/htslib/hfile.c linenumber=1559 memcmp linenumber=1560 perror linenumber=240 hts_log /src/htslib/hts.c linenumber=242 bgzf_read /src/htslib/bgzf.c linenumber=245 memcmp linenumber=246 hts_log /src/htslib/hts.c linenumber=247 sam_hdr_init /src/htslib/sam.c linenumber=250 bgzf_read /src/htslib/bgzf.c linenumber=254 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=256 bgzf_read /src/htslib/bgzf.c linenumber=266 bgzf_read /src/htslib/bgzf.c linenumber=269 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=271 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=1588 calloc linenumber=281 calloc linenumber=283 bgzf_read /src/htslib/bgzf.c linenumber=292 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=294 bgzf_read /src/htslib/bgzf.c linenumber=301 realloc linenumber=309 bgzf_read /src/htslib/bgzf.c linenumber=315 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=317 hts_log /src/htslib/hts.c linenumber=327 hts_log /src/htslib/hts.c linenumber=329 hts_log /src/htslib/hts.c linenumber=334 sam_hdr_destroy /src/htslib/sam.c linenumber=339 sam_hdr_sanitise /src/htslib/sam.c linenumber=1935 hts_log /src/htslib/hts.c linenumber=1862 sam_hdr_destroy /src/htslib/sam.c linenumber=1863 hts_log /src/htslib/hts.c linenumber=1875 hts_log /src/htslib/hts.c linenumber=1880 hts_log /src/htslib/hts.c linenumber=1884 sam_hdr_destroy /src/htslib/sam.c linenumber=1885 realloc linenumber=1889 sam_hdr_destroy /src/htslib/sam.c linenumber=1891 sam_hdr_dup /src/htslib/sam.c linenumber=1939 sam_hdr_init /src/htslib/sam.c linenumber=173 calloc linenumber=182 calloc linenumber=184 strdup linenumber=190 sam_hdr_dup_sdict /src/htslib/sam.c linenumber=197 kh_init_s2i /src/htslib/hts.c linenumber=147 kh_get_s2i /src/htslib/hts.c linenumber=155 kh_put_s2i /src/htslib/hts.c linenumber=157 kh_destroy_s2i /src/htslib/hts.c linenumber=159 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=203 kputsn /src/htslib/./htslib/kstring.h linenumber=2380 sam_hrecs_rebuild_lines /src/htslib/header.c linenumber=2382 kputsn /src/htslib/./htslib/kstring.h linenumber=762 build_header_line /src/htslib/header.c linenumber=766 kputc_ /src/htslib/./htslib/kstring.h linenumber=748 kputsn /src/htslib/./htslib/kstring.h linenumber=749 kputc_ /src/htslib/./htslib/kstring.h linenumber=751 kputsn /src/htslib/./htslib/kstring.h linenumber=752 kputc /src/htslib/./htslib/kstring.h linenumber=768 ks_release /src/htslib/./htslib/kstring.h linenumber=204 ks_release /src/htslib/./htslib/kstring.h linenumber=209 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=211 sam_hdr_destroy /src/htslib/sam.c linenumber=225 sam_hdr_sanitise /src/htslib/sam.c linenumber=1939 sam_hdr_create /src/htslib/sam.c linenumber=1943 sam_hdr_init /src/htslib/sam.c linenumber=1908 sam_hdr_build_from_sam_file /src/htslib/header.c linenumber=1912 sam_hrecs_new /src/htslib/header.c linenumber=1359 hts_getline /src/htslib/hts.c linenumber=1368 hts_log /src/htslib/hts.c linenumber=2039 abort linenumber=2040 kgetline2 /src/htslib/kstring.c linenumber=2046 ks_resize /src/htslib/./htslib/kstring.h linenumber=321 hgetln_wrapper /src/htslib/hts.c linenumber=2046 hgetln /src/htslib/./htslib/hfile.h linenumber=2032 herrno /src/htslib/./htslib/hfile.h linenumber=2048 __errno_location linenumber=2048 bgzf_getline /src/htslib/bgzf.c linenumber=2054 bgzf_read_block /src/htslib/bgzf.c linenumber=2305 memchr linenumber=2312 ks_expand /src/htslib/./htslib/kstring.h linenumber=2318 bgzf_htell /src/htslib/bgzf.c linenumber=2323 abort linenumber=2058 isalpha_c /src/htslib/./textutils_internal.h linenumber=1376 sam_hrecs_error /src/htslib/header.c linenumber=1377 strncmp linenumber=1382 kputc /src/htslib/./htslib/kstring.h linenumber=1385 valid_sam_header_type /src/htslib/header.c linenumber=1388 hts_log /src/htslib/hts.c linenumber=1389 warn_if_known_stderr /src/htslib/header.c linenumber=1390 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1394 TYPEKEY /src/htslib/./header.h linenumber=1399 kputsn /src/htslib/./htslib/kstring.h linenumber=1405 kputc /src/htslib/./htslib/kstring.h linenumber=1408 bgzf_peek /src/htslib/bgzf.c linenumber=1412 bgzf_read_block /src/htslib/bgzf.c linenumber=1297 hts_log /src/htslib/hts.c linenumber=1298 hpeek /src/htslib/hfile.c linenumber=1415 strstr linenumber=1433 hopen /src/htslib/hfile.c linenumber=1437 khgetline /src/htslib/hfile.c linenumber=1442 kgetline /src/htslib/kstring.c linenumber=310 ks_resize /src/htslib/./htslib/kstring.h linenumber=276 hgets_wrapper /src/htslib/hfile.c linenumber=310 hgets /src/htslib/hfile.c linenumber=303 strchr linenumber=1443 strtoll linenumber=1451 kputs /src/htslib/./htslib/kstring.h linenumber=1453 kputsn /src/htslib/./htslib/kstring.h linenumber=1454 kputs /src/htslib/./htslib/kstring.h linenumber=1455 kputll /src/htslib/./htslib/kstring.h linenumber=1456 kputc /src/htslib/./htslib/kstring.h linenumber=1457 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1461 ks_free /src/htslib/./htslib/kstring.h linenumber=1473 hclose /src/htslib/hfile.c linenumber=1474 hts_log /src/htslib/hts.c linenumber=1475 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1485 realloc linenumber=1489 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1503 kputsn /src/htslib/./htslib/kstring.h linenumber=1509 ks_release /src/htslib/./htslib/kstring.h linenumber=1511 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1513 ks_free /src/htslib/./htslib/kstring.h linenumber=1519 sam_hdr_destroy /src/htslib/sam.c linenumber=1913 sam_hdr_destroy /src/htslib/sam.c linenumber=1918 sam_hdr_sanitise /src/htslib/sam.c linenumber=1919 sam_hdr_init /src/htslib/sam.c linenumber=1948 __errno_location linenumber=1951 __errno_location linenumber=1955 sam_hdr_incr_ref /src/htslib/header.c linenumber=1962 hts_close_or_abort /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=89 hts_close /src/htslib/hts.c linenumber=41 abort linenumber=42 hts_close /src/htslib/hts.c linenumber=91 hts_close /src/htslib/hts.c linenumber=92 sam_hdr_count_lines /src/htslib/header.c linenumber=97 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2150 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2172 sam_hdr_write /src/htslib/sam.c linenumber=99 __errno_location linenumber=1970 bam_hdr_write /src/htslib/sam.c linenumber=1980 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=354 hts_log /src/htslib/hts.c linenumber=356 hts_log /src/htslib/hts.c linenumber=360 hts_log /src/htslib/hts.c linenumber=361 hts_log /src/htslib/hts.c linenumber=367 hts_log /src/htslib/hts.c linenumber=370 hts_log /src/htslib/hts.c linenumber=371 bgzf_write /src/htslib/bgzf.c linenumber=377 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=380 bgzf_write /src/htslib/bgzf.c linenumber=381 bgzf_write /src/htslib/bgzf.c linenumber=383 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=385 bgzf_write /src/htslib/bgzf.c linenumber=386 bgzf_write /src/htslib/bgzf.c linenumber=388 bgzf_write /src/htslib/bgzf.c linenumber=390 bgzf_write /src/htslib/bgzf.c linenumber=392 strlen linenumber=398 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=400 bgzf_write /src/htslib/bgzf.c linenumber=401 bgzf_write /src/htslib/bgzf.c linenumber=403 bgzf_write /src/htslib/bgzf.c linenumber=405 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=407 bgzf_write /src/htslib/bgzf.c linenumber=408 bgzf_write /src/htslib/bgzf.c linenumber=410 bgzf_flush /src/htslib/bgzf.c linenumber=413 cram_set_header2 /src/htslib/cram/cram_io.c linenumber=1985 sam_hdr_destroy /src/htslib/sam.c linenumber=2858 sam_hdr_dup /src/htslib/sam.c linenumber=2859 refs_from_header /src/htslib/cram/cram_io.c linenumber=2863 cram_load_reference /src/htslib/cram/cram_io.c linenumber=1987 cram_write_SAM_hdr /src/htslib/cram/cram_io.c linenumber=1988 cram_write_file_def /src/htslib/cram/cram_io.c linenumber=4897 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4695 sam_hrecs_find_rg /src/htslib/header.c linenumber=4903 sam_hdr_add_line /src/htslib/header.c linenumber=4904 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1700 sam_hrecs_vadd /src/htslib/header.c linenumber=1706 rebuild_target_arrays /src/htslib/header.c linenumber=1710 redact_header_text /src/htslib/header.c linenumber=1714 refs_from_header /src/htslib/cram/cram_io.c linenumber=4909 refs2id /src/htslib/cram/cram_io.c linenumber=4911 sam_hrecs_find_type_id /src/htslib/header.c linenumber=4921 sam_hrecs_find_key /src/htslib/header.c linenumber=4924 cram_get_ref /src/htslib/cram/cram_io.c linenumber=4936 hts_log /src/htslib/hts.c linenumber=4940 hts_log /src/htslib/hts.c linenumber=4942 hts_log /src/htslib/hts.c linenumber=4943 pthread_mutex_lock linenumber=4945 pthread_mutex_unlock linenumber=4949 hts_md5_init /src/htslib/md5.c linenumber=4955 hts_md5_update /src/htslib/md5.c linenumber=4959 hts_md5_final /src/htslib/md5.c linenumber=4970 hts_md5_destroy /src/htslib/md5.c linenumber=4971 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=4972 hts_md5_hex /src/htslib/md5.c linenumber=4974 sam_hdr_update_line /src/htslib/header.c linenumber=4976 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1916 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1922 check_for_name_update /src/htslib/header.c linenumber=1931 TYPEKEY /src/htslib/./header.h linenumber=1878 TYPEKEY /src/htslib/./header.h linenumber=1880 TYPEKEY /src/htslib/./header.h linenumber=1882 sam_hrecs_find_key /src/htslib/header.c linenumber=1891 __assert_fail linenumber=1894 strcmp linenumber=1900 strcmp linenumber=1901 kh_get_m_s2i /src/htslib/./header.h linenumber=1902 hts_log /src/htslib/hts.c linenumber=1935 TYPEKEY /src/htslib/./header.h linenumber=1939 hts_log /src/htslib/hts.c linenumber=1941 sam_hrecs_vupdate /src/htslib/header.c linenumber=1945 kh_get_m_s2i /src/htslib/./header.h linenumber=1956 sam_hrecs_find_key /src/htslib/header.c linenumber=1957 __assert_fail linenumber=1959 __assert_fail linenumber=1960 __assert_fail linenumber=1961 kh_del_m_s2i /src/htslib/./header.h linenumber=1963 kh_put_m_s2i /src/htslib/./header.h linenumber=1964 hts_log /src/htslib/hts.c linenumber=1966 TYPEKEY /src/htslib/./header.h linenumber=1972 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1972 rebuild_target_arrays /src/htslib/header.c linenumber=1975 redact_header_text /src/htslib/header.c linenumber=1978 full_path /src/htslib/cram/cram_io.c linenumber=4982 strlen linenumber=4851 hisremote /src/htslib/hfile.c linenumber=4852 hts_log /src/htslib/hts.c linenumber=4854 strncpy linenumber=4857 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=4863 strncpy linenumber=4865 getcwd linenumber=4871 strlen linenumber=4872 strncpy linenumber=4873 snprintf linenumber=4878 sam_hdr_update_line /src/htslib/header.c linenumber=4983 sam_hdr_length /src/htslib/header.c linenumber=4990 sam_hdr_rebuild /src/htslib/header.c linenumber=1579 rebuild_target_arrays /src/htslib/header.c linenumber=1613 hts_log /src/htslib/hts.c linenumber=1614 sam_hdr_link_pg /src/htslib/header.c linenumber=1623 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2476 realloc linenumber=2485 calloc linenumber=2489 __assert_fail linenumber=2500 kh_get_m_s2i /src/htslib/./header.h linenumber=2510 hts_log /src/htslib/hts.c linenumber=2513 hts_log /src/htslib/hts.c linenumber=2520 redact_header_text /src/htslib/header.c linenumber=2549 hts_log /src/htslib/hts.c linenumber=1624 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1629 ks_free /src/htslib/./htslib/kstring.h linenumber=1630 hts_log /src/htslib/hts.c linenumber=1631 ks_len /src/htslib/./htslib/kstring.h linenumber=1639 ks_release /src/htslib/./htslib/kstring.h linenumber=1640 hts_log /src/htslib/hts.c linenumber=4992 int32_encode /src/htslib/cram/cram_io.c linenumber=4996 sam_hdr_str /src/htslib/header.c linenumber=5000 sam_hdr_rebuild /src/htslib/header.c linenumber=1586 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=5000 cram_new_block /src/htslib/cram/cram_io.c linenumber=5004 cram_new_container /src/htslib/cram/cram_io.c linenumber=5005 calloc linenumber=3638 calloc linenumber=3666 cram_new_compression_header /src/htslib/cram/cram_io.c linenumber=3670 calloc linenumber=4331 cram_new_block /src/htslib/cram/cram_io.c linenumber=4335 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4340 cram_free_block /src/htslib/cram/cram_io.c linenumber=4341 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4346 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4347 cram_free_block /src/htslib/cram/cram_io.c linenumber=4348 cram_stats_create /src/htslib/cram/cram_stats.c linenumber=3675 calloc linenumber=49 kh_init_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3679 calloc linenumber=394 cram_free_block /src/htslib/cram/cram_io.c linenumber=5011 cram_free_container /src/htslib/cram/cram_io.c linenumber=5012 int32_put_blk /src/htslib/cram/cram_io.c linenumber=5016 block_append /src/htslib/cram/cram_io.h linenumber=1053 sam_hdr_str /src/htslib/header.c linenumber=5019 block_append /src/htslib/cram/cram_io.h linenumber=5019 cram_compress_block /src/htslib/cram/cram_io.c linenumber=5024 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=2324 cram_free_block /src/htslib/cram/cram_io.c linenumber=5036 cram_free_container /src/htslib/cram/cram_io.c linenumber=5037 calloc linenumber=5064 cram_free_block /src/htslib/cram/cram_io.c linenumber=5065 cram_free_container /src/htslib/cram/cram_io.c linenumber=5066 block_append /src/htslib/cram/cram_io.h