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=5194 get_severity_tag /src/htslib/hts.c linenumber=5198 fprintf linenumber=5198 vfprintf linenumber=5201 fprintf linenumber=5204 __errno_location linenumber=5206 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=1693 curl_global_init linenumber=1701 easy_errno /src/htslib/hfile_libcurl.c linenumber=1702 curl_easy_getinfo linenumber=179 curl_easy_getinfo linenumber=193 http_status_errno /src/htslib/hfile_libcurl.c linenumber=194 curl_easy_strerror linenumber=228 hts_log /src/htslib/hts.c linenumber=228 __errno_location linenumber=1702 curl_share_init linenumber=1704 curl_global_cleanup linenumber=1705 __errno_location linenumber=1705 curl_share_setopt linenumber=1706 share_lock /src/htslib/hfile_libcurl.c linenumber=1706 pthread_mutex_lock linenumber=312 curl_share_setopt linenumber=1707 share_unlock /src/htslib/hfile_libcurl.c linenumber=1707 pthread_mutex_unlock linenumber=316 curl_share_setopt linenumber=1708 curl_share_cleanup linenumber=1710 curl_global_cleanup linenumber=1711 __errno_location linenumber=1712 getenv linenumber=1716 strdup linenumber=1717 kh_init_auth_map /src/htslib/hfile_libcurl.c linenumber=1718 calloc linenumber=70 __errno_location linenumber=1720 kh_destroy_auth_map /src/htslib/hfile_libcurl.c linenumber=1722 curl_share_cleanup linenumber=1723 curl_global_cleanup linenumber=1724 __errno_location linenumber=1725 getenv linenumber=1729 strcmp linenumber=1730 getenv linenumber=1736 atoi linenumber=1737 getenv linenumber=1738 atol linenumber=1739 getenv linenumber=1740 atol linenumber=1741 getenv linenumber=1742 atol linenumber=1743 getenv linenumber=1744 atol linenumber=1745 curl_version_info linenumber=1748 ksprintf /src/htslib/kstring.c linenumber=1749 kvsprintf /src/htslib/kstring.c linenumber=183 kputd /src/htslib/kstring.c linenumber=151 kputsn /src/htslib/./htslib/kstring.h linenumber=44 __errno_location linenumber=245 ks_resize /src/htslib/./htslib/kstring.h linenumber=246 realloc linenumber=169 kputsn /src/htslib/./htslib/kstring.h linenumber=47 kputc /src/htslib/./htslib/kstring.h linenumber=53 ks_resize /src/htslib/./htslib/kstring.h linenumber=261 ks_resize /src/htslib/./htslib/kstring.h linenumber=58 snprintf linenumber=61 kputsn /src/htslib/./htslib/kstring.h linenumber=139 vsnprintf linenumber=165 ks_resize /src/htslib/./htslib/kstring.h linenumber=168 vsnprintf linenumber=171 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1755 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=2454 curl_global_init linenumber=2461 curl_share_init linenumber=2468 curl_global_cleanup linenumber=2471 __errno_location linenumber=2472 curl_share_setopt linenumber=2476 share_lock /src/htslib/hfile_s3.c linenumber=2476 pthread_mutex_lock linenumber=1136 curl_share_setopt linenumber=2477 share_unlock /src/htslib/hfile_s3.c linenumber=2477 pthread_mutex_unlock linenumber=1140 curl_share_setopt linenumber=2478 curl_share_cleanup linenumber=2481 curl_global_cleanup linenumber=2482 __errno_location linenumber=2483 curl_version_info linenumber=2487 ksprintf /src/htslib/kstring.c linenumber=2488 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2493 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2494 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2495 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=1468 strdup linenumber=1474 ed_is_big /src/htslib/./htslib/hts.h linenumber=1475 strchr linenumber=1478 strncpy linenumber=1479 strncpy linenumber=1483 strchr linenumber=1487 hts_detect_format2 /src/htslib/hts.c linenumber=1490 hpeek /src/htslib/hfile.c linenumber=562 refill_buffer /src/htslib/hfile.c linenumber=317 __errno_location linenumber=195 memcmp linenumber=577 memcmp linenumber=579 decompress_peek_gz /src/htslib/hts.c linenumber=585 hpeek /src/htslib/hfile.c linenumber=319 inflateInit2_ linenumber=329 inflate linenumber=334 inflateReset linenumber=340 inflateEnd linenumber=349 memcmp linenumber=587 memcmp linenumber=588 memcmp linenumber=589 memcmp linenumber=599 decompress_peek_xz /src/htslib/hts.c linenumber=602 hpeek /src/htslib/hfile.c linenumber=361 lzma_easy_decoder_memusage linenumber=365 lzma_stream_decoder linenumber=365 lzma_code linenumber=373 lzma_end linenumber=375 lzma_end linenumber=380 memcmp linenumber=608 hpeek /src/htslib/hfile.c linenumber=613 strcmp linenumber=627 find_file_extension /src/htslib/./hts_internal.h linenumber=629 strstr linenumber=142 strlen linenumber=144 tolower_c /src/htslib/./textutils_internal.h linenumber=630 memcmp linenumber=634 memcmp linenumber=642 memcmp linenumber=649 memcmp linenumber=655 memcmp linenumber=661 memcmp linenumber=668 memcmp linenumber=674 strcmp linenumber=681 memcmp linenumber=687 parse_version /src/htslib/hts.c linenumber=691 isdigit_c /src/htslib/./textutils_internal.h linenumber=398 __ctype_b_loc linenumber=171 isdigit_c /src/htslib/./textutils_internal.h linenumber=405 memcmp linenumber=695 memcmp linenumber=696 memcmp linenumber=697 memcmp linenumber=702 parse_version /src/htslib/hts.c linenumber=703 memcmp linenumber=708 cmp_nonblank /src/htslib/hts.c linenumber=715 isspace_c /src/htslib/./textutils_internal.h linenumber=422 __ctype_b_loc linenumber=176 memcmp linenumber=720 is_fastaq /src/htslib/hts.c linenumber=725 memchr linenumber=461 is_text_only /src/htslib/hts.c linenumber=464 toupper linenumber=472 is_fastaq /src/htslib/hts.c linenumber=730 parse_tabbed_text /src/htslib/hts.c linenumber=735 isdigit_c /src/htslib/./textutils_internal.h linenumber=500 strchr linenumber=504 isdigit_c /src/htslib/./textutils_internal.h linenumber=504 colmatch /src/htslib/hts.c linenumber=740 colmatch /src/htslib/hts.c linenumber=747 strstr linenumber=752 colmatch /src/htslib/hts.c linenumber=752 strstr linenumber=757 colmatch /src/htslib/hts.c linenumber=757 colmatch /src/htslib/hts.c linenumber=762 is_text_only /src/htslib/hts.c linenumber=770 __errno_location linenumber=1500 hopen_htsget_redirect /src/htslib/multipart.c linenumber=1505 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=5057 realloc linenumber=5061 __errno_location linenumber=5075 strerror linenumber=5075 hts_log /src/htslib/hts.c linenumber=5075 exit linenumber=5076 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=1510 __errno_location linenumber=522 hfile_destroy /src/htslib/hfile.c linenumber=526 __errno_location linenumber=527 hts_crypt4gh_redirect /src/htslib/hts.c linenumber=1518 strlen linenumber=1438 snprintf linenumber=1449 strchr linenumber=1450 snprintf linenumber=1450 hopen /src/htslib/hfile.c linenumber=1451 hts_detect_format2 /src/htslib/hts.c linenumber=1535 strchr linenumber=1538 strchr linenumber=1542 strchr linenumber=1543 strchr linenumber=1544 strchr linenumber=1545 strchr linenumber=1548 strchr linenumber=1549 strchr linenumber=1550 abort linenumber=1559 format_category /src/htslib/hts.c linenumber=1564 __errno_location linenumber=1570 bgzf_hopen /src/htslib/bgzf.c linenumber=1576 strchr linenumber=543 bgzf_read_init /src/htslib/bgzf.c linenumber=544 hpeek /src/htslib/hfile.c linenumber=388 calloc linenumber=391 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=395 hts_prod_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=121 hts_malloc /src/htslib/./htslib/hts_alloc.h linenumber=122 __errno_location linenumber=95 memcmp linenumber=399 memcmp linenumber=400 hts_log /src/htslib/hts.c linenumber=401 razf_info /src/htslib/bgzf.c linenumber=402 strcmp linenumber=321 hseek /src/htslib/hfile.c linenumber=324 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=325 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=326 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=326 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=1599 hts_log /src/htslib/hts.c linenumber=329 hts_log /src/htslib/hts.c linenumber=340 __errno_location linenumber=405 kh_init_bgzf_cache /src/htslib/bgzf.c linenumber=414 calloc linenumber=87 strchr linenumber=546 bgzf_write_init /src/htslib/bgzf.c linenumber=547 calloc linenumber=439 mode2level /src/htslib/bgzf.c linenumber=451 strchr linenumber=433 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=459 strchr linenumber=465 calloc linenumber=469 deflateInit2_ linenumber=475 bgzf_zerr /src/htslib/bgzf.c linenumber=477 __errno_location linenumber=364 strerror linenumber=364 snprintf linenumber=379 hts_log /src/htslib/hts.c linenumber=477 __errno_location linenumber=484 strerror linenumber=484 hts_log /src/htslib/hts.c linenumber=484 __errno_location linenumber=550 ed_is_big /src/htslib/./htslib/hts.h linenumber=553 cram_dopen /src/htslib/cram/cram_io.c linenumber=1582 calloc linenumber=5014 cram_read_file_def /src/htslib/cram/cram_io.c linenumber=5034 hread /src/htslib/cram/../htslib/hfile.h linenumber=4408 memcmp linenumber=4413 hts_log /src/htslib/hts.c linenumber=4419 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5040 cram_init_varint /src/htslib/cram/cram_io.c linenumber=4972 cram_read_SAM_hdr /src/htslib/cram/cram_io.c linenumber=5042 int32_decode /src/htslib/cram/cram_io.c linenumber=4466 hread /src/htslib/cram/../htslib/hfile.h linenumber=769 hread /src/htslib/cram/../htslib/hfile.h linenumber=4478 cram_read_container /src/htslib/cram/cram_io.c linenumber=4486 int32_decode /src/htslib/cram/cram_io.c linenumber=3568 crc32 linenumber=3579 calloc linenumber=3624 __errno_location linenumber=3630 cram_free_container /src/htslib/cram/cram_io.c linenumber=3631 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=3480 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=4101 cram_free_block /src/htslib/cram/cram_io.c linenumber=4131 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4133 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4135 cram_free_block /src/htslib/cram/cram_io.c linenumber=3483 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3489 free_bam_list /src/htslib/cram/cram_io.c linenumber=4162 bam_destroy1 /src/htslib/sam.c linenumber=3461 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=474 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=476 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=484 cram_free_block /src/htslib/cram/cram_io.c linenumber=4167 cram_free_block /src/htslib/cram/cram_io.c linenumber=4176 cram_free_block /src/htslib/cram/cram_io.c linenumber=4187 cram_free_slice_header /src/htslib/cram/cram_io.c linenumber=4194 cram_free_block /src/htslib/cram/cram_io.c linenumber=4197 cram_free_block /src/htslib/cram/cram_io.c linenumber=4200 cram_free_block /src/htslib/cram/cram_io.c linenumber=4203 cram_free_block /src/htslib/cram/cram_io.c linenumber=4206 cram_free_block /src/htslib/cram/cram_io.c linenumber=4209 cram_free_block /src/htslib/cram/cram_io.c linenumber=4212 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4227 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4230 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4232 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3498 cram_stats_free /src/htslib/cram/cram_stats.c linenumber=3503 kh_destroy_m_i2i /src/htslib/cram/cram_structs.h linenumber=214 cram_free_block /src/htslib/cram/cram_io.c linenumber=3525 cram_free_block /src/htslib/cram/cram_io.c linenumber=3526 kh_destroy_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3531 free_bam_list /src/htslib/cram/cram_io.c linenumber=3538 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3635 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=121 hts_malloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=122 __errno_location linenumber=3636 cram_free_container /src/htslib/cram/cram_io.c linenumber=3637 cram_free_container /src/htslib/cram/cram_io.c linenumber=3642 int32_decode /src/htslib/cram/cram_io.c linenumber=3650 cram_free_container /src/htslib/cram/cram_io.c linenumber=3651 hts_log /src/htslib/hts.c linenumber=3663 cram_free_container /src/htslib/cram/cram_io.c linenumber=3664 cram_free_container /src/htslib/cram/cram_io.c linenumber=4498 cram_read_block /src/htslib/cram/cram_io.c linenumber=4502 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1185 hts_log /src/htslib/hts.c linenumber=1187 crc32 linenumber=1190 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1191 crc32 linenumber=1192 hread /src/htslib/cram/../htslib/hfile.h linenumber=1207 hread /src/htslib/cram/../htslib/hfile.h linenumber=1219 int32_decode /src/htslib/cram/cram_io.c linenumber=1227 cram_free_container /src/htslib/cram/cram_io.c linenumber=4503 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=4506 crc32 linenumber=1348 hts_log /src/htslib/hts.c linenumber=1351 __assert_fail linenumber=1361 zlib_mem_inflate /src/htslib/cram/cram_io.c linenumber=1369 inflateInit2_ linenumber=942 hts_log /src/htslib/hts.c linenumber=944 inflate linenumber=955 hts_log /src/htslib/hts.c linenumber=960 inflateEnd linenumber=962 realloc linenumber=968 inflateEnd linenumber=971 inflateEnd linenumber=976 BZ2_bzBuffToBuffDecompress linenumber=1388 lzma_mem_inflate /src/htslib/cram/cram_io.c linenumber=1409 lzma_easy_decoder_memusage linenumber=1082 lzma_stream_decoder linenumber=1082 realloc linenumber=1092 lzma_code linenumber=1100 hts_log /src/htslib/hts.c linenumber=1102 lzma_code linenumber=1113 hts_log /src/htslib/hts.c linenumber=1115 realloc linenumber=1119 lzma_end linenumber=1124 lzma_end linenumber=1129 rans_uncompress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1430 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=1448 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=1461 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=1480 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=1499 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=4507 cram_free_block /src/htslib/cram/cram_io.c linenumber=4508 int32_get_blk /src/htslib/cram/cram_io.c linenumber=4518 cram_free_container /src/htslib/cram/cram_io.c linenumber=4521 cram_free_block /src/htslib/cram/cram_io.c linenumber=4522 cram_free_container /src/htslib/cram/cram_io.c linenumber=4526 cram_free_block /src/htslib/cram/cram_io.c linenumber=4527 cram_free_block /src/htslib/cram/cram_io.c linenumber=4532 cram_read_block /src/htslib/cram/cram_io.c linenumber=4536 cram_free_container /src/htslib/cram/cram_io.c linenumber=4537 cram_free_block /src/htslib/cram/cram_io.c linenumber=4545 cram_free_container /src/htslib/cram/cram_io.c linenumber=4552 hread /src/htslib/cram/../htslib/hfile.h linenumber=4557 cram_free_container /src/htslib/cram/cram_io.c linenumber=4558 cram_free_container /src/htslib/cram/cram_io.c linenumber=4566 sam_hdr_init /src/htslib/sam.c linenumber=4570 calloc linenumber=112 sam_hdr_add_lines /src/htslib/header.c linenumber=4576 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1668 sam_hrecs_new /src/htslib/header.c linenumber=1291 calloc linenumber=2735 kh_init_sam_hrecs_t /src/htslib/./header.h linenumber=2740 calloc linenumber=168 kh_init_m_s2i /src/htslib/./header.h linenumber=2749 calloc linenumber=169 kh_init_m_s2i /src/htslib/./header.h linenumber=2756 kh_init_m_s2i /src/htslib/./header.h linenumber=2764 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2767 next_power_2 /src/htslib/cram/pooled_alloc.c linenumber=76 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2770 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2773 sam_hrecs_init_type_order /src/htslib/header.c linenumber=2776 calloc linenumber=76 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2783 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2786 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2789 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2792 sam_hrecs_refs_from_targets_array /src/htslib/header.c linenumber=1297 hts_log /src/htslib/hts.c linenumber=1193 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1198 hts_prod_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=295 hts_realloc /src/htslib/./htslib/hts_alloc.h linenumber=296 __errno_location linenumber=268 realloc linenumber=271 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1207 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=1213 strlen linenumber=154 string_ndup /src/htslib/cram/string_alloc.c linenumber=154 string_alloc /src/htslib/cram/string_alloc.c linenumber=158 new_string_pool /src/htslib/cram/string_alloc.c linenumber=142 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=81 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=295 hts_realloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=296 hts_malloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=94 kh_get_s2i /src/htslib/hts.c linenumber=1219 __ac_FNV1a_hash_string /src/htslib/./cram/../htslib/khash.h linenumber=80 strcmp linenumber=80 kh_put_m_s2i /src/htslib/./header.h linenumber=1227 strcmp linenumber=169 hts_log /src/htslib/hts.c linenumber=1230 __errno_location linenumber=1242 strerror linenumber=1242 hts_log /src/htslib/hts.c linenumber=1242 kh_get_m_s2i /src/htslib/./header.h linenumber=1246 kh_del_m_s2i /src/htslib/./header.h linenumber=1247 sam_hrecs_free /src/htslib/header.c linenumber=1298 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2819 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2822 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2828 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2834 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2843 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2846 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2849 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1305 strlen linenumber=1003 sam_hrecs_error /src/htslib/header.c linenumber=1007 hts_log /src/htslib/hts.c linenumber=65 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1018 sam_hrecs_error /src/htslib/header.c linenumber=920 isalpha_c /src/htslib/./textutils_internal.h linenumber=925 __ctype_b_loc linenumber=170 sam_hrecs_error /src/htslib/header.c linenumber=926 TYPEKEY /src/htslib/./header.h linenumber=930 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=936 new_pool /src/htslib/cram/pooled_alloc.c linenumber=138 hts_realloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=101 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=320 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=321 hts_realloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=322 