linenumber=5069 cram_write_container /src/htslib/cram/cram_io.c linenumber=5074 cram_free_block /src/htslib/cram/cram_io.c linenumber=5075 cram_free_container /src/htslib/cram/cram_io.c linenumber=5076 cram_write_block /src/htslib/cram/cram_io.c linenumber=5080 cram_free_block /src/htslib/cram/cram_io.c linenumber=5081 cram_free_container /src/htslib/cram/cram_io.c linenumber=5082 block_resize /src/htslib/cram/cram_io.h linenumber=5087 cram_write_block /src/htslib/cram/cram_io.c linenumber=5092 cram_free_block /src/htslib/cram/cram_io.c linenumber=5093 cram_free_container /src/htslib/cram/cram_io.c linenumber=5094 cram_free_block /src/htslib/cram/cram_io.c linenumber=5099 cram_free_container /src/htslib/cram/cram_io.c linenumber=5100 hflush /src/htslib/hfile.c linenumber=5103 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=2006 strstr linenumber=2014 bgzf_write /src/htslib/bgzf.c linenumber=2022 hwrite /src/htslib/./htslib/hfile.h linenumber=2024 kputsn /src/htslib/./htslib/kstring.h linenumber=2034 kputs /src/htslib/./htslib/kstring.h linenumber=2035 kputsn /src/htslib/./htslib/kstring.h linenumber=2036 kputw /src/htslib/./htslib/kstring.h linenumber=2037 kputc /src/htslib/./htslib/kstring.h linenumber=2038 bgzf_write /src/htslib/bgzf.c linenumber=2043 hwrite /src/htslib/./htslib/hfile.h linenumber=2045 bgzf_flush /src/htslib/bgzf.c linenumber=2052 hflush /src/htslib/hfile.c linenumber=2054 __errno_location linenumber=2066 sam_hdr_dup /src/htslib/sam.c linenumber=2072 sam_hdr_destroy /src/htslib/sam.c linenumber=2073 bam_init1 /src/htslib/sam.c linenumber=102 calloc linenumber=433 sam_read1 /src/htslib/sam.c linenumber=106 sam_read1_bam /src/htslib/sam.c linenumber=4274 bam_read1 /src/htslib/sam.c linenumber=4133 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=793 bgzf_read /src/htslib/bgzf.c linenumber=163 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=798 bgzf_read /src/htslib/bgzf.c linenumber=806 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=809 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=810 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=816 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=819 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=820 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=821 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=822 realloc_bam_data /src/htslib/./sam_internal.h linenumber=829 sam_realloc_bam_data /src/htslib/sam.c linenumber=50 __errno_location linenumber=444 __errno_location linenumber=449 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=453 realloc linenumber=454 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=460 bam_set_mempolicy /src/htslib/./htslib/sam.h linenumber=460 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=832 fixup_missing_qname_nul /src/htslib/sam.c linenumber=834 realloc_bam_data /src/htslib/./sam_internal.h linenumber=772 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=839 swap_data /src/htslib/sam.c linenumber=841 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=759 bam_tag2cigar /src/htslib/sam.c linenumber=842 bam_aux_get /src/htslib/sam.c linenumber=695 __errno_location linenumber=696 __errno_location linenumber=698 __errno_location linenumber=699 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=710 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=720 __errno_location linenumber=57 sam_realloc_bam_data /src/htslib/sam.c linenumber=61 bam_endpos /src/htslib/sam.c linenumber=731 bam_cigar2rlen /src/htslib/sam.c linenumber=675 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=731 hts_log /src/htslib/hts.c linenumber=733 bam_cigar2rqlens /src/htslib/sam.c linenumber=848 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=850 hts_log /src/htslib/hts.c linenumber=853 __errno_location linenumber=4137 sam_read1_cram /src/htslib/sam.c linenumber=4278 cram_get_bam_seq /src/htslib/cram/cram_decode.c linenumber=4146 cram_get_seq /src/htslib/cram/cram_decode.c linenumber=3620 cram_next_slice /src/htslib/cram/cram_decode.c linenumber=3558 cram_first_slice /src/htslib/cram/cram_decode.c linenumber=3274 cram_free_container /src/htslib/cram/cram_io.c linenumber=3217 cram_read_container /src/htslib/cram/cram_io.c linenumber=3219 cram_seek /src/htslib/cram/cram_io.c linenumber=3235 cram_free_container /src/htslib/cram/cram_io.c linenumber=3237 cram_read_container /src/htslib/cram/cram_io.c linenumber=3239 cram_read_block /src/htslib/cram/cram_io.c linenumber=3250 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3255 calloc linenumber=147 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=155 kh_init_map /src/htslib/cram/cram_structs.h linenumber=189 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=197 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=216 kh_put_map /src/htslib/cram/cram_structs.h linenumber=229 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=231 kh_put_map /src/htslib/cram/cram_structs.h linenumber=241 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=243 kh_put_map /src/htslib/cram/cram_structs.h linenumber=253 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=255 kh_put_map /src/htslib/cram/cram_structs.h linenumber=265 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=267 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=277 kh_put_map /src/htslib/cram/cram_structs.h linenumber=308 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=310 cram_decode_TD /src/htslib/cram/cram_decode.c linenumber=317 cram_new_block /src/htslib/cram/cram_io.c linenumber=78 hts_log /src/htslib/hts.c linenumber=82 cram_free_block /src/htslib/cram/cram_io.c linenumber=83 cram_free_block /src/htslib/cram/cram_io.c linenumber=93 cram_free_block /src/htslib/cram/cram_io.c linenumber=98 block_append /src/htslib/cram/cram_io.h linenumber=102 block_append_char /src/htslib/cram/cram_io.h linenumber=107 calloc linenumber=120 cram_free_block /src/htslib/cram/cram_io.c linenumber=121 cram_free_block /src/htslib/cram/cram_io.c linenumber=135 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=319 kh_put_map /src/htslib/cram/cram_structs.h linenumber=326 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=328 hts_log /src/htslib/hts.c linenumber=336 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=343 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=361 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=375 hts_log /src/htslib/hts.c linenumber=458 hts_log /src/htslib/hts.c linenumber=463 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=467 cram_encoding2str /src/htslib/cram/cram_codecs.c linenumber=3886 hts_log /src/htslib/hts.c linenumber=3886 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=470 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=480 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=493 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=508 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=523 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=525 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=536 sam_hrecs_sort_order /src/htslib/header.c linenumber=3259 TYPEKEY /src/htslib/./header.h linenumber=3133 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3133 strcmp linenumber=3139 strcmp linenumber=3141 strcmp linenumber=3143 strcmp linenumber=3145 hts_log /src/htslib/hts.c linenumber=3146 pthread_mutex_lock linenumber=3260 pthread_mutex_unlock linenumber=3262 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3281 cram_free_container /src/htslib/cram/cram_io.c linenumber=3292 cram_read_container /src/htslib/cram/cram_io.c linenumber=3325 cram_free_container /src/htslib/cram/cram_io.c linenumber=3338 cram_free_container /src/htslib/cram/cram_io.c linenumber=3351 cram_free_container /src/htslib/cram/cram_io.c linenumber=3360 cram_free_container /src/htslib/cram/cram_io.c linenumber=3373 hseek /src/htslib/hfile.c linenumber=3376 cram_read_block /src/htslib/cram/cram_io.c linenumber=3386 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3392 sam_hrecs_sort_order /src/htslib/header.c linenumber=3397 pthread_mutex_lock linenumber=3398 pthread_mutex_unlock linenumber=3400 cram_free_container /src/htslib/cram/cram_io.c linenumber=3411 cram_read_slice /src/htslib/cram/cram_io.c linenumber=3416 cram_read_block /src/htslib/cram/cram_io.c linenumber=4567 calloc linenumber=4568 cram_decode_slice_header /src/htslib/cram/cram_decode.c linenumber=4578 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=963 calloc linenumber=973 hts_log /src/htslib/hts.c linenumber=989 cram_content_type2str /src/htslib/cram/cram_io.c linenumber=4583 hts_log /src/htslib/hts.c linenumber=4583 hts_log /src/htslib/hts.c linenumber=4589 calloc linenumber=4593 cram_read_block /src/htslib/cram/cram_io.c linenumber=4598 calloc linenumber=4609 cram_new_block /src/htslib/cram/cram_io.c linenumber=4626 cram_new_block /src/htslib/cram/cram_io.c linenumber=4627 cram_new_block /src/htslib/cram/cram_io.c linenumber=4628 cram_new_block /src/htslib/cram/cram_io.c linenumber=4629 cram_new_block /src/htslib/cram/cram_io.c linenumber=4630 cram_new_block /src/htslib/cram/cram_io.c linenumber=4631 cram_free_block /src/htslib/cram/cram_io.c linenumber=4642 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4645 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3431 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3440 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3449 cram_decode_slice_mt /src/htslib/cram/cram_decode.c linenumber=3461 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3053 hts_tpool_process_sz /src/htslib/thread_pool.c linenumber=3063 pthread_mutex_lock linenumber=306 pthread_mutex_unlock linenumber=308 __errno_location linenumber=3065 __errno_location linenumber=3066 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=3067 cram_decode_slice_thread /src/htslib/cram/cram_decode.c linenumber=3067 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3039 __errno_location linenumber=3070 __errno_location linenumber=3076 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3463 hts_tpool_process_len /src/htslib/thread_pool.c linenumber=3484 pthread_mutex_lock linenumber=292 pthread_mutex_unlock linenumber=294 hts_tpool_process_qsize /src/htslib/thread_pool.c linenumber=3485 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3496 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3501 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3503 hts_log /src/htslib/hts.c linenumber=3504 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3508 hts_log /src/htslib/hts.c linenumber=3513 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3515 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3519 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3583 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3590 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3626 strlen linenumber=3124 append_uint64 /src/htslib/cram/cram_io.h linenumber=3129 append_uint32 /src/htslib/cram/cram_io.h linenumber=344 append_uint32 /src/htslib/cram/cram_io.h linenumber=347 append_sub32 /src/htslib/cram/cram_io.h linenumber=349 append_uint32 /src/htslib/cram/cram_io.h linenumber=351 append_sub32 /src/htslib/cram/cram_io.h linenumber=353 append_uint64 /src/htslib/cram/cram_io.h linenumber=3133 bam_set1 /src/htslib/sam.c linenumber=3168 bam_cigar2rqlens /src/htslib/sam.c linenumber=553 hts_log /src/htslib/hts.c linenumber=561 __errno_location linenumber=562 hts_log /src/htslib/hts.c linenumber=566 __errno_location linenumber=567 hts_log /src/htslib/hts.c linenumber=571 __errno_location linenumber=572 hts_log /src/htslib/hts.c linenumber=576 __errno_location linenumber=577 subtract_check_underflow /src/htslib/sam.c linenumber=582 subtract_check_underflow /src/htslib/sam.c linenumber=583 subtract_check_underflow /src/htslib/sam.c linenumber=584 subtract_check_underflow /src/htslib/sam.c linenumber=585 subtract_check_underflow /src/htslib/sam.c linenumber=586 hts_log /src/htslib/hts.c linenumber=588 __errno_location linenumber=589 realloc_bam_data /src/htslib/./sam_internal.h linenumber=595 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=602 strncpy linenumber=614 cram_eof /src/htslib/cram/cram_io.c linenumber=4148 bam_tag2cigar /src/htslib/sam.c linenumber=4150 sam_read1_sam /src/htslib/sam.c linenumber=4282 sam_parse1 /src/htslib/sam.c linenumber=4162 strchr linenumber=2716 hts_log /src/htslib/hts.c linenumber=2718 hts_log /src/htslib/hts.c linenumber=2719 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2721 parse_sam_flag /src/htslib/sam.c linenumber=2731 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2500 strtoul linenumber=2506 strchr linenumber=2735 strcmp linenumber=2736 hts_log /src/htslib/hts.c linenumber=2737 bam_name2id /src/htslib/./htslib/sam.h linenumber=2738 sam_hdr_name2tid /src/htslib/header.c linenumber=780 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2400 kh_get_m_s2i /src/htslib/./header.h linenumber=2408 hts_log /src/htslib/hts.c linenumber=2739 hts_strprint /src/htslib/textutils.c linenumber=2740 isprint_c /src/htslib/./textutils_internal.h linenumber=473 __ctype_b_loc linenumber=174 strcpy linenumber=480 snprintf linenumber=485 hts_log /src/htslib/hts.c linenumber=2740 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2744 hts_log /src/htslib/hts.c linenumber=2747 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2753 bam_parse_cigar /src/htslib/sam.c linenumber=2759 hts_log /src/htslib/hts.c linenumber=2933 read_ncigar /src/htslib/sam.c linenumber=2938 isdigit_c /src/htslib/./textutils_internal.h linenumber=2847 hts_log /src/htslib/hts.c linenumber=2849 hts_log /src/htslib/hts.c linenumber=2853 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2946 hts_log /src/htslib/hts.c linenumber=2947 parse_cigar /src/htslib/sam.c linenumber=2959 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2873 hts_log /src/htslib/hts.c linenumber=2875 hts_log /src/htslib/hts.c linenumber=2885 bam_cigar2rlen /src/htslib/sam.c linenumber=2764 hts_log /src/htslib/hts.c linenumber=2767 strchr linenumber=2769 hts_log /src/htslib/hts.c linenumber=2772 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2774 strchr linenumber=2776 strcmp linenumber=2777 strcmp linenumber=2779 bam_name2id /src/htslib/./htslib/sam.h linenumber=2782 hts_log /src/htslib/hts.c linenumber=2783 hts_strprint /src/htslib/textutils.c linenumber=2784 hts_log /src/htslib/hts.c linenumber=2784 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2787 hts_log /src/htslib/hts.c linenumber=2790 hts_str2int /src/htslib/./textutils_internal.h linenumber=2794 hts_log /src/htslib/hts.c linenumber=2796 strchr linenumber=2798 strcmp linenumber=2799 hts_log /src/htslib/hts.c linenumber=2800 bam_cigar2qlen /src/htslib/sam.c linenumber=2802 hts_log /src/htslib/hts.c linenumber=2803 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2805 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2814 hts_log /src/htslib/hts.c linenumber=2820 hts_log /src/htslib/hts.c linenumber=2824 aux_parse /src/htslib/sam.c linenumber=2829 hts_log /src/htslib/hts.c linenumber=2555 isspace_c /src/htslib/./textutils_internal.h linenumber=2559 hts_log /src/htslib/hts.c linenumber=2559 isspace_c /src/htslib/./textutils_internal.h linenumber=2562 isspace_c /src/htslib/./textutils_internal.h linenumber=2564 kh_get_tag /src/htslib/sam.c linenumber=2571 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2579 isspace_c /src/htslib/./textutils_internal.h linenumber=2583 hts_log /src/htslib/hts.c linenumber=2583 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2586 hts_str2int /src/htslib/./textutils_internal.h linenumber=2593 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2599 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=275 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2603 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=283 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2607 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2613 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2617 strtod linenumber=2623 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2623 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=345 strtod linenumber=2627 double_to_le /src/htslib/./htslib/hts_endian.h linenumber=2627 u64_to_le /src/htslib/./htslib/hts_endian.h linenumber=359 strchr linenumber=2630 strlen linenumber=2631 isspace_c /src/htslib/./textutils_internal.h linenumber=2632 hts_log /src/htslib/hts.c linenumber=2632 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2635 isspace_c /src/htslib/./textutils_internal.h linenumber=2642 hts_log /src/htslib/hts.c linenumber=2642 sam_parse_B_vals /src/htslib/sam.c linenumber=2645 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2495 hts_log /src/htslib/hts.c linenumber=2375 aux_type2size /src/htslib/sam.c linenumber=2385 hts_log /src/htslib/hts.c linenumber=2387 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2404 hts_log /src/htslib/hts.c linenumber=2405 sam_parse_Bc_vals /src/htslib/sam.c linenumber=2418 grow_B_array /src/htslib/sam.c linenumber=2249 __errno_location linenumber=2224 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2229 hts_log /src/htslib/hts.c linenumber=2230 hts_str2int /src/htslib/./textutils_internal.h linenumber=2252 sam_parse_BC_vals /src/htslib/sam.c linenumber=2421 grow_B_array /src/htslib/sam.c linenumber=2263 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2267 sam_parse_Bs_vals /src/htslib/sam.c linenumber=2424 grow_B_array /src/htslib/sam.c linenumber=2283 hts_str2int /src/htslib/./textutils_internal.h linenumber=2286 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2286 sam_parse_BS_vals /src/htslib/sam.c linenumber=2427 grow_B_array /src/htslib/sam.c linenumber=2298 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2302 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2302 sam_parse_Bi_vals /src/htslib/sam.c linenumber=2430 grow_B_array /src/htslib/sam.c linenumber=2319 hts_str2int /src/htslib/./textutils_internal.h linenumber=2322 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2322 sam_parse_BI_vals /src/htslib/sam.c linenumber=2433 grow_B_array /src/htslib/sam.c linenumber=2334 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2338 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2338 sam_parse_Bf_vals /src/htslib/sam.c linenumber=2436 grow_B_array /src/htslib/sam.c linenumber=2355 strtod linenumber=2358 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2358 hts_log /src/htslib/hts.c linenumber=2441 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2444 hts_str2int /src/htslib/./textutils_internal.h linenumber=2458 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2467 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2469 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2471 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2475 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2477 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2479 hts_log /src/htslib/hts.c linenumber=2484 isspace_c /src/htslib/./textutils_internal.h linenumber=2647 hts_strprint /src/htslib/textutils.c linenumber=2647 hts_log /src/htslib/hts.c linenumber=2647 isspace_c /src/htslib/./textutils_internal.h linenumber=2653 hts_log /src/htslib/hts.c linenumber=2653 bam_tag2cigar /src/htslib/sam.c linenumber=2832 sam_state_destroy /src/htslib/sam.c linenumber=4173 __errno_location linenumber=4174 bgzf_seek /src/htslib/bgzf.c linenumber=4177 bgzf_seek_common /src/htslib/bgzf.c linenumber=2257 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=4188 pthread_create linenumber=4192 sam_dispatcher_read /src/htslib/sam.c linenumber=4192 ks_resize /src/htslib/./htslib/kstring.h linenumber=3334 pthread_mutex_lock linenumber=3339 pthread_cond_signal linenumber=3343 pthread_mutex_unlock linenumber=3344 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3345 pthread_mutex_unlock linenumber=3351 pthread_mutex_lock linenumber=3353 pthread_mutex_unlock linenumber=3359 calloc linenumber=3363 realloc linenumber=3378 bgzf_read /src/htslib/bgzf.c linenumber=3390 hread /src/htslib/./htslib/hfile.h linenumber=3392 __errno_location linenumber=3394 sam_state_err /src/htslib/sam.c linenumber=3394 realloc linenumber=3411 __assert_fail linenumber=3416 __assert_fail linenumber=3417 __assert_fail linenumber=3418 ks_resize /src/htslib/./htslib/kstring.h linenumber=3424 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=3436 sam_parse_worker /src/htslib/sam.c linenumber=3436 pthread_mutex_lock linenumber=3224 pthread_mutex_unlock linenumber=3229 calloc linenumber=3232 calloc linenumber=3237 sam_state_err /src/htslib/sam.c linenumber=3239 sam_state_err /src/htslib/sam.c linenumber=3250 realloc linenumber=3260 sam_state_err /src/htslib/sam.c linenumber=3263 strchr linenumber=3279 sam_parse1 /src/htslib/sam.c linenumber=3291 __errno_location linenumber=3292 sam_state_err /src/htslib/sam.c linenumber=3292 cleanup_sp_lines /src/htslib/sam.c linenumber=3293 __assert_fail linenumber=3205 sam_free_sp_bams /src/htslib/sam.c linenumber=3208 pthread_mutex_lock linenumber=3302 pthread_mutex_unlock linenumber=3305 sam_free_sp_bams /src/htslib/sam.c linenumber=3309 cleanup_sp_lines /src/htslib/sam.c linenumber=3436 cleanup_sp_bams /src/htslib/sam.c linenumber=3436 sam_free_sp_bams /src/htslib/sam.c linenumber=3319 pthread_mutex_lock linenumber=3439 pthread_mutex_unlock linenumber=3441 pthread_mutex_unlock linenumber=3446 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3450 sam_parse_eof /src/htslib/sam.c linenumber=3450 pthread_cond_wait linenumber=3458 pthread_cond_signal linenumber=3461 pthread_mutex_unlock linenumber=3462 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3463 pthread_mutex_unlock linenumber=3467 pthread_mutex_lock linenumber=3473 pthread_cond_signal linenumber=3475 pthread_mutex_unlock linenumber=3476 pthread_mutex_lock linenumber=3479 pthread_mutex_unlock linenumber=3482 __errno_location linenumber=3489 sam_state_err /src/htslib/sam.c linenumber=3489 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3490 hts_log /src/htslib/hts.c linenumber=4199 __errno_location linenumber=4207 pthread_mutex_lock linenumber=4211 pthread_mutex_unlock linenumber=4213 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=4217 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4220 pthread_mutex_lock linenumber=4224 pthread_mutex_unlock linenumber=4226 bam_copy1 /src/htslib/sam.c linenumber=4231 realloc_bam_data /src/htslib/./sam_internal.h linenumber=488 pthread_mutex_lock linenumber=4234 pthread_mutex_unlock linenumber=4237 hts_getline /src/htslib/hts.c linenumber=4250 sam_parse1 /src/htslib/sam.c linenumber=4253 hts_log /src/htslib/hts.c linenumber=4256 fastq_state_init /src/htslib/sam.c linenumber=4289 fastq_parse1 /src/htslib/sam.c linenumber=4294 hts_getline /src/htslib/hts.c linenumber=3944 strpbrk linenumber=3960 isspace_c /src/htslib/./textutils_internal.h linenumber=3972 isspace_c /src/htslib/./textutils_internal.h linenumber=3980 hts_getline /src/htslib/hts.c linenumber=3988 kputsn /src/htslib/./htslib/kstring.h linenumber=3994 hts_getline /src/htslib/hts.c linenumber=4003 kputsn /src/htslib/./htslib/kstring.h linenumber=4007 isdigit_c /src/htslib/./textutils_internal.h linenumber=4020 regexec linenumber=4034 hts_log /src/htslib/hts.c linenumber=4039 isalpha_c /src/htslib/./textutils_internal.h linenumber=4047 bam_set1 /src/htslib/sam.c linenumber=4067 bam_aux_append /src/htslib/sam.c linenumber=4079 __assert_fail linenumber=4765 realloc_bam_data /src/htslib/./sam_internal.h linenumber=4769 __errno_location linenumber=4789 isdigit_c /src/htslib/./textutils_internal.h linenumber=4091 strtol linenumber=4092 isdigit_c /src/htslib/./textutils_internal.h linenumber=4106 isspace_c /src/htslib/./textutils_internal.h linenumber=4109 bam_aux_append /src/htslib/sam.c linenumber=4118 aux_parse /src/htslib/sam.c linenumber=4125 __errno_location linenumber=4298 __errno_location linenumber=4302 sam_passes_filter /src/htslib/sam.c linenumber=4307 hts_filter_eval2 /src/htslib/hts_expr.c linenumber=1539 ks_free /src/htslib/./htslib/kstring.h linenumber=923 hts_filter_eval_ /src/htslib/hts_expr.c linenumber=926 expression /src/htslib/hts_expr.c linenumber=881 and_expr /src/htslib/hts_expr.c linenumber=846 eq_expr /src/htslib/hts_expr.c linenumber=797 cmp_expr /src/htslib/hts_expr.c linenumber=698 bitor_expr /src/htslib/hts_expr.c linenumber=625 bitxor_expr /src/htslib/hts_expr.c linenumber=587 bitand_expr /src/htslib/hts_expr.c linenumber=552 add_expr /src/htslib/hts_expr.c linenumber=517 mul_expr /src/htslib/hts_expr.c linenumber=472 unary_expr /src/htslib/hts_expr.c linenumber=425 ws /src/htslib/hts_expr.c linenumber=367 simple_expr /src/htslib/hts_expr.c linenumber=369 ws /src/htslib/hts_expr.c linenumber=287 expression /src/htslib/hts_expr.c linenumber=289 ws /src/htslib/hts_expr.c linenumber=290 fprintf linenumber=292 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=302 __ctype_b_loc linenumber=365 strtod linenumber=386 strtod linenumber=409 ks_clear /src/htslib/./htslib/kstring.h linenumber=320 kputsn /src/htslib/./htslib/kstring.h linenumber=320 func_expr /src/htslib/hts_expr.c linenumber=347 strncmp linenumber=159 expression /src/htslib/hts_expr.c linenumber=160 expr_func_avg /src/htslib/hts_expr.c linenumber=161 strncmp linenumber=166 expression /src/htslib/hts_expr.c linenumber=167 ws /src/htslib/hts_expr.c linenumber=172 expression /src/htslib/hts_expr.c linenumber=172 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=174 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=72 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=178 ks_free /src/htslib/./htslib/kstring.h linenumber=85 strncmp linenumber=184 expression /src/htslib/hts_expr.c linenumber=185 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=187 strncmp linenumber=189 expression /src/htslib/hts_expr.c linenumber=190 exp linenumber=192 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=195 ks_clear /src/htslib/./htslib/kstring.h linenumber=77 strncmp linenumber=201 expression /src/htslib/hts_expr.c linenumber=202 expr_func_length /src/htslib/hts_expr.c linenumber=203 strncmp linenumber=204 expression /src/htslib/hts_expr.c linenumber=205 log linenumber=207 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=210 strncmp linenumber=215 expression /src/htslib/hts_expr.c linenumber=216 expr_func_min /src/htslib/hts_expr.c linenumber=217 strncmp linenumber=218 expression /src/htslib/hts_expr.c linenumber=219 expr_func_max /src/htslib/hts_expr.c linenumber=220 strncmp linenumber=225 expression /src/htslib/hts_expr.c linenumber=226 ws /src/htslib/hts_expr.c linenumber=233 expression /src/htslib/hts_expr.c linenumber=233 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=234 