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=106 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=941 kh_resize_sam_hrecs_t /src/htslib/./header.h linenumber=168 realloc linenumber=168 TYPEKEY /src/htslib/./header.h linenumber=948 parse_comment_line /src/htslib/header.c linenumber=950 sam_hrecs_error /src/htslib/header.c linenumber=807 warn_if_known_stderr /src/htslib/header.c linenumber=808 kmemmem /src/htslib/kstring.c linenumber=791 boyer_moore /src/htslib/kstring.c linenumber=499 memchr linenumber=468 ksBM_prep /src/htslib/kstring.c linenumber=473 hts_calloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=411 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=228 hts_calloc /src/htslib/./htslib/hts_alloc.h linenumber=229 __errno_location linenumber=201 calloc linenumber=204 calloc linenumber=418 karp_rabin /src/htslib/kstring.c linenumber=474 fast_exp /src/htslib/kstring.c linenumber=373 memcmp linenumber=393 known_stderr /src/htslib/header.c linenumber=792 hts_log /src/htslib/hts.c linenumber=782 hts_log /src/htslib/hts.c linenumber=783 kmemmem /src/htslib/kstring.c linenumber=793 known_stderr /src/htslib/header.c linenumber=794 kmemmem /src/htslib/kstring.c linenumber=795 known_stderr /src/htslib/header.c linenumber=796 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=815 string_ndup /src/htslib/cram/string_alloc.c linenumber=817 parse_noncomment_line /src/htslib/header.c linenumber=957 TYPEKEY /src/htslib/./header.h linenumber=832 sam_hrecs_error /src/htslib/header.c linenumber=842 warn_if_known_stderr /src/htslib/header.c linenumber=843 sam_hrecs_error /src/htslib/header.c linenumber=853 warn_if_known_stderr /src/htslib/header.c linenumber=854 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=866 string_ndup /src/htslib/cram/string_alloc.c linenumber=868 sam_hrecs_global_list_add /src/htslib/header.c linenumber=965 TYPEKEY /src/htslib/./header.h linenumber=504 __assert_fail linenumber=972 sam_hrecs_free_tags /src/htslib/header.c linenumber=989 sam_hrecs_free_tags /src/htslib/header.c linenumber=699 pool_free /src/htslib/cram/pooled_alloc.c linenumber=701 pool_free /src/htslib/cram/pooled_alloc.c linenumber=990 TYPEKEY /src/htslib/./header.h linenumber=1030 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1045 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1049 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1063 TYPEKEY /src/htslib/./header.h linenumber=146 __assert_fail linenumber=157 __assert_fail linenumber=160 strtoll linenumber=162 __assert_fail linenumber=167 hts_log /src/htslib/hts.c linenumber=174 hts_log /src/htslib/hts.c linenumber=179 hts_log /src/htslib/hts.c linenumber=185 kh_get_m_s2i /src/htslib/./header.h linenumber=191 snprintf linenumber=203 sam_hrecs_update /src/htslib/header.c linenumber=205 sam_hrecs_vupdate /src/htslib/header.c linenumber=2996 sam_hrecs_find_key /src/htslib/header.c linenumber=2954 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=2956 strlen linenumber=2966 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=2967 string_alloc /src/htslib/cram/string_alloc.c linenumber=2967 snprintf linenumber=2971 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=209 kstrtok /src/htslib/kstring.c linenumber=96 strchr linenumber=216 strlen linenumber=217 string_ndup /src/htslib/cram/string_alloc.c linenumber=100 kh_put_m_s2i /src/htslib/./header.h linenumber=104 hts_log /src/htslib/hts.c linenumber=110 strcmp linenumber=223 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=227 strcmp linenumber=237 hts_log /src/htslib/hts.c linenumber=238 hts_log /src/htslib/hts.c linenumber=246 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=252 kh_put_m_s2i /src/htslib/./header.h linenumber=263 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=267 TYPEKEY /src/htslib/./header.h linenumber=276 sam_hrecs_find_key /src/htslib/header.c linenumber=277 hts_log /src/htslib/hts.c linenumber=282 __assert_fail linenumber=285 kh_get_m_s2i /src/htslib/./header.h linenumber=288 __assert_fail linenumber=291 hts_log /src/htslib/hts.c linenumber=293 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=304 kh_put_m_s2i /src/htslib/./header.h linenumber=316 TYPEKEY /src/htslib/./header.h linenumber=324 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=331 __assert_fail linenumber=349 hts_log /src/htslib/hts.c linenumber=353 kh_get_m_s2i /src/htslib/./header.h linenumber=358 kh_put_m_s2i /src/htslib/./header.h linenumber=388 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=400 sam_hrecs_free /src/htslib/header.c linenumber=1306 add_stub_ref_sq_lines /src/htslib/header.c linenumber=1311 snprintf linenumber=1273 sam_hrecs_add /src/htslib/header.c linenumber=1274 sam_hrecs_vadd /src/htslib/header.c linenumber=686 TYPEKEY /src/htslib/./header.h linenumber=558 strncmp linenumber=560 sam_hrecs_find_type_id /src/htslib/header.c linenumber=560 kh_get_m_s2i /src/htslib/./header.h linenumber=2881 kh_get_m_s2i /src/htslib/./header.h linenumber=2889 kh_get_m_s2i /src/htslib/./header.h linenumber=2897 TYPEKEY /src/htslib/./header.h linenumber=2904 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=2904 sam_hrecs_vupdate /src/htslib/header.c linenumber=561 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=563 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=565 __assert_fail linenumber=576 sam_hrecs_global_list_add /src/htslib/header.c linenumber=590 __assert_fail linenumber=593 __assert_fail linenumber=594 __assert_fail linenumber=595 __assert_fail linenumber=596 strncmp linenumber=605 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=610 strncmp linenumber=613 strlen linenumber=614 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=615 string_alloc /src/htslib/cram/string_alloc.c linenumber=615 snprintf linenumber=616 strlen linenumber=620 string_ndup /src/htslib/cram/string_alloc.c linenumber=621 strncmp linenumber=642 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=645 strncmp linenumber=648 strlen linenumber=649 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=650 string_alloc /src/htslib/cram/string_alloc.c linenumber=650 snprintf linenumber=651 strlen linenumber=655 string_ndup /src/htslib/cram/string_alloc.c linenumber=656 TYPEKEY /src/htslib/./header.h linenumber=670 sam_hrecs_update_hashes /src/htslib/header.c linenumber=670 strncmp linenumber=673 hts_log /src/htslib/hts.c linenumber=1281 sam_hrecs_free /src/htslib/header.c linenumber=1312 rebuild_target_arrays /src/htslib/header.c linenumber=1318 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1162 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1084 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1089 strcmp linenumber=1104 strdup linenumber=1107 kh_get_s2i /src/htslib/hts.c linenumber=1118 kh_del_s2i /src/htslib/hts.c linenumber=1120 kh_init_s2i /src/htslib/hts.c linenumber=1126 calloc linenumber=80 kh_put_s2i /src/htslib/hts.c linenumber=1132 kh_resize_s2i /src/htslib/hts.c linenumber=80 realloc linenumber=80 kh_get_s2i /src/htslib/hts.c linenumber=1143 kh_del_s2i /src/htslib/hts.c linenumber=1145 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1673 rebuild_target_arrays /src/htslib/header.c linenumber=1676 redact_header_text /src/htslib/header.c linenumber=1680 __assert_fail linenumber=1532 sam_hdr_destroy /src/htslib/sam.c linenumber=4578 sam_hrecs_free /src/htslib/header.c linenumber=138 kh_destroy_s2i /src/htslib/hts.c linenumber=140 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5043 calloc linenumber=5049 strncpy linenumber=5062 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5065 strrchr linenumber=5070 strdup linenumber=5070 refs_create /src/htslib/cram/cram_io.c linenumber=5078 calloc linenumber=2230 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2237 kh_init_refs /src/htslib/cram/cram_structs.h linenumber=2245 calloc linenumber=684 pthread_mutex_init linenumber=2248 refs_free /src/htslib/cram/cram_io.c linenumber=2253 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2199 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2211 mfclose /src/htslib/cram/mFILE.c linenumber=2181 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=2215 bgzf_close /src/htslib/bgzf.c linenumber=2222 bgzf_flush /src/htslib/bgzf.c linenumber=2087 mt_queue /src/htslib/bgzf.c linenumber=1957 pthread_mutex_lock linenumber=1861 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=1862 pthread_mutex_unlock linenumber=1864 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=1873 pthread_mutex_lock linenumber=854 pthread_mutex_unlock linenumber=860 __errno_location linenumber=861 pthread_mutex_unlock linenumber=866 pthread_cond_wait linenumber=881 pthread_mutex_unlock linenumber=885 wake_next_worker /src/htslib/thread_pool.c linenumber=913 pthread_mutex_lock linenumber=659 __assert_fail linenumber=663 __assert_fail linenumber=677 pthread_cond_signal linenumber=714 pthread_mutex_unlock linenumber=717 pthread_mutex_unlock linenumber=915 bgzf_encode_level0_func /src/htslib/bgzf.c linenumber=1873 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1356 