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=235 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=237 pow linenumber=241 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=242 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=247 strncmp linenumber=252 expression /src/htslib/hts_expr.c linenumber=253 sqrt linenumber=255 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=258 ws /src/htslib/hts_expr.c linenumber=266 fprintf linenumber=268 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=370 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=371 unary_expr /src/htslib/hts_expr.c linenumber=379 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=383 unary_expr /src/htslib/hts_expr.c linenumber=396 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=397 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=398 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=401 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=402 simple_expr /src/htslib/hts_expr.c linenumber=409 ws /src/htslib/hts_expr.c linenumber=431 unary_expr /src/htslib/hts_expr.c linenumber=433 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=434 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=435 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=437 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=450 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=454 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=458 ws /src/htslib/hts_expr.c linenumber=478 mul_expr /src/htslib/hts_expr.c linenumber=481 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=482 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=485 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=498 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=505 ws /src/htslib/hts_expr.c linenumber=522 add_expr /src/htslib/hts_expr.c linenumber=524 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=525 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=528 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=538 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=540 ws /src/htslib/hts_expr.c linenumber=557 bitand_expr /src/htslib/hts_expr.c linenumber=559 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=560 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=563 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=573 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=575 ws /src/htslib/hts_expr.c linenumber=592 bitxor_expr /src/htslib/hts_expr.c linenumber=594 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=595 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=598 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=608 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=610 ws /src/htslib/hts_expr.c linenumber=627 cmp_expr /src/htslib/hts_expr.c linenumber=633 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=634 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=635 strcmp linenumber=639 cmp_expr /src/htslib/hts_expr.c linenumber=645 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=646 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=647 strcmp linenumber=651 cmp_expr /src/htslib/hts_expr.c linenumber=657 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=658 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=659 strcmp linenumber=663 cmp_expr /src/htslib/hts_expr.c linenumber=669 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=670 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=671 strcmp linenumber=675 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=681 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=682 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=683 ws /src/htslib/hts_expr.c linenumber=700 eq_expr /src/htslib/hts_expr.c linenumber=710 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=713 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=714 strcmp linenumber=717 eq_expr /src/htslib/hts_expr.c linenumber=725 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=728 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=729 strcmp linenumber=732 eq_expr /src/htslib/hts_expr.c linenumber=741 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=743 regcomp linenumber=757 regerror linenumber=760 fprintf linenumber=761 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=762 regexec linenumber=768 regfree linenumber=772 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=782 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=783 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=784 ws /src/htslib/hts_expr.c linenumber=801 eq_expr /src/htslib/hts_expr.c linenumber=803 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=804 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=805 eq_expr /src/htslib/hts_expr.c linenumber=814 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=815 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=817 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=819 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=822 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=824 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=827 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=838 ws /src/htslib/hts_expr.c linenumber=884 fprintf linenumber=885 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=896 bam_sym_lookup /src/htslib/sam.c linenumber=1539 memcmp linenumber=1218 ks_clear /src/htslib/./htslib/kstring.h linenumber=1221 kputw /src/htslib/./htslib/kstring.h linenumber=1226 kputc_ /src/htslib/./htslib/kstring.h linenumber=1227 kputs /src/htslib/./htslib/kstring.h linenumber=1229 kputs /src/htslib/./htslib/kstring.h linenumber=1231 memcmp linenumber=1238 bam_endpos /src/htslib/sam.c linenumber=1240 memcmp linenumber=1246 memcmp linenumber=1253 memcmp linenumber=1257 memcmp linenumber=1261 memcmp linenumber=1265 memcmp linenumber=1269 memcmp linenumber=1273 memcmp linenumber=1277 memcmp linenumber=1281 memcmp linenumber=1285 memcmp linenumber=1289 memcmp linenumber=1293 memcmp linenumber=1297 hts_log /src/htslib/hts.c linenumber=1302 memcmp linenumber=1310 memcmp linenumber=1330 bam_get_library /src/htslib/sam.c linenumber=1333 bam_aux_get /src/htslib/sam.c linenumber=1177 sam_hdr_find_tag_id /src/htslib/header.c linenumber=1184 ks_clear /src/htslib/./htslib/kstring.h linenumber=1334 kputs /src/htslib/./htslib/kstring.h linenumber=1334 memcmp linenumber=1340 memcmp linenumber=1344 memcmp linenumber=1348 sam_hdr_tid2name /src/htslib/header.c linenumber=1351 ks_clear /src/htslib/./htslib/kstring.h linenumber=1352 kputs /src/htslib/./htslib/kstring.h linenumber=1352 memcmp linenumber=1354 memcmp linenumber=1362 memcmp linenumber=1370 memcmp linenumber=1374 memcmp linenumber=1382 bam_cigar2qlen /src/htslib/sam.c linenumber=1384 memcmp linenumber=1386 ks_clear /src/htslib/./htslib/kstring.h linenumber=1389 kputs /src/htslib/./htslib/kstring.h linenumber=1389 memcmp linenumber=1391 ks_clear /src/htslib/./htslib/kstring.h linenumber=1393 ks_resize /src/htslib/./htslib/kstring.h linenumber=1394 memcmp linenumber=1404 bam_cigar2rlen /src/htslib/sam.c linenumber=1406 memcmp linenumber=1408 sam_hdr_tid2name /src/htslib/header.c linenumber=1411 ks_clear /src/htslib/./htslib/kstring.h linenumber=1412 kputs /src/htslib/./htslib/kstring.h linenumber=1412 memcmp linenumber=1414 sam_hdr_tid2name /src/htslib/header.c linenumber=1417 ks_clear /src/htslib/./htslib/kstring.h linenumber=1418 kputs /src/htslib/./htslib/kstring.h linenumber=1418 memcmp linenumber=1420 memcmp linenumber=1428 ks_clear /src/htslib/./htslib/kstring.h linenumber=1430 ks_resize /src/htslib/./htslib/kstring.h linenumber=1431 nibble2base /src/htslib/./sam_internal.h linenumber=1433 memcmp linenumber=1438 memcmp linenumber=1469 bam_aux_get /src/htslib/sam.c linenumber=1481 ks_clear /src/htslib/./htslib/kstring.h linenumber=1489 kputs /src/htslib/./htslib/kstring.h linenumber=1489 ks_clear /src/htslib/./htslib/kstring.h linenumber=1494 kputsn /src/htslib/./htslib/kstring.h linenumber=1494 bam_aux2i /src/htslib/sam.c linenumber=1501 get_int_aux_val /src/htslib/sam.c linenumber=5121 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=5105 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=5107 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=5108 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=5109 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=5110 __errno_location linenumber=5112 bam_aux2f /src/htslib/sam.c linenumber=1507 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=5128 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=5129 get_int_aux_val /src/htslib/sam.c linenumber=5130 hts_log /src/htslib/hts.c linenumber=1511 hts_log /src/htslib/hts.c linenumber=1540 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1541 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1546 sam_write1 /src/htslib/sam.c linenumber=107 bam_write_idx1 /src/htslib/sam.c linenumber=4561 bam_write1 /src/htslib/sam.c linenumber=937 hts_log /src/htslib/hts.c linenumber=868 __errno_location linenumber=869 hts_log /src/htslib/hts.c linenumber=876 bgzf_flush_try /src/htslib/bgzf.c linenumber=888 lazy_flush /src/htslib/bgzf.c linenumber=1998 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=890 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=892 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=892 bgzf_write /src/htslib/bgzf.c linenumber=193 swap_data /src/htslib/sam.c linenumber=893 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=895 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=897 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=898 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=900 bam_cigar2rlen /src/htslib/sam.c linenumber=904 hts_log /src/htslib/hts.c linenumber=908 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=917 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=918 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=919 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=920 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=921 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=922 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=923 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=924 swap_data /src/htslib/sam.c linenumber=926 bgzf_flush_try /src/htslib/bgzf.c linenumber=940 hts_idx_amend_last /src/htslib/hts.c linenumber=943 bam_write1 /src/htslib/sam.c linenumber=945 bam_endpos /src/htslib/sam.c linenumber=949 bgzf_idx_push /src/htslib/bgzf.c linenumber=949 hts_idx_push /src/htslib/hts.c linenumber=194 hts_idx_check_range /src/htslib/hts.c linenumber=2562 hts_idx_maxpos /src/htslib/hts.c linenumber=2540 hts_bin_maxpos /src/htslib/./htslib/hts.h linenumber=2535 hts_log /src/htslib/hts.c linenumber=2545 idx_format_name /src/htslib/hts.c linenumber=2550 hts_log /src/htslib/hts.c linenumber=2550 __errno_location linenumber=2554 realloc linenumber=2569 realloc linenumber=2573 hts_log /src/htslib/hts.c linenumber=2586 hts_log /src/htslib/hts.c linenumber=2591 hts_log /src/htslib/hts.c linenumber=2597 hts_log /src/htslib/hts.c linenumber=2602 kh_init_bin /src/htslib/hts.c linenumber=2607 calloc linenumber=2242 insert_to_l /src/htslib/hts.c linenumber=2612 realloc linenumber=2357 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2616 insert_to_b /src/htslib/hts.c linenumber=2619 kh_put_bin /src/htslib/hts.c linenumber=2325 kh_resize_bin /src/htslib/hts.c linenumber=2242 realloc linenumber=2242 calloc linenumber=2330 kh_del_bin /src/htslib/hts.c linenumber=2332 realloc linenumber=2337 insert_to_b /src/htslib/hts.c linenumber=2624 insert_to_b /src/htslib/hts.c linenumber=2626 hts_idx_check_range /src/htslib/hts.c linenumber=197 pthread_mutex_lock linenumber=200 realloc linenumber=207 pthread_mutex_unlock linenumber=208 pthread_mutex_unlock linenumber=223 sam_hdr_tid2name /src/htslib/header.c linenumber=950 sam_hdr_tid2len /src/htslib/header.c linenumber=950 kh_get_s2i /src/htslib/hts.c linenumber=2442 hts_log /src/htslib/hts.c linenumber=950 cram_put_bam_seq /src/htslib/cram/cram_encode.c linenumber=4564 cram_new_container /src/htslib/cram/cram_io.c linenumber=4049 pthread_mutex_lock linenumber=4055 pthread_mutex_unlock linenumber=4058 hts_log /src/htslib/hts.c linenumber=4083 pthread_mutex_lock linenumber=4086 hts_log /src/htslib/hts.c linenumber=4089 pthread_mutex_unlock linenumber=4091 cram_next_container /src/htslib/cram/cram_encode.c linenumber=4100 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=3304 hts_log /src/htslib/hts.c linenumber=3310 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=3315 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3321 cram_free_container /src/htslib/cram/cram_io.c linenumber=3329 cram_new_container /src/htslib/cram/cram_io.c linenumber=3332 pthread_mutex_lock linenumber=3337 pthread_mutex_unlock linenumber=3341 cram_new_slice /src/htslib/cram/cram_io.c linenumber=3349 calloc linenumber=4505 calloc linenumber=4509 cram_new_block /src/htslib/cram/cram_io.c linenumber=4522 cram_new_block /src/htslib/cram/cram_io.c linenumber=4523 cram_new_block /src/htslib/cram/cram_io.c linenumber=4524 cram_new_block /src/htslib/cram/cram_io.c linenumber=4525 cram_new_block /src/htslib/cram/cram_io.c linenumber=4526 cram_new_block /src/htslib/cram/cram_io.c linenumber=4527 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4538 