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1360 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1361 hts_crc32 /src/htslib/bgzf.c linenumber=1364 crc32 linenumber=622 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1365 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1366 job_cleanup /src/htslib/bgzf.c linenumber=1873 pthread_mutex_lock linenumber=1326 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1327 pthread_mutex_unlock linenumber=1328 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=1882 bgzf_encode_func /src/htslib/bgzf.c linenumber=1882 bgzf_compress /src/htslib/bgzf.c linenumber=1335 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=636 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=637 deflateInit2_ linenumber=648 bgzf_zerr /src/htslib/bgzf.c linenumber=650 hts_log /src/htslib/hts.c linenumber=650 deflate linenumber=653 deflateEnd linenumber=655 bgzf_zerr /src/htslib/bgzf.c linenumber=658 hts_log /src/htslib/hts.c linenumber=658 deflateEnd linenumber=666 deflateEnd linenumber=669 bgzf_zerr /src/htslib/bgzf.c linenumber=670 hts_log /src/htslib/hts.c linenumber=670 packInt16 /src/htslib/bgzf.c linenumber=678 crc32 linenumber=680 packInt32 /src/htslib/bgzf.c linenumber=681 packInt32 /src/htslib/bgzf.c linenumber=682 job_cleanup /src/htslib/bgzf.c linenumber=1882 job_cleanup /src/htslib/bgzf.c linenumber=1892 pthread_mutex_lock linenumber=1893 pthread_mutex_unlock linenumber=1895 mt_flush_queue /src/htslib/bgzf.c linenumber=1958 pthread_mutex_lock linenumber=1908 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=1911 pthread_mutex_lock linenumber=335 pthread_mutex_unlock linenumber=337 pthread_mutex_unlock linenumber=1913 hts_usleep /src/htslib/./hts_internal.h linenumber=1914 nanosleep linenumber=162 pthread_mutex_lock linenumber=1915 pthread_mutex_unlock linenumber=1917 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=1923 pthread_mutex_lock linenumber=949 pthread_cond_signal linenumber=954 pthread_cond_wait linenumber=967 gettimeofday linenumber=976 pthread_cond_timedwait linenumber=979 gettimeofday linenumber=986 pthread_cond_timedwait linenumber=989 pthread_mutex_unlock linenumber=995 pthread_mutex_lock linenumber=1964 pthread_mutex_unlock linenumber=1966 hflush /src/htslib/hfile.c linenumber=1973 flush_buffer /src/htslib/hfile.c linenumber=392 __errno_location linenumber=394 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1980 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2381 deflate_block /src/htslib/bgzf.c linenumber=1983 bgzf_compress /src/htslib/bgzf.c linenumber=715 bgzf_gzip_compress /src/htslib/bgzf.c linenumber=717 deflate linenumber=696 bgzf_zerr /src/htslib/bgzf.c linenumber=698 hts_log /src/htslib/hts.c linenumber=698 hts_log /src/htslib/hts.c linenumber=702 hts_log /src/htslib/hts.c linenumber=721 bgzf_zerr /src/htslib/bgzf.c linenumber=1985 hts_log /src/htslib/hts.c linenumber=1985 hwrite /src/htslib/./htslib/hfile.h linenumber=1988 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=1989 bgzf_close_mt /src/htslib/bgzf.c linenumber=2088 mt_destroy /src/htslib/bgzf.c linenumber=2077 pthread_mutex_lock linenumber=1812 pthread_cond_signal linenumber=1814 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=1815 pthread_mutex_lock linenumber=925 pthread_cond_signal linenumber=927 pthread_mutex_unlock linenumber=928 pthread_mutex_unlock linenumber=1816 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=1821 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=1825 pthread_mutex_lock linenumber=421 pthread_mutex_unlock linenumber=423 hts_tpool_process_reset /src/htslib/thread_pool.c linenumber=426 pthread_mutex_lock linenumber=1018 pthread_mutex_unlock linenumber=1031 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1047 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=1053 pthread_mutex_lock linenumber=1057 pthread_cond_signal linenumber=1064 pthread_mutex_unlock linenumber=1065 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1075 pthread_mutex_lock linenumber=427 hts_tpool_process_detach_locked /src/htslib/thread_pool.c linenumber=428 hts_tpool_process_shutdown_locked /src/htslib/thread_pool.c linenumber=429 pthread_cond_broadcast linenumber=322 pthread_cond_broadcast linenumber=323 pthread_cond_broadcast linenumber=324 pthread_cond_broadcast linenumber=325 pthread_mutex_unlock linenumber=433 pthread_cond_destroy linenumber=437 pthread_cond_destroy linenumber=438 pthread_cond_destroy linenumber=439 pthread_cond_destroy linenumber=440 pthread_mutex_unlock linenumber=441 pthread_join linenumber=1830 pthread_mutex_destroy linenumber=1833 pthread_mutex_destroy linenumber=1834 pthread_mutex_destroy linenumber=1835 pthread_cond_destroy linenumber=1836 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1838 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=1841 pthread_mutex_lock linenumber=1096 pthread_cond_signal linenumber=1102 pthread_mutex_unlock linenumber=1104 pthread_join linenumber=1109 pthread_mutex_destroy linenumber=1111 pthread_cond_destroy linenumber=1113 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=1843 fflush linenumber=1849 deflate_block /src/htslib/bgzf.c linenumber=2092 bgzf_zerr /src/htslib/bgzf.c linenumber=2094 hts_log /src/htslib/hts.c linenumber=2094 bgzf_close_mt /src/htslib/bgzf.c linenumber=2095 hwrite /src/htslib/./htslib/hfile.h linenumber=2098 hflush /src/htslib/hfile.c linenumber=2099 hts_log /src/htslib/hts.c linenumber=2100 bgzf_close_mt /src/htslib/bgzf.c linenumber=2106 inflateEnd linenumber=2111 deflateEnd linenumber=2112 bgzf_zerr /src/htslib/bgzf.c linenumber=2114 hts_log /src/htslib/hts.c linenumber=2114 hclose /src/htslib/hfile.c linenumber=2118 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=2120 free_cache /src/htslib/bgzf.c linenumber=2122 kh_destroy_bgzf_cache /src/htslib/bgzf.c linenumber=913 bgzf_clear_private_data /src/htslib/./bgzf_internal.h linenumber=915 __assert_fail linenumber=59 pthread_mutex_destroy linenumber=2224 pthread_mutex_init linenumber=5114 pthread_mutex_init linenumber=5115 pthread_mutex_init linenumber=5116 pthread_mutex_init linenumber=5117 cram_new_metrics /src/htslib/cram/cram_io.c linenumber=5120 calloc linenumber=2090 kh_init_m_metrics /src/htslib/cram/cram_structs.h linenumber=5125 calloc linenumber=294 refs_from_header /src/htslib/cram/cram_io.c linenumber=5135 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2543 hts_realloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=2553 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2567 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=684 strcmp linenumber=684 calloc linenumber=2572 string_dup /src/htslib/cram/string_alloc.c linenumber=2578 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2583 sam_hrecs_find_key /src/htslib/header.c linenumber=2584 string_dup /src/htslib/cram/string_alloc.c linenumber=2585 sam_hrecs_find_key /src/htslib/header.c linenumber=2587 strtoll linenumber=2589 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2596 kh_resize_refs /src/htslib/cram/cram_structs.h linenumber=684 realloc linenumber=684 cram_set_option /src/htslib/cram/cram_io.c linenumber=1585 cram_set_voption /src/htslib/cram/cram_io.c linenumber=5392 __errno_location linenumber=5409 strdup linenumber=5421 refs_free /src/htslib/cram/cram_io.c linenumber=5497 cram_seek_to_refpos /src/htslib/cram/cram_index.c linenumber=5504 cram_index_query /src/htslib/cram/cram_index.c linenumber=585 cram_seek /src/htslib/cram/cram_io.c linenumber=586 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5156 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3683 pthread_mutex_lock linenumber=262 pthread_mutex_unlock linenumber=264 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3684 pthread_mutex_lock linenumber=228 hts_tpool_next_result_locked /src/htslib/thread_pool.c linenumber=229 pthread_cond_signal linenumber=182 wake_next_worker /src/htslib/thread_pool.c linenumber=184 gettimeofday linenumber=234 pthread_mutex_unlock linenumber=241 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=243 pthread_cond_timedwait linenumber=246 pthread_mutex_unlock linenumber=250 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3687 cram_free_container /src/htslib/cram/cram_io.c linenumber=3696 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3700 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3701 cram_free_container /src/htslib/cram/cram_io.c linenumber=3716 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3720 cram_free_container /src/htslib/cram/cram_io.c linenumber=3730 hseek /src/htslib/hfile.c linenumber=5158 pthread_mutex_lock linenumber=594 pthread_mutex_unlock linenumber=602 cram_free_container /src/htslib/cram/cram_io.c linenumber=605 cram_free_container /src/htslib/cram/cram_io.c linenumber=607 pthread_mutex_lock linenumber=619 pthread_mutex_unlock linenumber=621 pthread_mutex_lock linenumber=5505 pthread_mutex_unlock linenumber=5510 pthread_mutex_lock linenumber=5516 pthread_mutex_unlock linenumber=5529 cram_load_reference /src/htslib/cram/cram_io.c linenumber=5534 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3364 strlen linenumber=2308 refs_create /src/htslib/cram/cram_io.c linenumber=2314 bgzf_close /src/htslib/bgzf.c linenumber=2318 strstr linenumber=2323 string_ndup /src/htslib/cram/string_alloc.c linenumber=2325 snprintf linenumber=2328 strcmp linenumber=2331 string_ndup /src/htslib/cram/string_alloc.c linenumber=2333 snprintf linenumber=2336 string_dup /src/htslib/cram/string_alloc.c linenumber=2339 snprintf linenumber=2341 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=2345 strncmp linenumber=2268 hisremote /src/htslib/hfile.c linenumber=2271 find_scheme_handler /src/htslib/hfile.c linenumber=1347 snprintf linenumber=2274 access linenumber=2275 fai_build /src/htslib/faidx.c linenumber=2276 fai_build3 /src/htslib/faidx.c linenumber=583 fai_build3_core /src/htslib/faidx.c linenumber=578 bgzf_open /src/htslib/bgzf.c linenumber=490 strchr linenumber=499 hopen /src/htslib/hfile.c linenumber=501 bgzf_read_init /src/htslib/bgzf.c linenumber=502 hclose_abruptly /src/htslib/hfile.c linenumber=503 strchr linenumber=505 hopen /src/htslib/hfile.c linenumber=507 bgzf_write_init /src/htslib/bgzf.c linenumber=508 __errno_location linenumber=512 ed_is_big /src/htslib/./htslib/hts.h linenumber=514 strerror linenumber=493 hts_log /src/htslib/hts.c linenumber=493 bgzf_index_build_init /src/htslib/bgzf.c linenumber=498 bgzf_index_destroy /src/htslib/bgzf.c linenumber=2367 calloc linenumber=2368 hts_log /src/htslib/hts.c linenumber=499 fai_build_core /src/htslib/faidx.c linenumber=504 calloc linenumber=159 kh_init_s /src/htslib/faidx.c linenumber=160 bgzf_getc_ /src/htslib/faidx.c linenumber=166 bgzf_getc /src/htslib/bgzf.c linenumber=66 bgzf_read_block /src/htslib/bgzf.c linenumber=2306 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=1018 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=1019 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1023 mt_destroy /src/htslib/bgzf.c linenumber=1027 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1031 hts_log /src/htslib/hts.c linenumber=1040 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1043 hts_log /src/htslib/hts.c linenumber=1050 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1060 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1074 pthread_mutex_lock linenumber=1081 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1082 pthread_mutex_unlock linenumber=1083 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1092 bgzf_htell /src/htslib/bgzf.c linenumber=1103 pthread_mutex_lock linenumber=996 pthread_mutex_unlock linenumber=998 htell /src/htslib/./htslib/hfile.h linenumber=1001 hread /src/htslib/./htslib/hfile.h linenumber=1108 __errno_location linenumber=1111 strerror linenumber=1111 hts_log /src/htslib/hts.c linenumber=1111 inflate_gzip_block /src/htslib/bgzf.c linenumber=1131 hread /src/htslib/./htslib/hfile.h linenumber=845 inflate linenumber=859 bgzf_zerr /src/htslib/bgzf.c linenumber=863 hts_log /src/htslib/hts.c linenumber=863 hpeek /src/htslib/hfile.c linenumber=871 inflateReset linenumber=873 bgzf_zerr /src/htslib/bgzf.c linenumber=875 hts_log /src/htslib/hts.c linenumber=875 hts_log /src/htslib/hts.c linenumber=886 hts_log /src/htslib/hts.c linenumber=1134 load_block_from_cache /src/htslib/bgzf.c linenumber=1143 kh_get_bgzf_cache /src/htslib/bgzf.c linenumber=925 hseek /src/htslib/hfile.c linenumber=932 hts_log /src/htslib/hts.c linenumber=935 exit linenumber=936 hread /src/htslib/./htslib/hfile.h linenumber=1148 hts_log /src/htslib/hts.c linenumber=1152 check_header /src/htslib/bgzf.c linenumber=1158 unpackInt16 /src/htslib/bgzf.c linenumber=901 unpackInt16 /src/htslib/bgzf.c linenumber=903 hts_log /src/htslib/hts.c linenumber=1161 hread /src/htslib/./htslib/hfile.h linenumber=1171 calloc linenumber=1174 inflateInit2_ linenumber=1176 bgzf_zerr /src/htslib/bgzf.c linenumber=1179 hts_log /src/htslib/hts.c linenumber=1179 inflate_gzip_block /src/htslib/bgzf.c linenumber=1185 hts_log /src/htslib/hts.c linenumber=1188 unpackInt16 /src/htslib/bgzf.c linenumber=1199 hts_log /src/htslib/hts.c linenumber=1202 hread /src/htslib/./htslib/hfile.h linenumber=1210 hts_log /src/htslib/hts.c linenumber=1212 inflate_block /src/htslib/bgzf.c linenumber=1219 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=812 bgzf_uncompress /src/htslib/bgzf.c linenumber=813 inflateInit2_ linenumber=776 bgzf_zerr /src/htslib/bgzf.c linenumber=778 hts_log /src/htslib/hts.c linenumber=778 inflate linenumber=781 bgzf_zerr /src/htslib/bgzf.c linenumber=782 inflateEnd linenumber=783 bgzf_zerr /src/htslib/bgzf.c linenumber=784 hts_log /src/htslib/hts.c linenumber=784 inflateEnd linenumber=788 bgzf_zerr /src/htslib/bgzf.c linenumber=789 hts_log /src/htslib/hts.c linenumber=789 crc32 linenumber=794 hts_log /src/htslib/hts.c linenumber=800 bgzf_zerr /src/htslib/bgzf.c linenumber=1220 hts_log /src/htslib/hts.c linenumber=1220 bgzf_htell /src/htslib/bgzf.c linenumber=1228 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1235 cache_block /src/htslib/bgzf.c linenumber=1238 kh_del_bgzf_cache /src/htslib/bgzf.c linenumber=970 kh_put_bgzf_cache /src/htslib/bgzf.c linenumber=976 kh_resize_bgzf_cache /src/htslib/bgzf.c linenumber=87 realloc linenumber=87 bgzf_htell /src/htslib/bgzf.c linenumber=2311 hts_log /src/htslib/hts.c linenumber=172 hts_log /src/htslib/hts.c linenumber=182 bgzf_getc_ /src/htslib/faidx.c linenumber=192 hts_log /src/htslib/hts.c linenumber=195 __ctype_b_loc linenumber=207 hts_log /src/htslib/hts.c linenumber=207 fai_insert_index /src/htslib/faidx.c linenumber=215 hts_log /src/htslib/hts.c linenumber=100 hts_log /src/htslib/hts.c linenumber=104 hts_log /src/htslib/hts.c linenumber=108 hts_log /src/htslib/hts.c linenumber=113 strdup linenumber=118 kh_put_s /src/htslib/faidx.c linenumber=120 kh_resize_s /src/htslib/faidx.c linenumber=80 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=80 hts_log /src/htslib/hts.c linenumber=124 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=132 hts_log /src/htslib/hts.c linenumber=133 __ctype_b_loc linenumber=224 kputc /src/htslib/./htslib/kstring.h linenumber=225 bgzf_getc_ /src/htslib/faidx.c linenumber=229 kputsn /src/htslib/./htslib/kstring.h linenumber=231 hts_log /src/htslib/hts.c linenumber=234 bgzf_getc_ /src/htslib/faidx.c linenumber=239 bgzf_utell /src/htslib/bgzf.c linenumber=242 bgzf_getc_ /src/htslib/faidx.c linenumber=259 bgzf_utell /src/htslib/bgzf.c linenumber=260 hts_log /src/htslib/hts.c linenumber=264 isgraph_ /src/htslib/faidx.c linenumber=275 bgzf_getc_ /src/htslib/faidx.c linenumber=276 hts_log /src/htslib/hts.c linenumber=291 bgzf_getc_ /src/htslib/faidx.c linenumber=301 bgzf_utell /src/htslib/bgzf.c linenumber=302 hts_log /src/htslib/hts.c linenumber=305 hts_log /src/htslib/hts.c linenumber=313 isgraph_ /src/htslib/faidx.c linenumber=329 bgzf_getc_ /src/htslib/faidx.c linenumber=330 hts_log /src/htslib/hts.c linenumber=335 hts_log /src/htslib/hts.c linenumber=343 fai_insert_index /src/htslib/faidx.c linenumber=353 hts_log /src/htslib/hts.c linenumber=356 fai_destroy /src/htslib/faidx.c linenumber=365 kh_destroy_s /src/htslib/faidx.c linenumber=474 bgzf_close /src/htslib/bgzf.c linenumber=475 hts_log /src/htslib/hts.c linenumber=508 ksprintf /src/htslib/kstring.c linenumber=520 ksprintf /src/htslib/kstring.c linenumber=525 bgzf_index_dump /src/htslib/bgzf.c linenumber=530 hts_log /src/htslib/hts.c linenumber=2447 __errno_location linenumber=2448 get_name_suffix /src/htslib/bgzf.c linenumber=2454 strlen linenumber=2399 snprintf linenumber=2402 hopen /src/htslib/hfile.c linenumber=2459 bgzf_index_dump_hfile /src/htslib/bgzf.c linenumber=2465 hts_log /src/htslib/hts.c linenumber=2415 __errno_location linenumber=2416 bgzf_flush /src/htslib/bgzf.c linenumber=2420 hwrite_uint64 /src/htslib/bgzf.c linenumber=2426 ed_is_big /src/htslib/./htslib/hts.h linenumber=2392 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2392 hwrite /src/htslib/./htslib/hfile.h linenumber=2393 hwrite_uint64 /src/htslib/bgzf.c linenumber=2430 hwrite_uint64 /src/htslib/bgzf.c linenumber=2431 __errno_location linenumber=2436 strerror linenumber=2436 hts_log /src/htslib/hts.c linenumber=2436 hclose /src/htslib/hfile.c linenumber=2467 __errno_location linenumber=2479 strerror linenumber=2479 hts_log /src/htslib/hts.c linenumber=2479 hclose_abruptly /src/htslib/hfile.c linenumber=2481 hts_log /src/htslib/hts.c linenumber=531 bgzf_close /src/htslib/bgzf.c linenumber=536 __errno_location linenumber=540 strerror linenumber=540 hts_log /src/htslib/hts.c linenumber=540 hopen /src/htslib/hfile.c linenumber=544 __errno_location linenumber=547 strerror linenumber=547 hts_log /src/htslib/hts.c linenumber=547 fai_save /src/htslib/faidx.c linenumber=551 kh_get_s /src/htslib/faidx.c linenumber=377 __assert_fail linenumber=378 snprintf linenumber=382 snprintf linenumber=386 hputs /src/htslib/./htslib/hfile.h linenumber=392 strlen linenumber=280 hputs2 /src/htslib/hfile.c linenumber=284 hwrite2 /src/htslib/hfile.c linenumber=443 hputs /src/htslib/./htslib/hfile.h linenumber=393 __errno_location linenumber=552 strerror linenumber=552 hts_log /src/htslib/hts.c