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4539 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4540 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4550 pthread_mutex_lock linenumber=4132 hts_log /src/htslib/hts.c linenumber=4134 pthread_mutex_unlock linenumber=4145 pthread_mutex_lock linenumber=4148 calloc linenumber=4149 pthread_mutex_unlock linenumber=4150 pthread_mutex_lock linenumber=4164 calloc linenumber=4165 pthread_mutex_unlock linenumber=4166 pthread_mutex_lock linenumber=4170 pthread_mutex_unlock linenumber=4173 pthread_mutex_lock linenumber=4183 calloc linenumber=4190 pthread_mutex_unlock linenumber=4192 pthread_mutex_unlock linenumber=4196 bam_copy1 /src/htslib/sam.c linenumber=4201 bam_dup1 /src/htslib/sam.c linenumber=4204 bam_init1 /src/htslib/sam.c linenumber=499 bam_copy1 /src/htslib/sam.c linenumber=501 bam_destroy1 /src/htslib/sam.c linenumber=502 bam_cigar2qlen /src/htslib/sam.c linenumber=4216 hts_log /src/htslib/hts.c linenumber=4218 pthread_create linenumber=4587 sam_dispatcher_write /src/htslib/sam.c linenumber=4587 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3503 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3504 sam_state_err /src/htslib/sam.c linenumber=3506 bgzf_flush_try /src/htslib/bgzf.c linenumber=3521 bgzf_write /src/htslib/bgzf.c linenumber=3523 hwrite /src/htslib/./htslib/hfile.h linenumber=3526 bam_endpos /src/htslib/sam.c linenumber=3533 bgzf_idx_push /src/htslib/bgzf.c linenumber=3532 __errno_location linenumber=3536 sam_state_err /src/htslib/sam.c linenumber=3536 sam_hdr_tid2name /src/htslib/header.c linenumber=3537 sam_hdr_tid2len /src/htslib/header.c linenumber=3537 hts_log /src/htslib/hts.c linenumber=3537 bam_endpos /src/htslib/sam.c linenumber=3542 hts_idx_push /src/htslib/hts.c linenumber=3542 __errno_location linenumber=3544 sam_state_err /src/htslib/sam.c linenumber=3544 sam_hdr_tid2name /src/htslib/header.c linenumber=3545 sam_hdr_tid2len /src/htslib/header.c linenumber=3545 hts_log /src/htslib/hts.c linenumber=3545 __assert_fail linenumber=3552 pthread_mutex_lock linenumber=3555 pthread_mutex_unlock linenumber=3559 bgzf_write /src/htslib/bgzf.c linenumber=3606 bgzf_flush_try /src/htslib/bgzf.c linenumber=3614 bgzf_write /src/htslib/bgzf.c linenumber=3619 hwrite /src/htslib/./htslib/hfile.h linenumber=3626 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3631 pthread_mutex_lock linenumber=3634 pthread_mutex_unlock linenumber=3637 sam_state_err /src/htslib/sam.c linenumber=3640 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3641 __errno_location linenumber=3645 sam_state_err /src/htslib/sam.c linenumber=3645 hts_log /src/htslib/hts.c linenumber=4594 pthread_mutex_lock linenumber=4601 pthread_mutex_unlock linenumber=4608 pthread_mutex_unlock linenumber=4610 calloc linenumber=4611 calloc linenumber=4612 bam_copy1 /src/htslib/sam.c linenumber=4625 pthread_mutex_lock linenumber=4632 pthread_mutex_unlock linenumber=4634 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=4637 sam_format_worker /src/htslib/sam.c linenumber=4637 cleanup_sp_bams /src/htslib/sam.c linenumber=4637 cleanup_sp_lines /src/htslib/sam.c linenumber=4637 pthread_mutex_unlock linenumber=4640 pthread_mutex_unlock linenumber=4643 sam_format1 /src/htslib/sam.c linenumber=4652 sam_format1_append /src/htslib/sam.c linenumber=4409 kputc /src/htslib/./htslib/kstring.h linenumber=4653 bgzf_flush_try /src/htslib/bgzf.c linenumber=4655 bgzf_write /src/htslib/bgzf.c linenumber=4657 hwrite /src/htslib/./htslib/hfile.h linenumber=4659 bam_endpos /src/htslib/sam.c linenumber=4664 bgzf_idx_push /src/htslib/bgzf.c linenumber=4664 sam_hdr_tid2name /src/htslib/header.c linenumber=4666 sam_hdr_tid2len /src/htslib/header.c linenumber=4666 hts_log /src/htslib/hts.c linenumber=4666 bam_endpos /src/htslib/sam.c linenumber=4671 hts_idx_push /src/htslib/hts.c linenumber=4671 sam_hdr_tid2name /src/htslib/header.c linenumber=4673 sam_hdr_tid2len /src/htslib/header.c linenumber=4673 hts_log /src/htslib/hts.c linenumber=4673 fastq_state_init /src/htslib/sam.c linenumber=4688 fastq_format1 /src/htslib/sam.c linenumber=4693 kputc /src/htslib/./htslib/kstring.h linenumber=4422 kputs /src/htslib/./htslib/kstring.h linenumber=4422 bam_aux_get /src/htslib/sam.c linenumber=4444 kputc /src/htslib/./htslib/kstring.h linenumber=4446 isalpha_c /src/htslib/./textutils_internal.h linenumber=4449 toupper_c /src/htslib/./textutils_internal.h linenumber=4449 kputc /src/htslib/./htslib/kstring.h linenumber=4449 kputs /src/htslib/./htslib/kstring.h linenumber=4454 kputs /src/htslib/./htslib/kstring.h linenumber=4462 kputs /src/htslib/./htslib/kstring.h linenumber=4465 bam_aux_get /src/htslib/sam.c linenumber=4475 ksprintf /src/htslib/kstring.c linenumber=4476 isupper_c /src/htslib/./textutils_internal.h linenumber=4480 __ctype_b_loc linenumber=177 islower_c /src/htslib/./textutils_internal.h linenumber=4480 __ctype_b_loc linenumber=173 hts_log /src/htslib/hts.c linenumber=4481 strlen linenumber=4482 strlen linenumber=4490 isalpha_c /src/htslib/./textutils_internal.h linenumber=4493 islower_c /src/htslib/./textutils_internal.h linenumber=4495 toupper_c /src/htslib/./textutils_internal.h linenumber=4496 kh_get_tag /src/htslib/sam.c linenumber=4507 kputc_ /src/htslib/./htslib/kstring.h linenumber=4508 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4509 skip_aux /src/htslib/sam.c linenumber=4512 kputsn /src/htslib/./htslib/kstring.h linenumber=4515 ks_resize /src/htslib/./htslib/kstring.h linenumber=4518 kputc_ /src/htslib/./htslib/kstring.h linenumber=4519 kputc_ /src/htslib/./htslib/kstring.h linenumber=4525 kputc_ /src/htslib/./htslib/kstring.h linenumber=4528 kputsn /src/htslib/./htslib/kstring.h linenumber=4533 kputc_ /src/htslib/./htslib/kstring.h linenumber=4537 kputc_ /src/htslib/./htslib/kstring.h linenumber=4540 kputc_ /src/htslib/./htslib/kstring.h linenumber=4543 kputc /src/htslib/./htslib/kstring.h linenumber=4546 bgzf_flush_try /src/htslib/bgzf.c linenumber=4696 bgzf_write /src/htslib/bgzf.c linenumber=4698 hwrite /src/htslib/./htslib/hfile.h linenumber=4701 __errno_location linenumber=4708 bam_destroy1 /src/htslib/sam.c linenumber=110 sam_hdr_destroy /src/htslib/sam.c linenumber=113 hts_close_or_abort /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=115 hts_close /src/htslib/hts.c linenumber=117 hts_close /src/htslib/hts.c linenumber=118 view_sam /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=202 view_sam /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=203 view_vcf /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=206 abort linenumber=124 hopen /src/htslib/hfile.c linenumber=128 hts_hopen /src/htslib/hts.c linenumber=134 hclose /src/htslib/hfile.c linenumber=136 abort linenumber=137 hts_open /src/htslib/hts.c linenumber=141 abort linenumber=143 bcf_hdr_read /src/htslib/vcf.c linenumber=145 vcf_hdr_read /src/htslib/vcf.c linenumber=1713 bcf_hdr_init /src/htslib/vcf.c linenumber=2601 calloc linenumber=1639 kh_init_vdict /src/htslib/vcf.c linenumber=1642 calloc linenumber=74 kh_resize_vdict /src/htslib/vcf.c linenumber=1645 realloc linenumber=74 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=74 calloc linenumber=1648 kh_init_hdict /src/htslib/vcf.c linenumber=1650 strchr linenumber=1658 bcf_hdr_append /src/htslib/vcf.c linenumber=1660 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1494 calloc linenumber=667 isalpha_c /src/htslib/./textutils_internal.h linenumber=696 isalnum_c /src/htslib/./textutils_internal.h linenumber=699 bcf_hrec_add_key /src/htslib/vcf.c linenumber=707 __assert_fail linenumber=444 realloc linenumber=445 realloc linenumber=448 is_escaped /src/htslib/vcf.c linenumber=727 hts_strprint /src/htslib/textutils.c linenumber=745 hts_log /src/htslib/hts.c linenumber=745 bcf_hrec_set_val /src/htslib/vcf.c linenumber=752 __errno_location linenumber=471 __errno_location linenumber=484 hts_log /src/htslib/hts.c linenumber=762 isspace_c /src/htslib/./textutils_internal.h linenumber=767 hts_strprint /src/htslib/textutils.c linenumber=770 hts_log /src/htslib/hts.c linenumber=770 bcf_hrec_destroy /src/htslib/vcf.c linenumber=780 hts_strprint /src/htslib/textutils.c linenumber=787 hts_log /src/htslib/hts.c linenumber=787 bcf_hrec_destroy /src/htslib/vcf.c linenumber=791 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1496 get_hdr_aux /src/htslib/vcf.c linenumber=1127 bcf_hrec_check /src/htslib/vcf.c linenumber=1132 bcf_hrec_set_type /src/htslib/vcf.c linenumber=599 strcmp linenumber=529 strcmp linenumber=530 strcmp linenumber=531 strcmp linenumber=532 bcf_hrec_find_key /src/htslib/vcf.c linenumber=603 strcasecmp linenumber=523 bcf_hrec_find_key /src/htslib/vcf.c linenumber=613 strcmp linenumber=616 bcf_hrec_find_key /src/htslib/vcf.c linenumber=624 hts_log /src/htslib/hts.c linenumber=635 hts_log /src/htslib/hts.c linenumber=639 hts_log /src/htslib/hts.c linenumber=643 bcf_hdr_register_hrec /src/htslib/vcf.c linenumber=1134 bcf_hrec_set_type /src/htslib/vcf.c linenumber=838 bcf_hrec_find_key /src/htslib/vcf.c linenumber=845 strtoll linenumber=849 bcf_hrec_find_key /src/htslib/vcf.c linenumber=853 strdup linenumber=855 kh_get_vdict /src/htslib/vcf.c linenumber=860 strcmp linenumber=74 kh_put_vdict /src/htslib/vcf.c linenumber=867 kh_resize_vdict /src/htslib/vcf.c linenumber=74 bcf_hrec_find_key /src/htslib/vcf.c linenumber=871 strtol linenumber=875 kh_del_vdict /src/htslib/vcf.c linenumber=879 hts_log /src/htslib/hts.c linenumber=882 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=891 hts_log /src/htslib/hts.c linenumber=805 __errno_location linenumber=807 hts_resize_array_ /src/htslib/hts.c linenumber=817 hts_log /src/htslib/hts.c linenumber=5115 __errno_location linenumber=5116 realloc linenumber=5120 __errno_location linenumber=5122 __errno_location linenumber=5123 strerror linenumber=5123 hts_log /src/htslib/hts.c linenumber=5123 __errno_location linenumber=5124 abort linenumber=5133 abort linenumber=5144 kh_del_vdict /src/htslib/vcf.c linenumber=893 hrec_add_idx /src/htslib/vcf.c linenumber=899 realloc linenumber=498 realloc linenumber=502 strdup linenumber=506 kputw /src/htslib/./htslib/kstring.h linenumber=510 strcmp linenumber=916 strcmp linenumber=917 strtol linenumber=920 hts_log /src/htslib/hts.c linenumber=923 strcmp linenumber=927 strcmp linenumber=929 strcmp linenumber=930 strcmp linenumber=931 strcmp linenumber=932 strcmp linenumber=933 hts_log /src/htslib/hts.c linenumber=936 strcmp linenumber=940 strcmp linenumber=943 strcmp linenumber=944 strcmp linenumber=945 strcmp linenumber=946 strcmp linenumber=947 strcmp linenumber=948 strcmp linenumber=949 strcmp linenumber=950 strcmp linenumber=951 __isoc99_sscanf linenumber=954 hts_log /src/htslib/hts.c linenumber=962 hts_log /src/htslib/hts.c linenumber=967 hts_log /src/htslib/hts.c linenumber=973 strdup linenumber=984 kh_get_vdict /src/htslib/vcf.c linenumber=988 hrec_add_idx /src/htslib/vcf.c linenumber=997 kh_put_vdict /src/htslib/vcf.c linenumber=1003 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=1012 kh_del_vdict /src/htslib/vcf.c linenumber=1013 hrec_add_idx /src/htslib/vcf.c linenumber=1018 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1141 ksprintf /src/htslib/kstring.c linenumber=1145 kh_get_hdict /src/htslib/vcf.c linenumber=1150 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=79 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1154 strcmp linenumber=1158 bcf_get_version /src/htslib/vcf.c linenumber=1159 get_hdr_aux /src/htslib/vcf.c linenumber=158 bcf_hdr_get_version /src/htslib/vcf.c linenumber=162 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=1598 ksprintf /src/htslib/kstring.c linenumber=1220 get_hdr_aux /src/htslib/vcf.c linenumber=1221 kh_get_hdict /src/htslib/vcf.c linenumber=1222 strcmp linenumber=1230 strcmp linenumber=1240 ksprintf /src/htslib/kstring.c linenumber=1243 get_hdr_aux /src/htslib/vcf.c linenumber=1244 kh_get_hdict /src/htslib/vcf.c linenumber=1245 strcmp linenumber=1253 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1254 strcmp linenumber=1255 kh_get_vdict /src/htslib/vcf.c linenumber=1260 hts_log /src/htslib/hts.c linenumber=1601 strstr linenumber=167 strchr linenumber=171 strtol linenumber=174 __errno_location linenumber=175 __errno_location linenumber=176 strtol linenumber=180 __errno_location linenumber=181 __errno_location linenumber=182 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1164 ksprintf /src/htslib/kstring.c linenumber=1166 kh_get_hdict /src/htslib/vcf.c linenumber=1171 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1175 realloc linenumber=1183 bcf_hdr_unregister_hrec /src/htslib/vcf.c linenumber=1186 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1032 kh_get_vdict /src/htslib/vcf.c linenumber=1038 kh_put_hdict /src/htslib/vcf.c linenumber=1193 kh_resize_hdict /src/htslib/vcf.c linenumber=79 bcf_hdr_append /src/htslib/vcf.c linenumber=1662 kh_destroy_vdict /src/htslib/vcf.c linenumber=1669 hts_log /src/htslib/hts.c linenumber=2603 hts_getline /src/htslib/hts.c linenumber=2607 hts_log /src/htslib/hts.c linenumber=2611 hopen /src/htslib/hfile.c linenumber=2616 hts_log /src/htslib/hts.c linenumber=2618 khgetline /src/htslib/hfile.c linenumber=2621 strchr linenumber=2622 kputs /src/htslib/./htslib/kstring.h linenumber=2624 kputsn /src/htslib/./htslib/kstring.h linenumber=2625 kputs /src/htslib/./htslib/kstring.h linenumber=2626 atol