linenumber=552 hclose /src/htslib/hfile.c linenumber=556 __errno_location linenumber=557 strerror linenumber=557 hts_log /src/htslib/hts.c linenumber=557 fai_destroy /src/htslib/faidx.c linenumber=563 __errno_location linenumber=567 bgzf_close /src/htslib/bgzf.c linenumber=570 fai_destroy /src/htslib/faidx.c linenumber=571 __errno_location linenumber=572 bgzf_open /src/htslib/bgzf.c linenumber=2280 perror linenumber=2281 bgzf_index_load /src/htslib/bgzf.c linenumber=2285 get_name_suffix /src/htslib/bgzf.c linenumber=2534 hopen /src/htslib/hfile.c linenumber=2539 bgzf_index_load_hfile /src/htslib/bgzf.c linenumber=2545 calloc linenumber=2495 hread_uint64 /src/htslib/bgzf.c linenumber=2498 hread /src/htslib/./htslib/hfile.h linenumber=2488 ed_is_big /src/htslib/./htslib/hts.h linenumber=2489 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2489 hread_uint64 /src/htslib/bgzf.c linenumber=2511 hread_uint64 /src/htslib/bgzf.c linenumber=2512 __errno_location linenumber=2518 strerror linenumber=2518 hts_log /src/htslib/hts.c linenumber=2518 hclose /src/htslib/hfile.c linenumber=2547 __errno_location linenumber=2558 strerror linenumber=2558 hts_log /src/htslib/hts.c linenumber=2558 hclose_abruptly /src/htslib/hfile.c linenumber=2560 hts_log /src/htslib/hts.c linenumber=2286 bgzf_close /src/htslib/bgzf.c linenumber=2287 hts_log /src/htslib/hts.c linenumber=2346 hopen /src/htslib/hfile.c linenumber=2350 hts_log /src/htslib/hts.c linenumber=2351 perror linenumber=2353 hgets /src/htslib/hfile.c linenumber=2356 __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=2366 string_dup /src/htslib/cram/string_alloc.c linenumber=2369 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2372 strtoll linenumber=2374 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2377 strtoll linenumber=2379 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2382 strtol linenumber=2384 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2387 strtol linenumber=2389 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2400 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2426 hclose /src/htslib/hfile.c linenumber=2438 hclose_abruptly /src/htslib/hfile.c linenumber=2444 refs_free /src/htslib/cram/cram_io.c linenumber=2447 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3369 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2466 strcmp linenumber=2478 __assert_fail linenumber=2478 hts_log /src/htslib/hts.c linenumber=2482 refs_free /src/htslib/cram/cram_io.c linenumber=3375 refs_create /src/htslib/cram/cram_io.c linenumber=3376 refs_from_header /src/htslib/cram/cram_io.c linenumber=3378 refs2id /src/htslib/cram/cram_io.c linenumber=3383 calloc linenumber=2508 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2514 __isoc99_sscanf linenumber=5539 hts_log /src/htslib/hts.c linenumber=5540 hts_log /src/htslib/hts.c linenumber=5546 __errno_location linenumber=5548 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5558 hts_tpool_init /src/htslib/thread_pool.c linenumber=5572 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=742 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=747 pthread_mutexattr_init linenumber=756 pthread_mutexattr_settype linenumber=757 pthread_mutex_init linenumber=758 pthread_mutexattr_destroy linenumber=759 pthread_mutex_lock linenumber=761 pthread_attr_init linenumber=767 pthread_attr_getstacksize linenumber=770 pthread_attr_setstacksize linenumber=773 pthread_cond_init linenumber=782 pthread_create linenumber=783 tpool_worker /src/htslib/thread_pool.c linenumber=783 pthread_mutex_lock linenumber=524 __assert_fail linenumber=528 pthread_cond_wait linenumber=558 __assert_fail linenumber=588 pthread_cond_broadcast linenumber=601 pthread_cond_signal linenumber=604 pthread_mutex_unlock linenumber=608 hts_tpool_add_result /src/htslib/thread_pool.c linenumber=613 pthread_mutex_lock linenumber=100 pthread_cond_signal linenumber=106 pthread_mutex_unlock linenumber=110 pthread_mutex_unlock linenumber=115 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=116 pthread_mutex_lock linenumber=329 hts_tpool_process_shutdown_locked /src/htslib/thread_pool.c linenumber=330 pthread_mutex_unlock linenumber=331 __assert_fail linenumber=133 pthread_cond_broadcast linenumber=138 pthread_mutex_unlock linenumber=142 pthread_mutex_lock linenumber=618 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=621 pthread_mutex_unlock linenumber=631 pthread_mutex_lock linenumber=642 hts_tpool_process_shutdown_locked /src/htslib/thread_pool.c linenumber=646 pthread_mutex_unlock linenumber=651 pthread_mutex_unlock linenumber=787 pthread_attr_destroy linenumber=788 __errno_location linenumber=797 __errno_location linenumber=798 strerror linenumber=798 hts_log /src/htslib/hts.c linenumber=798 pthread_mutex_unlock linenumber=801 pthread_join linenumber=803 pthread_cond_destroy linenumber=804 pthread_mutex_destroy linenumber=806 pthread_attr_destroy linenumber=808 __errno_location linenumber=812 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5575 pthread_cond_init linenumber=378 pthread_cond_init linenumber=379 pthread_cond_init linenumber=380 pthread_cond_init linenumber=381 hts_tpool_process_attach /src/htslib/thread_pool.c linenumber=403 pthread_mutex_lock linenumber=458 __assert_fail linenumber=469 pthread_mutex_unlock linenumber=470 hts_tpool_size /src/htslib/thread_pool.c linenumber=5589 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5588 hts_log /src/htslib/hts.c linenumber=5655 __errno_location linenumber=5656 bgzf_hopen /src/htslib/bgzf.c linenumber=1597 __errno_location linenumber=1606 hts_process_opts /src/htslib/hts.c linenumber=1611 hts_parse_opt_list /src/htslib/hts.c linenumber=1418 strncpy linenumber=1314 hts_opt_add /src/htslib/hts.c linenumber=1317 strdup linenumber=1038 strchr linenumber=1043 strcmp linenumber=1048 strcmp linenumber=1049 atoi linenumber=1050 strcmp linenumber=1052 strcmp linenumber=1053 atoi linenumber=1054 strcmp linenumber=1056 strcmp linenumber=1057 atoi linenumber=1058 strcmp linenumber=1060 strcmp linenumber=1061 atoi linenumber=1062 strcmp linenumber=1064 strcmp linenumber=1065 atoi linenumber=1066 strcmp linenumber=1068 strcmp linenumber=1069 atoi linenumber=1070 strcmp linenumber=1072 strcmp linenumber=1073 atoi linenumber=1074 strcmp linenumber=1076 strcmp linenumber=1077 atoi linenumber=1078 strcmp linenumber=1080 strcmp linenumber=1081 atoi linenumber=1082 strcmp linenumber=1084 strcmp linenumber=1085 atoi linenumber=1086 strcmp linenumber=1088 strcmp linenumber=1089 atoi linenumber=1090 strcmp linenumber=1092 strcmp linenumber=1093 atoi linenumber=1094 strcmp linenumber=1096 strcmp linenumber=1097 atoi linenumber=1098 strcmp linenumber=1100 strcmp linenumber=1101 atoi linenumber=1102 strcmp linenumber=1105 atoi linenumber=1106 strcmp linenumber=1108 strcmp linenumber=1109 strcmp linenumber=1112 strcmp linenumber=1113 strcmp linenumber=1116 strcmp linenumber=1117 strcmp linenumber=1120 strcmp linenumber=1121 strcmp linenumber=1124 strcmp linenumber=1125 strcmp linenumber=1128 strcmp linenumber=1129 strcmp linenumber=1132 strcmp linenumber=1133 atoi linenumber=1134 strcmp linenumber=1136 strcmp linenumber=1137 atoi linenumber=1138 strcmp linenumber=1140 strcmp linenumber=1141 strtol linenumber=1144 hts_log /src/htslib/hts.c linenumber=1153 strcmp linenumber=1160 strcmp linenumber=1161 strtol linenumber=1162 strcmp linenumber=1164 strcmp linenumber=1165 strtol linenumber=1166 strcmp linenumber=1168 strcmp linenumber=1169 strcmp linenumber=1172 strcmp linenumber=1173 atoi linenumber=1174 strcmp linenumber=1176 strcmp linenumber=1177 atoi linenumber=1178 strcmp linenumber=1180 strcmp linenumber=1181 strtol linenumber=1182 strcmp linenumber=1184 strcmp linenumber=1185 strtol linenumber=1186 strcmp linenumber=1188 strcmp linenumber=1189 strcmp linenumber=1192 strcmp linenumber=1193 strcmp linenumber=1196 strcmp linenumber=1197 strcmp linenumber=1200 strcmp linenumber=1201 strcmp linenumber=1204 strcmp linenumber=1205 strcmp linenumber=1208 strcmp linenumber=1209 strcmp linenumber=1212 strcmp linenumber=1213 strcmp linenumber=1216 strcmp linenumber=1217 hts_log /src/htslib/hts.c linenumber=1221 hts_opt_apply /src/htslib/hts.c linenumber=1421 strdup linenumber=1254 hts_set_opt /src/htslib/hts.c linenumber=1264 hts_set_threads /src/htslib/hts.c linenumber=1801 sam_set_threads /src/htslib/sam.c linenumber=1926 hts_tpool_init /src/htslib/thread_pool.c linenumber=3735 sam_set_thread_pool /src/htslib/sam.c linenumber=3738 sam_state_create /src/htslib/sam.c linenumber=3707 calloc linenumber=3039 pthread_mutex_init linenumber=3711 pthread_mutex_init linenumber=3712 pthread_cond_init linenumber=3713 hts_tpool_size /src/htslib/thread_pool.c linenumber=3717 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=3718 sam_state_destroy /src/htslib/sam.c linenumber=3720 pthread_mutex_lock linenumber=3085 pthread_cond_signal linenumber=3088 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3091 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3098 pthread_mutex_unlock linenumber=3099 hts_usleep /src/htslib/./hts_internal.h linenumber=3100 pthread_mutex_lock linenumber=3101 pthread_mutex_unlock linenumber=3104 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3110 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=832 sam_format_worker /src/htslib/sam.c linenumber=3110 pthread_mutex_lock linenumber=3644 pthread_mutex_unlock linenumber=3649 calloc linenumber=3652 sam_state_err /src/htslib/sam.c linenumber=3654 pthread_mutex_lock linenumber=3053 pthread_mutex_unlock linenumber=3056 sam_format1_append /src/htslib/sam.c linenumber=3666 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4313 __errno_location linenumber=279 ks_resize /src/htslib/./htslib/kstring.h linenumber=280 kputc_ /src/htslib/./htslib/kstring.h linenumber=4314 ks_resize /src/htslib/./htslib/kstring.h linenumber=270 kputw /src/htslib/./htslib/kstring.h linenumber=4315 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=4315 kputs /src/htslib/./htslib/kstring.h linenumber=4317 kputc_ /src/htslib/./htslib/kstring.h linenumber=4318 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4319 kputll /src/htslib/./htslib/kstring.h linenumber=4320 ks_resize /src/htslib/./htslib/kstring.h linenumber=388 kputuw /src/htslib/./htslib/kstring.h linenumber=398 kputc_ /src/htslib/./htslib/kstring.h linenumber=4320 kputw /src/htslib/./htslib/kstring.h linenumber=4321 kputc_ /src/htslib/./htslib/kstring.h linenumber=4321 kputw /src/htslib/./htslib/kstring.h linenumber=4325 kputc_ /src/htslib/./htslib/kstring.h linenumber=4326 kputc_ /src/htslib/./htslib/kstring.h linenumber=4328 kputc_ /src/htslib/./htslib/kstring.h linenumber=4329 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4330 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4331 kputs /src/htslib/./htslib/kstring.h linenumber=4333 kputc_ /src/htslib/./htslib/kstring.h linenumber=4334 kputll /src/htslib/./htslib/kstring.h linenumber=4336 kputc_ /src/htslib/./htslib/kstring.h linenumber=4336 kputll /src/htslib/./htslib/kstring.h linenumber=4337 kputc_ /src/htslib/./htslib/kstring.h linenumber=4337 ks_resize /src/htslib/./htslib/kstring.h linenumber=4340 nibble2base /src/htslib/./sam_internal.h linenumber=4344 add33 /src/htslib/sam.c linenumber=4354 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4360 kputc_ /src/htslib/./htslib/kstring.h linenumber=4366 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4367 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=4370 hts_log /src/htslib/hts.c linenumber=4376 __errno_location linenumber=4378 hts_log /src/htslib/hts.c linenumber=4382 __errno_location linenumber=4383 __errno_location linenumber=3667 sam_state_err /src/htslib/sam.c linenumber=3667 kputc /src/htslib/./htslib/kstring.h linenumber=3670 pthread_mutex_lock linenumber=3673 pthread_mutex_unlock linenumber=3687 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3114 pthread_mutex_lock linenumber=3115 pthread_mutex_unlock linenumber=3117 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3119 hts_usleep /src/htslib/./hts_internal.h linenumber=3120 pthread_mutex_lock linenumber=3121 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=3124 pthread_mutex_unlock linenumber=3126 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3129 pthread_join linenumber=3134 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=3140 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3143 pthread_mutex_destroy linenumber=3146 pthread_mutex_destroy linenumber=3147 pthread_cond_destroy linenumber=3148 sam_free_sp_bams /src/htslib/sam.c linenumber=3163 sam_free_sp_bams /src/htslib/sam.c linenumber=3168 bam_hdr_destroy /src/htslib/./htslib/sam.h linenumber=3174 sam_hdr_destroy /src/htslib/sam.c linenumber=401 bgzf_thread_pool /src/htslib/bgzf.c linenumber=3725 calloc linenumber=1750 hts_tpool_size /src/htslib/thread_pool.c linenumber=1755 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=1758 hts_tpool_process_ref_incr /src/htslib/thread_pool.c linenumber=1760 pthread_mutex_lock linenumber=270 pthread_mutex_unlock linenumber=272 pool_create /src/htslib/cram/pooled_alloc.c linenumber=1762 pthread_mutex_init linenumber=1766 pthread_mutex_init linenumber=1767 pthread_mutex_init linenumber=1768 pthread_cond_init linenumber=1769 pthread_create linenumber=1774 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3741 hts_get_bgzfp /src/htslib/hts.c linenumber=1928 bgzf_mt /src/htslib/bgzf.c linenumber=1928 hts_tpool_init /src/htslib/thread_pool.c linenumber=1792 bgzf_thread_pool /src/htslib/bgzf.c linenumber=1797 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=1798 hts_set_opt /src/htslib/hts.c linenumber=1930 hts_hfile /src/htslib/hts.c linenumber=1805 bgzf_hfile /src/htslib/bgzf.c linenumber=1779 cram_hfile /src/htslib/./cram/cram_io.h linenumber=1780 bgzf_hfile /src/htslib/bgzf.c linenumber=1786 hfile_set_blksize /src/htslib/hfile.c linenumber=1809 hts_log /src/htslib/hts.c linenumber=1810 hts_log /src/htslib/hts.c linenumber=1815 hts_set_thread_pool /src/htslib/hts.c linenumber=1825 sam_set_thread_pool /src/htslib/sam.c linenumber=1937 hts_get_bgzfp /src/htslib/hts.c linenumber=1939 bgzf_thread_pool /src/htslib/bgzf.c linenumber=1939 hts_set_opt /src/htslib/hts.c linenumber=1941 hts_set_cache_size /src/htslib/hts.c linenumber=1832 hts_get_bgzfp /src/htslib/hts.c linenumber=1949 bgzf_set_cache_size /src/htslib/bgzf.c linenumber=1949 fastq_state_set /src/htslib/sam.c linenumber=1841 fastq_state_init /src/htslib/sam.c linenumber=3805 calloc linenumber=3771 strcpy linenumber=3774 regcomp linenumber=3778 strcmp linenumber=3825 kh_init_tag /src/htslib/sam.c linenumber=3827 calloc linenumber=64 strlen linenumber=3830 hts_log /src/htslib/hts.c linenumber=3834 kh_put_tag /src/htslib/sam.c linenumber=3838 kh_resize_tag /src/htslib/sam.c linenumber=64 realloc linenumber=64 strncpy linenumber=3850 strcmp linenumber=3860 __ctype_b_loc linenumber=3864 isalnum_c /src/htslib/./textutils_internal.h linenumber=3864 strncpy linenumber=3869 hts_log /src/htslib/hts.c linenumber=3883 regfree linenumber=3893 regcomp linenumber=3894 hts_log /src/htslib/hts.c linenumber=3895 fastq_state_set /src/htslib/sam.c linenumber=1850 fastq_state_set /src/htslib/sam.c linenumber=1862 cram_set_option /src/htslib/cram/cram_io.c linenumber=1874 hts_set_filter_expression /src/htslib/hts.c linenumber=1882 hts_filter_free /src/htslib/hts_expr.c linenumber=1971 regfree linenumber=870 hts_filter_init /src/htslib/hts_expr.c linenumber=1976 calloc linenumber=851 strlen linenumber=855 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=856 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=146 hts_prod_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=147 hts_malloc /src/htslib/./htslib/hts_alloc.h linenumber=148 cram_set_voption /src/htslib/cram/cram_io.c linenumber=1915 hts_set_opt /src/htslib/hts.c linenumber=1268 hts_opt_free /src/htslib/hts.c linenumber=1422 hts_opt_free /src/htslib/hts.c linenumber=1426 hclose_abruptly /src/htslib/hfile.c linenumber=1619 hts_log /src/htslib/hts.c linenumber=1624 hclose_abruptly /src/htslib/hfile.c linenumber=1627 hclose /src/htslib/hfile.c linenumber=188 abort linenumber=189 hts_close /src/htslib/hts.c linenumber=194 __errno_location linenumber=1644 bgzf_close /src/htslib/bgzf.c linenumber=1652 cram_eof /src/htslib/cram/cram_io.c linenumber=1657 hts_log /src/htslib/hts.c linenumber=1659 cram_close /src/htslib/cram/cram_io.c linenumber=1666 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=5280 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=5282 pthread_mutex_lock linenumber=4024 reset_metrics /src/htslib/cram/cram_io.c linenumber=4027 pthread_mutex_unlock linenumber=3992 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3993 pthread_mutex_lock linenumber=3994 pthread_mutex_unlock linenumber=4030 cram_flush_container /src/htslib/cram/cram_io.c linenumber=4033 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=3881 pthread_mutex_lock linenumber=1797 hts_log /src/htslib/hts.c linenumber=1800 hts_log /src/htslib/hts.c linenumber=1805 pthread_mutex_unlock linenumber=1808 pthread_mutex_unlock linenumber=1814 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1826 pthread_mutex_lock linenumber=3186 hts_log /src/htslib/hts.c linenumber=3201 pthread_mutex_unlock linenumber=3202 pthread_mutex_lock linenumber=3219 hts_log /src/htslib/hts.c linenumber=3222 cram_populate_ref /src/htslib/cram/cram_io.c linenumber=3224 getenv linenumber=2741 getenv linenumber=2746 hts_log /src/htslib/hts.c linenumber=2750 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2755 sam_hrecs_find_key /src/htslib/header.c linenumber=2758 hts_log /src/htslib/hts.c linenumber=2761 expand_cache_path /src/htslib/cram/cram_io.c linenumber=2766 strchr linenumber=2652 strncpy linenumber=2654 strlen linenumber=2659 strcpy linenumber=2661 strtol linenumber=2670 strlen linenumber=2671 strncpy linenumber=2674 strlen linenumber=2693 strcpy linenumber=2695 strlen linenumber=2699 strcpy linenumber=2703 stat linenumber=2767 stat linenumber=2788 bgzf_open /src/htslib/bgzf.c linenumber=2790 string_dup /src/htslib/cram/string_alloc.c linenumber=2794 bgzf_close /src/htslib/bgzf.c