linenumber=2627 kputl /src/htslib/./htslib/kstring.h linenumber=2627 kputll /src/htslib/./htslib/kstring.h linenumber=446 kputsn /src/htslib/./htslib/kstring.h linenumber=2628 hclose /src/htslib/hfile.c linenumber=2631 kputsn /src/htslib/./htslib/kstring.h linenumber=2637 kputc /src/htslib/./htslib/kstring.h linenumber=2638 hts_log /src/htslib/hts.c linenumber=2644 bcf_hdr_parse /src/htslib/vcf.c linenumber=2647 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1416 strcasecmp linenumber=1417 hts_log /src/htslib/hts.c linenumber=1418 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1419 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1420 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1425 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1426 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1427 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1433 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1434 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1435 __assert_fail linenumber=1440 __errno_location linenumber=1443 strerror linenumber=1443 hts_log /src/htslib/hts.c linenumber=1443 strncmp linenumber=1458 strchr linenumber=1459 hts_strprint /src/htslib/textutils.c linenumber=1462 hts_log /src/htslib/hts.c linenumber=1462 hts_log /src/htslib/hts.c linenumber=1479 bcf_hdr_parse_sample_line /src/htslib/vcf.c linenumber=1483 strlen linenumber=289 strncmp linenumber=289 hts_log /src/htslib/hts.c linenumber=291 strlen linenumber=295 strncmp linenumber=297 hts_log /src/htslib/hts.c linenumber=299 bcf_hdr_add_sample_len /src/htslib/vcf.c linenumber=309 isspace_c /src/htslib/./textutils_internal.h linenumber=235 hts_log /src/htslib/hts.c linenumber=238 kh_put_vdict /src/htslib/vcf.c linenumber=258 hts_log /src/htslib/hts.c linenumber=267 bcf_hdr_sync /src/htslib/vcf.c linenumber=1485 realloc linenumber=327 get_hdr_aux /src/htslib/vcf.c linenumber=341 bcf_hdr_check_sanity /src/htslib/vcf.c linenumber=1487 bcf_get_version /src/htslib/vcf.c linenumber=1271 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1350 kh_get_vdict /src/htslib/vcf.c linenumber=4625 atoi linenumber=1356 hts_log /src/htslib/hts.c linenumber=1361 hts_log /src/htslib/hts.c linenumber=1366 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1377 atoi linenumber=1392 hts_log /src/htslib/hts.c linenumber=1397 hts_log /src/htslib/hts.c linenumber=1402 tbx_index_load3 /src/htslib/tbx.c linenumber=2650 index_load /src/htslib/tbx.c linenumber=601 calloc linenumber=558 hts_idx_load3 /src/htslib/hts.c linenumber=561 idx_find_and_load /src/htslib/hts.c linenumber=4993 strstr linenumber=4927 strdup linenumber=4931 __errno_location linenumber=4933 strerror linenumber=4933 hts_log /src/htslib/hts.c linenumber=4933 hts_idx_load3 /src/htslib/hts.c linenumber=4938 hisremote /src/htslib/hfile.c linenumber=4997 stat linenumber=4999 hts_log /src/htslib/hts.c linenumber=5002 idx_test_and_fetch /src/htslib/hts.c linenumber=5007 hisremote /src/htslib/hfile.c linenumber=4632 strncmp linenumber=4637 strcspn linenumber=4637 kputsn /src/htslib/./htslib/kstring.h linenumber=4644 access linenumber=4645 hopen /src/htslib/hfile.c linenumber=4654 hts_log /src/htslib/hts.c linenumber=4655 hts_detect_format2 /src/htslib/hts.c linenumber=4659 hts_log /src/htslib/hts.c linenumber=4660 hts_log /src/htslib/hts.c linenumber=4665 hts_open_tmpfile /src/htslib/hts.c linenumber=4670 hts_log /src/htslib/hts.c linenumber=4671 hts_log /src/htslib/hts.c linenumber=4674 calloc linenumber=4675 __errno_location linenumber=4677 strerror linenumber=4677 hts_log /src/htslib/hts.c linenumber=4677 hread /src/htslib/./htslib/hfile.h linenumber=4680 hwrite /src/htslib/./htslib/hfile.h linenumber=4681 __errno_location linenumber=4682 strerror linenumber=4682 hts_log /src/htslib/hts.c linenumber=4682 hts_log /src/htslib/hts.c linenumber=4690 hclose /src/htslib/hfile.c linenumber=4693 __errno_location linenumber=4694 strerror linenumber=4694 hts_log /src/htslib/hts.c linenumber=4694 rename linenumber=4699 __errno_location linenumber=4700 strerror linenumber=4700 hts_log /src/htslib/hts.c linenumber=4700 ks_clear /src/htslib/./htslib/kstring.h linenumber=4703 hclose /src/htslib/hfile.c linenumber=4712 hts_log /src/htslib/hts.c linenumber=4713 hopen /src/htslib/hfile.c linenumber=4721 hclose_abruptly /src/htslib/hfile.c linenumber=4722 strlen linenumber=4724 __errno_location linenumber=4729 hclose_abruptly /src/htslib/hfile.c linenumber=4730 hclose_abruptly /src/htslib/hfile.c linenumber=4731 unlink linenumber=4732 __errno_location linenumber=4735 strdup linenumber=5009 idx_read /src/htslib/hts.c linenumber=5017 bgzf_open /src/htslib/bgzf.c linenumber=2996 ed_is_big /src/htslib/./htslib/hts.h linenumber=2998 bgzf_read /src/htslib/bgzf.c linenumber=2999 memcmp linenumber=3001 bgzf_read /src/htslib/bgzf.c linenumber=3003 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3004 bgzf_read /src/htslib/bgzf.c linenumber=3008 bgzf_read /src/htslib/bgzf.c linenumber=3012 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3013 hts_idx_init /src/htslib/hts.c linenumber=3015 calloc linenumber=2408 calloc linenumber=2420 calloc linenumber=2422 idx_read_core /src/htslib/hts.c linenumber=3019 ed_is_big /src/htslib/./htslib/hts.h linenumber=2928 kh_init_bin /src/htslib/hts.c linenumber=2936 bgzf_read /src/htslib/bgzf.c linenumber=2937 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2938 bgzf_read /src/htslib/bgzf.c linenumber=2942 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2943 kh_put_bin /src/htslib/hts.c linenumber=2944 bgzf_read /src/htslib/bgzf.c linenumber=2949 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2950 bgzf_read /src/htslib/bgzf.c linenumber=2952 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2953 bgzf_read /src/htslib/bgzf.c linenumber=2959 swap_bins /src/htslib/hts.c linenumber=2960 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2743 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2744 bgzf_read /src/htslib/bgzf.c linenumber=2965 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2966 bgzf_read /src/htslib/bgzf.c linenumber=2973 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2974 update_loff /src/htslib/hts.c linenumber=2978 hts_bin_bot /src/htslib/./htslib/hts.h linenumber=2448 hts_bin_level /src/htslib/./htslib/hts.h linenumber=1552 bgzf_read /src/htslib/bgzf.c linenumber=2981 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2982 memcmp linenumber=3021 bgzf_read /src/htslib/bgzf.c linenumber=3025 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3026 hts_idx_init /src/htslib/hts.c linenumber=3028 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3029 bgzf_read /src/htslib/bgzf.c linenumber=3037 idx_read_core /src/htslib/hts.c linenumber=3040 memcmp linenumber=3042 bgzf_read /src/htslib/bgzf.c linenumber=3044 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3045 hts_idx_init /src/htslib/hts.c linenumber=3047 idx_read_core /src/htslib/hts.c linenumber=3048 __errno_location linenumber=3050 bgzf_close /src/htslib/bgzf.c linenumber=3052 bgzf_close /src/htslib/bgzf.c linenumber=3056 hts_idx_destroy /src/htslib/hts.c linenumber=3057 __errno_location linenumber=5019 strerror linenumber=5019 hts_log /src/htslib/hts.c linenumber=5019 hts_idx_check_local /src/htslib/hts.c linenumber=4943 hisremote /src/htslib/hfile.c linenumber=4770 strlen linenumber=4771 strncmp linenumber=4778 strncmp linenumber=4779 hts_log /src/htslib/hts.c linenumber=4789 strlen linenumber=4790 calloc linenumber=4791 strcpy linenumber=4797 stat linenumber=4798 strcpy linenumber=4804 stat linenumber=4805 strcpy linenumber=4814 stat linenumber=4815 strcpy linenumber=4821 stat linenumber=4822 strcpy linenumber=4830 stat linenumber=4831 strcpy linenumber=4837 stat linenumber=4838 strcpy linenumber=4846 stat linenumber=4847 strcpy linenumber=4853 stat linenumber=4854 strcpy linenumber=4863 strcmp linenumber=4865 strcmp linenumber=4866 strcpy linenumber=4867 stat linenumber=4868 strcpy linenumber=4873 stat linenumber=4875 hisremote /src/htslib/hfile.c linenumber=4943 idx_filename /src/htslib/hts.c linenumber=4945 haddextension /src/htslib/hfile.c linenumber=4892 find_scheme_handler /src/htslib/hfile.c linenumber=1369 strncmp linenumber=1372 strcspn linenumber=1372 strchr linenumber=1376 strip_extension /src/htslib/hfile.c linenumber=1379 kputsn /src/htslib/./htslib/kstring.h linenumber=1382 kputs /src/htslib/./htslib/kstring.h linenumber=1383 kputs /src/htslib/./htslib/kstring.h linenumber=1384 idx_test_and_fetch /src/htslib/hts.c linenumber=4896 haddextension /src/htslib/hfile.c linenumber=4898 idx_test_and_fetch /src/htslib/hts.c linenumber=4902 idx_filename /src/htslib/hts.c linenumber=4948 idx_filename /src/htslib/hts.c linenumber=4949 idx_filename /src/htslib/hts.c linenumber=4954 idx_filename /src/htslib/hts.c linenumber=4957 idx_filename /src/htslib/hts.c linenumber=4958 hts_log /src/htslib/hts.c linenumber=4966 hts_idx_load3 /src/htslib/hts.c linenumber=4971 idx_read /src/htslib/hts.c linenumber=4973 hts_idx_get_meta /src/htslib/hts.c linenumber=567 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=570 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=571 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=572 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=573 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=574 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=575 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=576 get_tid /src/htslib/tbx.c linenumber=584 kh_init_s2i /src/htslib/hts.c linenumber=69 kh_put_s2i /src/htslib/hts.c linenumber=74 strdup linenumber=78 kh_del_s2i /src/htslib/hts.c linenumber=83 kh_get_s2i /src/htslib/hts.c linenumber=87 __errno_location linenumber=585 strerror linenumber=585 hts_log /src/htslib/hts.c linenumber=585 strlen linenumber=583 hts_log /src/htslib/hts.c linenumber=592 tbx_destroy /src/htslib/tbx.c linenumber=595 hts_idx_destroy /src/htslib/hts.c linenumber=521 kh_destroy_s2i /src/htslib/hts.c linenumber=522 tbx_seqnames /src/htslib/tbx.c linenumber=2654 calloc linenumber=620 calloc linenumber=623 __assert_fail linenumber=633 __assert_fail linenumber=638 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=2658 add_missing_contig_hrec /src/htslib/vcf.c linenumber=2660 calloc linenumber=2572 strdup linenumber=2576 bcf_hrec_add_key /src/htslib/vcf.c linenumber=2579 strlen linenumber=2580 bcf_hrec_set_val /src/htslib/vcf.c linenumber=2580 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=2582 __errno_location linenumber=2587 __errno_location linenumber=2588 strerror linenumber=2588 hts_log /src/htslib/hts.c linenumber=2588 bcf_hrec_destroy /src/htslib/vcf.c linenumber=2589 __errno_location linenumber=2590 bcf_hdr_sync /src/htslib/vcf.c linenumber=2664 tbx_destroy /src/htslib/tbx.c linenumber=2667 tbx_destroy /src/htslib/tbx.c linenumber=2673 bcf_hdr_destroy /src/htslib/vcf.c linenumber=2676 get_hdr_aux /src/htslib/vcf.c linenumber=1679 kh_destroy_hdict /src/htslib/vcf.c linenumber=1694 kh_destroy_vdict /src/htslib/vcf.c linenumber=1697 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1701 hts_log /src/htslib/hts.c linenumber=1715 __assert_fail linenumber=1719 bcf_hdr_init /src/htslib/vcf.c linenumber=1724 hts_log /src/htslib/hts.c linenumber=1726 bgzf_read /src/htslib/bgzf.c linenumber=1729 hts_log /src/htslib/hts.c linenumber=1731 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1732 strncmp linenumber=1735 strncmp linenumber=1737 hts_log /src/htslib/hts.c linenumber=1738 hts_log /src/htslib/hts.c linenumber=1740 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1741 bgzf_read /src/htslib/bgzf.c linenumber=1747 __errno_location linenumber=1749 __errno_location linenumber=1751 bgzf_read /src/htslib/bgzf.c linenumber=1755 bcf_hdr_parse /src/htslib/vcf.c linenumber=1757 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1760 get_hdr_aux /src/htslib/vcf.c linenumber=198 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1761 __assert_fail linenumber=53 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1761 bcf_hdr_decr_ref /src/htslib/vcf.c linenumber=215 get_hdr_aux /src/htslib/vcf.c linenumber=204 bcf_hdr_destroy /src/htslib/vcf.c linenumber=209 hts_log /src/htslib/hts.c linenumber=1765 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1767 hts_close_or_abort /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=147 hts_close /src/htslib/hts.c linenumber=148 bcf_hdr_write /src/htslib/vcf.c linenumber=152 __errno_location linenumber=1774 bcf_hdr_sync /src/htslib/vcf.c linenumber=1778 vcf_hdr_write /src/htslib/vcf.c linenumber=1783 bcf_hdr_format /src/htslib/vcf.c linenumber=2814 _bcf_hrec_format /src/htslib/vcf.c linenumber=2744 ksprintf /src/htslib/kstring.c linenumber=2718 strcmp linenumber=2722 kputc /src/htslib/./htslib/kstring.h linenumber=2723 ksprintf /src/htslib/kstring.c linenumber=2724 ksprintf /src/htslib/kstring.c linenumber=2727 ksprintf /src/htslib/kstring.c linenumber=2730 ksprintf /src/htslib/kstring.c linenumber=2746 ksprintf /src/htslib/kstring.c linenumber=2749 ksprintf /src/htslib/kstring.c linenumber=2751 ksprintf /src/htslib/kstring.c linenumber=2753 bgzf_write /src/htslib/bgzf.c linenumber=2821 bgzf_flush /src/htslib/bgzf.c linenumber=2822 hwrite /src/htslib/./htslib/hfile.h linenumber=2824 bcf_hdr_format /src/htslib/vcf.c linenumber=1790 kputc /src/htslib/./htslib/kstring.h linenumber=1794 bgzf_write /src/htslib/bgzf.c linenumber=1797 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1799 bgzf_write /src/htslib/bgzf.c linenumber=1800 bgzf_write /src/htslib/bgzf.c linenumber=1801 bgzf_flush /src/htslib/bgzf.c linenumber=1802 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1804 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1805 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1805 bcf_init /src/htslib/vcf.c linenumber=155 calloc linenumber=1818 bcf_read /src/htslib/vcf.c linenumber=159 vcf_read /src/htslib/vcf.c linenumber=2258 hts_getline /src/htslib/hts.c linenumber=4173 vcf_parse /src/htslib/vcf.c linenumber=4175 ks_resize /src/htslib/./htslib/kstring.h linenumber=4010 bcf_clear /src/htslib/vcf.c linenumber=4023 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=1842 kstrtok /src/htslib/kstring.c linenumber=4028 kh_get_vdict /src/htslib/vcf.c linenumber=4033 hts_log /src/htslib/hts.c linenumber=4035 fix_chromosome /src/htslib/vcf.c linenumber=4037 ksprintf /src/htslib/kstring.c linenumber=3751 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3753 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3755 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3756 bcf_hdr_sync /src/htslib/vcf.c linenumber=3757 kh_get_vdict /src/htslib/vcf.c linenumber=3758 hts_log /src/htslib/hts.c linenumber=4038 kstrtok /src/htslib/kstring.c linenumber=4046 hts_str2uint /src/htslib/./textutils_internal.h linenumber=4052 hts_log /src/htslib/hts.c linenumber=4054 hts_log /src/htslib/hts.c linenumber=4057 kstrtok /src/htslib/kstring.c linenumber=4066 memcmp linenumber=4070 bcf_enc_vchar /src/htslib/vcf.c linenumber=4070 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2972 ks_resize /src/htslib/./htslib/kstring.h linenumber=1544 ks_resize /src/htslib/./htslib/kstring.h linenumber=1552 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1564 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1568 kputsn /src/htslib/./htslib/kstring.h linenumber=2973 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=4071 kstrtok /src/htslib/kstring.c linenumber=4074 bcf_enc_vchar /src/htslib/vcf.c linenumber=4078 kstrtok /src/htslib/kstring.c linenumber=4082 memcmp linenumber=4086 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4090 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=1239 bcf_hdr_id2name /src/htslib/./htslib/vcf.h linenumber=1228 hts_log /src/htslib/hts.c linenumber=4090 bcf_enc_vchar /src/htslib/vcf.c linenumber=4095 kstrtok /src/htslib/kstring.c linenumber=4104 memcmp linenumber=4108 atof linenumber=4108 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4109 kstrtok /src/htslib/kstring.c linenumber=4113 memcmp linenumber=4117 vcf_parse_filter /src/htslib/vcf.c linenumber=4118 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3777 hts_log /src/htslib/hts.c linenumber=3777 kstrtok /src/htslib/kstring.c linenumber=3784 kh_get_vdict /src/htslib/vcf.c linenumber=3786 hts_log /src/htslib/hts.c linenumber=3791 ksprintf /src/htslib/kstring.c linenumber=3794 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3795 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3797 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3798 bcf_hdr_sync /src/htslib/vcf.c linenumber=3799 kh_get_vdict /src/htslib/vcf.c linenumber=3800 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3803 hts_log /src/htslib/hts.c linenumber=3803 bcf_enc_vint /src/htslib/vcf.c linenumber=3812 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2839 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=2841 ks_resize /src/htslib/./htslib/kstring.h linenumber=1584 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1604 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1608 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2881 ks_resize /src/htslib/./htslib/kstring.h linenumber=2882 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2893 ks_resize /src/htslib/./htslib/kstring.h linenumber=2894 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2903 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2909 ks_resize /src/htslib/./htslib/kstring.h linenumber=2910 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2914 bcf_enc_vint /src/htslib/vcf.c linenumber=4121 kstrtok /src/htslib/kstring.c linenumber=4125 memcmp linenumber=4129 vcf_parse_info /src/htslib/vcf.c linenumber=4130 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3833 hts_log /src/htslib/hts.c linenumber=3833 kh_get_vdict /src/htslib/vcf.c linenumber=3847 ksprintf /src/htslib/kstring.c linenumber=3853 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3854 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3856 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3857 bcf_hdr_sync /src/htslib/vcf.c linenumber=3858 kh_get_vdict /src/htslib/vcf.c linenumber=3859 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3862 hts_log /src/htslib/hts.c linenumber=3862 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3869 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3871 bcf_enc_vchar /src/htslib/vcf.c linenumber=3873 realloc linenumber=3881 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3883 hts_log /src/htslib/hts.c linenumber=3883 hts_str2int /src/htslib/./textutils_internal.h linenumber=3919 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3925 hts_log /src/htslib/hts.c linenumber=3925 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3944 bcf_enc_vint /src/htslib/vcf.c linenumber=3947 memcmp linenumber=3950 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3956 hts_log /src/htslib/hts.c linenumber=3956 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3966 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3968 bcf_enc_vfloat /src/htslib/vcf.c linenumber=3971 __assert_fail linenumber=2964 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2965 serialize_float_array /src/htslib/vcf.c linenumber=2966 ks_resize /src/htslib/./htslib/kstring.h linenumber=2950 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2954 kstrtok /src/htslib/kstring.c linenumber=4137 vcf_parse_format /src/htslib/vcf.c linenumber=4141 vcf_parse_format_empty1 /src/htslib/vcf.c linenumber=3697 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3142 hts_log /src/htslib/hts.c linenumber=3142 vcf_parse_format_dict2 /src/htslib/vcf.c linenumber=3701 kstrtok /src/htslib/kstring.c linenumber=3165 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3168 hts_log /src/htslib/hts.c linenumber=3168 kh_get_vdict /src/htslib/vcf.c linenumber=3174 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3178 hts_log /src/htslib/hts.c linenumber=3178 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3182 hts_log /src/htslib/hts.c linenumber=3182 ksprintf /src/htslib/kstring.c linenumber=3185 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3186 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3188 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3189 bcf_hdr_sync /src/htslib/vcf.c linenumber=3190 kh_get_vdict /src/htslib/vcf.c linenumber=3192 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3195 hts_log /src/htslib/hts.c linenumber=3195 vcf_parse_format_max3 /src/htslib/vcf.c linenumber=3722 hts_log /src/htslib/hts.c linenumber=3276 vcf_parse_format_alloc4 /src/htslib/vcf.c linenumber=3726 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3312 hts_log /src/htslib/hts.c linenumber=3312 align_mem /src/htslib/vcf.c linenumber=3317 kputsn /src/htslib/./htslib/kstring.h linenumber=3129 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3318 hts_log /src/htslib/hts.c linenumber=3318 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3328 hts_log /src/htslib/hts.c linenumber=3328 ks_resize /src/htslib/./htslib/kstring.h linenumber=3337 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3338 hts_log /src/htslib/hts.c linenumber=3338 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3363 hts_log /src/htslib/hts.c linenumber=3363 vcf_parse_format_fill5 /src/htslib/vcf.c linenumber=3730 bcf_get_version /src/htslib/vcf.c linenumber=3385 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3408 hts_log /src/htslib/hts.c linenumber=3408 hts_str2uint /src/htslib/./textutils_internal.h linenumber=3456 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3481 hts_log /src/htslib/hts.c linenumber=3481 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3485 hts_log /src/htslib/hts.c linenumber=3485 hts_str2int /src/htslib/./textutils_internal.h linenumber=3511 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3516 hts_log /src/htslib/hts.c linenumber=3516 isdigit_c /src/htslib/./textutils_internal.h linenumber=3537 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3538 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3542 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=3545 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3555 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3557 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3559 hts_log /src/htslib/hts.c linenumber=3559 hts_strprint /src/htslib/textutils.c linenumber=3572 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3572 hts_log /src/htslib/hts.c linenumber=3572 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3607 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3608 vcf_parse_format_gt6 /src/htslib/vcf.c linenumber=3734 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3630 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3632 kputsn /src/htslib/./htslib/kstring.h linenumber=3633 bcf_enc_vint /src/htslib/vcf.c linenumber=3635 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3637 serialize_float_array /src/htslib/vcf.c linenumber=3638 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3641 hts_log /src/htslib/hts.c linenumber=3641 vcf_parse_format_check7 /src/htslib/vcf.c linenumber=3738 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3667 hts_log /src/htslib/hts.c linenumber=3667 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3674 hts_log /src/htslib/hts.c linenumber=3674 get_rlen /src/htslib/vcf.c linenumber=4147 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6433 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6444 strlen linenumber=186 memcmp linenumber=191 memcmp linenumber=192 memcmp linenumber=193 memcmp linenumber=194 strcmp linenumber=6448 strcmp linenumber=6449 strlen linenumber=6454 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6457 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=1676 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=1667 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=1634 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1637 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1640 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=1643 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=263 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6462 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6466 strncmp linenumber=6470 strncmp linenumber=6471 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6482 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6487 bcf_get_info /src/htslib/vcf.c linenumber=6492 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6040 bcf_get_info_id /src/htslib/vcf.c linenumber=6042 bcf_unpack /src/htslib/vcf.c linenumber=6059 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4249 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=3084 bcf_fmt_array /src/htslib/vcf.c linenumber=3085 kputc_ /src/htslib/./htslib/kstring.h linenumber=3041 memchr linenumber=3050 kputsn /src/htslib/./htslib/kstring.h linenumber=3051 kputc /src/htslib/./htslib/kstring.h linenumber=3054 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=3070 kputc_ /src/htslib/./htslib/kstring.h linenumber=3070 kputc /src/htslib/./htslib/kstring.h linenumber=3070 kputw /src/htslib/./htslib/kstring.h linenumber=3070 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3071 kputc_ /src/htslib/./htslib/kstring.h linenumber=3071 kputc /src/htslib/./htslib/kstring.h linenumber=3071 kputw /src/htslib/./htslib/kstring.h linenumber=3071 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3072 kputc_ /src/htslib/./htslib/kstring.h linenumber=3072 kputc /src/htslib/./htslib/kstring.h linenumber=3072 kputw /src/htslib/./htslib/kstring.h linenumber=3072 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3073 kputc_ /src/htslib/./htslib/kstring.h linenumber=3073 kputc /src/htslib/./htslib/kstring.h linenumber=3073 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3073 kputd /src/htslib/kstring.c linenumber=3073 hts_log /src/htslib/hts.c linenumber=3074 exit linenumber=3074 kputc_ /src/htslib/./htslib/kstring.h linenumber=4251 hts_realloc_or_die /src/htslib/hts.c linenumber=4255 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4261 kputc_ /src/htslib/./htslib/kstring.h linenumber=4262 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4277 hts_realloc_or_die /src/htslib/hts.c linenumber=4278 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=4280 hts_realloc_or_die /src/htslib/hts.c linenumber=4287 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=4290 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4196 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4197 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=4209 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=4213 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=4217 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=4221 hts_realloc_or_die /src/htslib/hts.c linenumber=4295 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=4298 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4181 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4182 bcf_get_info /src/htslib/vcf.c linenumber=6493 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6496 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6498 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6504 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6511 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6520 bcf_get_fmt /src/htslib/vcf.c linenumber=6527 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6033 bcf_get_fmt_id /src/htslib/vcf.c linenumber=6035 bcf_unpack /src/htslib/vcf.c linenumber=6048 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6530 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=6532 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6537 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6567 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6571 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6575 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6579 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6611 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6615 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6619 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6623 bgzf_get_private_data /src/htslib/./bgzf_internal.h linenumber=2260 __assert_fail linenumber=68 bcf_read1_core /src/htslib/vcf.c linenumber=2261 bgzf_read /src/htslib/bgzf.c linenumber=1879 bcf_clear /src/htslib/vcf.c linenumber=1883 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1884 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1887 ks_resize /src/htslib/./htslib/kstring.h linenumber=1892 ks_resize /src/htslib/./htslib/kstring.h linenumber=1893 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1894 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1895 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1897 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1898 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1899 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1900 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1901 bgzf_read /src/htslib/bgzf.c linenumber=1908 bgzf_read /src/htslib/bgzf.c linenumber=1909 bcf_record_check /src/htslib/vcf.c linenumber=2262 bcf_get_version /src/htslib/vcf.c linenumber=2062 bcf_hdr_id2int /src/htslib/vcf.c linenumber=2063 hts_log /src/htslib/hts.c linenumber=2070 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2077 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=1960 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1930 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1933 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2079 get_type_name /src/htslib/vcf.c linenumber=2079 hts_log /src/htslib/hts.c linenumber=2079 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2088 hts_log /src/htslib/hts.c linenumber=2088 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2095 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2098 get_type_name /src/htslib/vcf.c linenumber=2098 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2108 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2112 get_type_name /src/htslib/vcf.c linenumber=2112 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=2119 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2124 hts_log /src/htslib/hts.c linenumber=2124 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2136 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2140 hts_log /src/htslib/hts.c linenumber=2140 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2143 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2147 get_type_name /src/htslib/vcf.c linenumber=2147 hts_log /src/htslib/hts.c linenumber=2147 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2161 bcf_record_check_err /src/htslib/vcf.c linenumber=2165 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2034 hts_log /src/htslib/hts.c linenumber=2034 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2168 bcf_record_check_err /src/htslib/vcf.c linenumber=2171 updatephasing /src/htslib/vcf.c linenumber=2176 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2191 hts_log /src/htslib/hts.c linenumber=2191 get_rlen /src/htslib/vcf.c linenumber=2197 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2206 hts_log /src/htslib/hts.c linenumber=2206 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2210 hts_log /src/htslib/hts.c linenumber=2210 bcf_subset_format /src/htslib/vcf.c linenumber=2264 hts_realloc_or_die /src/htslib/hts.c linenumber=2227 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=2232 bcf_write /src/htslib/vcf.c linenumber=160 bcf_hdr_sync /src/htslib/vcf.c linenumber=2513 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2517 hts_log /src/htslib/hts.c linenumber=2517 vcf_write /src/htslib/vcf.c linenumber=2523 vcf_format /src/htslib/vcf.c linenumber=4591 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=4308 hts_log /src/htslib/hts.c linenumber=4310 __errno_location linenumber=4312 bcf_unpack /src/htslib/vcf.c linenumber=4316 get_hdr_aux /src/htslib/vcf.c linenumber=4327 calloc linenumber=4329 kputs /src/htslib/./htslib/kstring.h linenumber=4334 kputc_ /src/htslib/./htslib/kstring.h linenumber=4335 kputll /src/htslib/./htslib/kstring.h linenumber=4335 kputc_ /src/htslib/./htslib/kstring.h linenumber=4336 kputs /src/htslib/./htslib/kstring.h linenumber=4338 kputc_ /src/htslib/./htslib/kstring.h linenumber=4343 kputs /src/htslib/./htslib/kstring.h linenumber=4344 kputc_ /src/htslib/./htslib/kstring.h linenumber=4346 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4348 kputd /src/htslib/kstring.c linenumber=4349 kputc_ /src/htslib/./htslib/kstring.h linenumber=4350 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4356 hts_log /src/htslib/hts.c linenumber=4356 __errno_location linenumber=4358 kputc_ /src/htslib/./htslib/kstring.h linenumber=4361 strlen linenumber=4363 kputsn /src/htslib/./htslib/kstring.h linenumber=4364 kputc_ /src/htslib/./htslib/kstring.h linenumber=4366 kputc_ /src/htslib/./htslib/kstring.h linenumber=4368 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4388 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4389 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4405 hts_log /src/htslib/hts.c linenumber=4405 __errno_location linenumber=4410 strlen linenumber=4416 ks_resize /src/htslib/./htslib/kstring.h linenumber=4418 bcf_fmt_array /src/htslib/vcf.c linenumber=4435 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4440 kputc_ /src/htslib/./htslib/kstring.h linenumber=4441 kputd /src/htslib/kstring.c linenumber=4443 kputc_ /src/htslib/./htslib/kstring.h linenumber=4445 kputc_ /src/htslib/./htslib/kstring.h linenumber=4454 kputw /src/htslib/./htslib/kstring.h linenumber=4456 kputc_ /src/htslib/./htslib/kstring.h linenumber=4459 kputll /src/htslib/./htslib/kstring.h linenumber=4461 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4463 hts_log /src/htslib/hts.c linenumber=4463 __errno_location linenumber=4464 kputc_ /src/htslib/./htslib/kstring.h linenumber=4469 kputc_ /src/htslib/./htslib/kstring.h linenumber=4470 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4499 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4500 kputc_ /src/htslib/./htslib/kstring.h linenumber=4506 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4513 hts_log /src/htslib/hts.c linenumber=4513 __errno_location linenumber=4514 strlen linenumber=4521 kputsn /src/htslib/./htslib/kstring.h linenumber=4523 kputsn /src/htslib/./htslib/kstring.h linenumber=4527 kputc_ /src/htslib/./htslib/kstring.h linenumber=4531 kputc_ /src/htslib/./htslib/kstring.h linenumber=4536 bcf_format_gt_v2 /src/htslib/vcf.c linenumber=4539 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6371 kputc /src/htslib/./htslib/kstring.h linenumber=6371 kputw /src/htslib/./htslib/kstring.h linenumber=6371 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6373 kputc /src/htslib/./htslib/kstring.h linenumber=6373 kputw /src/htslib/./htslib/kstring.h linenumber=6373 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6375 kputc /src/htslib/./htslib/kstring.h linenumber=6375 kputw /src/htslib/./htslib/kstring.h linenumber=6375 kputc /src/htslib/./htslib/kstring.h linenumber=6377 hts_log /src/htslib/hts.c linenumber=6378 get_hdr_aux /src/htslib/vcf.c linenumber=6382 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6392 ks_resize /src/htslib/./htslib/kstring.h linenumber=474 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6394 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6401 hts_log /src/htslib/hts.c linenumber=4540 __errno_location linenumber=4541 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4549 kputc_ /src/htslib/./htslib/kstring.h linenumber=2991 kputc_ /src/htslib/./htslib/kstring.h linenumber=2997 kputw /src/htslib/./htslib/kstring.h linenumber=2998 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3002 kputc_ /src/htslib/./htslib/kstring.h linenumber=3005 kputw /src/htslib/./htslib/kstring.h linenumber=3006 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3011 kputc_ /src/htslib/./htslib/kstring.h linenumber=3014 kputw /src/htslib/./htslib/kstring.h linenumber=3015 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3020 kputc_ /src/htslib/./htslib/kstring.h linenumber=3023 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3024 kputd /src/htslib/kstring.c linenumber=3024 hts_log /src/htslib/hts.c linenumber=3029 bcf_fmt_array /src/htslib/vcf.c linenumber=4551 kputc_ /src/htslib/./htslib/kstring.h linenumber=4557 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4559 bcf_fmt_array /src/htslib/vcf.c linenumber=4561 kputc_ /src/htslib/./htslib/kstring.h linenumber=4563 kputsn /src/htslib/./htslib/kstring.h linenumber=4570 kputc /src/htslib/./htslib/kstring.h linenumber=4572 bgzf_flush_try /src/htslib/bgzf.c linenumber=4594 hts_idx_amend_last /src/htslib/hts.c linenumber=4597 bgzf_write /src/htslib/bgzf.c linenumber=4598 hwrite /src/htslib/./htslib/hfile.h linenumber=4600 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4605 hts_idx_tbi_name /src/htslib/hts.c linenumber=4605 strlen linenumber=2655 realloc linenumber=2656 strcpy linenumber=2662 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=2666 u32_to_le /src/htslib/./cram/../htslib/hts_endian.h linenumber=2666 bgzf_idx_push /src/htslib/bgzf.c linenumber=4608 bcf_strerror /src/htslib/vcf.c linenumber=2532 add_desc_to_buffer /src/htslib/vcf.c linenumber=6319 strlen linenumber=6293 snprintf linenumber=6294 snprintf linenumber=6297 add_desc_to_buffer /src/htslib/vcf.c linenumber=6328 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2532 bcf1_sync /src/htslib/vcf.c linenumber=2535 bcf1_sync_id /src/htslib/vcf.c linenumber=2342 strcmp linenumber=2281 strlen linenumber=2282 bcf_enc_vchar /src/htslib/vcf.c linenumber=2282 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2284 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2345 strlen linenumber=2292 bcf_enc_vchar /src/htslib/vcf.c linenumber=2292 strlen linenumber=2295 bcf1_sync_filter /src/htslib/vcf.c linenumber=2348 bcf_enc_vint /src/htslib/vcf.c linenumber=2302 bcf_enc_vint /src/htslib/vcf.c linenumber=2304 bcf1_sync_info /src/htslib/vcf.c linenumber=2351 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2321 bcf_unpack /src/htslib/vcf.c linenumber=2358 bcf1_sync_id /src/htslib/vcf.c linenumber=2365 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2367 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2373 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2376 strlen linenumber=2377 bcf1_sync_filter /src/htslib/vcf.c linenumber=2386 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2388 bcf_enc_vint /src/htslib/vcf.c linenumber=2390 bcf1_sync_info /src/htslib/vcf.c linenumber=2399 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2406 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2443 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2539 hts_log /src/htslib/hts.c linenumber=2539 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2545 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2546 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2547 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2548 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2549 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2550 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2551 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2552 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2553 bgzf_write /src/htslib/bgzf.c linenumber=2554 bgzf_write /src/htslib/bgzf.c linenumber=2555 bgzf_write /src/htslib/bgzf.c linenumber=2556 bgzf_idx_push /src/htslib/bgzf.c linenumber=2559 bcf_destroy /src/htslib/vcf.c linenumber=163 bcf_empty /src/htslib/vcf.c linenumber=1870 bcf_clear /src/htslib/vcf.c linenumber=1856 bcf_hdr_destroy /src/htslib/vcf.c linenumber=166 hts_close_or_abort /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=167 hts_close /src/htslib/hts.c linenumber=168 view_vcf /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=207 ====================================