linenumber=2797 open_path_mfile /src/htslib/cram/open_trace_file.c linenumber=2813 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=2815 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=2833 strstr linenumber=2836 strncmp linenumber=2837 hts_log /src/htslib/hts.c linenumber=2839 strncmp linenumber=2843 bgzf_close /src/htslib/bgzf.c linenumber=2848 refs_load_fai /src/htslib/cram/cram_io.c linenumber=2852 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=2854 bgzf_close /src/htslib/bgzf.c linenumber=2858 refs2id /src/htslib/cram/cram_io.c linenumber=2866 expand_cache_path /src/htslib/cram/cram_io.c linenumber=2879 hts_log /src/htslib/hts.c linenumber=2882 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2883 strrchr linenumber=2711 is_directory /src/htslib/cram/cram_io.c linenumber=2716 stat linenumber=2638 mkdir linenumber=2721 chmod linenumber=2722 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2727 mkdir linenumber=2728 chmod linenumber=2729 hts_open_tmpfile /src/htslib/hts.c linenumber=2885 getpid linenumber=1982 time linenumber=1989 clock linenumber=1989 ks_clear /src/htslib/./htslib/kstring.h linenumber=1992 ksprintf /src/htslib/kstring.c linenumber=1993 hopen /src/htslib/hfile.c linenumber=1995 __errno_location linenumber=1996 perror linenumber=2887 hts_md5_init /src/htslib/md5.c linenumber=2899 hts_md5_reset /src/htslib/md5.c linenumber=329 hclose_abruptly /src/htslib/hfile.c linenumber=2900 unlink linenumber=2901 hts_md5_update /src/htslib/md5.c linenumber=2905 body /src/htslib/md5.c linenumber=260 body /src/htslib/md5.c linenumber=264 hts_md5_final /src/htslib/md5.c linenumber=2906 body /src/htslib/md5.c linenumber=283 body /src/htslib/md5.c linenumber=300 hts_md5_destroy /src/htslib/md5.c linenumber=2907 hts_md5_hex /src/htslib/md5.c linenumber=2908 strncmp linenumber=2910 hts_log /src/htslib/hts.c linenumber=2911 hclose_abruptly /src/htslib/hfile.c linenumber=2912 unlink linenumber=2913 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=2918 hclose /src/htslib/hfile.c linenumber=2919 chmod linenumber=2920 rename linenumber=2921 __errno_location linenumber=2922 strerror linenumber=2922 hts_log /src/htslib/hts.c linenumber=2922 unlink linenumber=2924 hts_log /src/htslib/hts.c linenumber=3225 hts_log /src/htslib/hts.c linenumber=3227 pthread_mutex_unlock linenumber=3228 pthread_mutex_unlock linenumber=3229 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3234 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3266 cram_ref_load /src/htslib/cram/cram_io.c linenumber=3269 __assert_fail linenumber=3095 __assert_fail linenumber=3105 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3109 strcmp linenumber=3117 bgzf_close /src/htslib/bgzf.c linenumber=3119 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3122 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3128 bgzf_useek /src/htslib/bgzf.c linenumber=3017 hseek /src/htslib/hfile.c linenumber=2580 bgzf_read_block /src/htslib/bgzf.c linenumber=2588 bgzf_seek_common /src/htslib/bgzf.c linenumber=2613 pthread_mutex_lock linenumber=2194 pthread_cond_signal linenumber=2201 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=2202 pthread_cond_wait linenumber=2204 pthread_cond_signal linenumber=2209 abort linenumber=2212 __errno_location linenumber=2220 pthread_mutex_unlock linenumber=2221 pthread_mutex_unlock linenumber=2229 hseek /src/htslib/hfile.c linenumber=2231 bgzf_read_block /src/htslib/bgzf.c linenumber=2616 __assert_fail linenumber=2628 perror linenumber=3018 bgzf_read /src/htslib/bgzf.c linenumber=3026 __assert_fail linenumber=1247 bgzf_read_block /src/htslib/bgzf.c linenumber=1252 hts_log /src/htslib/hts.c linenumber=1254 bgzf_htell /src/htslib/bgzf.c linenumber=1264 hts_log /src/htslib/hts.c linenumber=1269 bgzf_htell /src/htslib/bgzf.c linenumber=1284 perror linenumber=3027 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3044 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3049 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3058 hts_log /src/htslib/hts.c linenumber=3065 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=3072 toupper linenumber=180 pthread_mutex_unlock linenumber=3270 pthread_mutex_unlock linenumber=3271 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3279 pthread_mutex_unlock linenumber=3295 pthread_mutex_unlock linenumber=3296 pthread_mutex_unlock linenumber=3316 pthread_mutex_unlock linenumber=3317 strcmp linenumber=3322 bgzf_close /src/htslib/bgzf.c linenumber=3324 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3327 pthread_mutex_unlock linenumber=3328 pthread_mutex_unlock linenumber=3329 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3334 pthread_mutex_unlock linenumber=3335 pthread_mutex_unlock linenumber=3336 pthread_mutex_unlock linenumber=3349 pthread_mutex_unlock linenumber=3350 hts_log /src/htslib/hts.c linenumber=1830 hts_log /src/htslib/hts.c linenumber=1832 pthread_mutex_lock linenumber=1834 pthread_mutex_unlock linenumber=1837 hts_log /src/htslib/hts.c linenumber=1842 hts_log /src/htslib/hts.c linenumber=1845 hts_log /src/htslib/hts.c linenumber=1846 hts_log /src/htslib/hts.c linenumber=1849 pthread_mutex_lock linenumber=1851 pthread_mutex_unlock linenumber=1853 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1856 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1738 sam_hrecs_find_key /src/htslib/header.c linenumber=1743 hts_md5_init /src/htslib/md5.c linenumber=1754 hts_md5_update /src/htslib/md5.c linenumber=1756 hts_md5_final /src/htslib/md5.c linenumber=1757 hts_md5_destroy /src/htslib/md5.c linenumber=1758 hts_md5_hex /src/htslib/md5.c linenumber=1759 strcmp linenumber=1762 hts_log /src/htslib/hts.c linenumber=1763 hts_log /src/htslib/hts.c linenumber=1765 cram_ref_incr /src/htslib/cram/cram_io.c linenumber=1889 pthread_mutex_lock linenumber=2947 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=2948 pthread_mutex_unlock linenumber=2949 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1896 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1897 hts_log /src/htslib/hts.c linenumber=1900 __assert_fail linenumber=1915 lossy_read_names /src/htslib/cram/cram_encode.c linenumber=1919 kh_init_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1287 calloc linenumber=55 expected_template_count /src/htslib/cram/cram_encode.c linenumber=1305 bam_aux_get /src/htslib/sam.c linenumber=1240 bam_aux_first /src/htslib/sam.c linenumber=4826 __errno_location linenumber=4804 skip_aux /src/htslib/sam.c linenumber=4829 aux_type2size /src/htslib/sam.c linenumber=4779 memchr linenumber=4783 aux_type2size /src/htslib/sam.c linenumber=4787 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=4788 bam_aux_next /src/htslib/sam.c linenumber=4826 skip_aux /src/htslib/sam.c linenumber=4811 __errno_location linenumber=4813 hts_log /src/htslib/hts.c linenumber=4817 __errno_location linenumber=4819 hts_log /src/htslib/hts.c linenumber=4840 __errno_location linenumber=4842 bam_data_end /src/htslib/cram/cram_encode.c linenumber=1242 bam_aux2i_end /src/htslib/cram/cram_encode.c linenumber=1242 __errno_location linenumber=1194 __errno_location linenumber=1200 __errno_location linenumber=1206 le_to_i16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1209 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=241 __errno_location linenumber=1212 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1215 __errno_location linenumber=1218 le_to_i32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1221 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=252 __errno_location linenumber=1224 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1227 __errno_location linenumber=1229 bam_aux_get /src/htslib/sam.c linenumber=1247 kh_put_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1308 kh_resize_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=55 realloc linenumber=55 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=55 strcmp linenumber=55 kh_get_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1340 kh_destroy_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1353 cram_generate_reference /src/htslib/cram/cram_encode.c linenumber=1930 extend_ref /src/htslib/cram/cram_encode.c linenumber=1677 realloc linenumber=1460 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1465 hts_log /src/htslib/hts.c linenumber=1688 cram_add_to_ref /src/htslib/cram/cram_encode.c linenumber=1692 bam_aux_get /src/htslib/sam.c linenumber=1595 cram_add_to_ref_MD /src/htslib/cram/cram_encode.c linenumber=1599 bam_cigar2rlen /src/htslib/sam.c linenumber=1495 extend_ref /src/htslib/cram/cram_encode.c linenumber=1499 __ctype_b_loc linenumber=1509 hts_str2uint /src/htslib/cram/../textutils_internal.h linenumber=1512 extend_ref /src/htslib/cram/cram_encode.c linenumber=1514 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1519 hts_log /src/htslib/hts.c linenumber=1526 __ctype_b_loc linenumber=1545 extend_ref /src/htslib/cram/cram_encode.c linenumber=1546 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1549 hts_log /src/htslib/hts.c linenumber=1555 extend_ref /src/htslib/cram/cram_encode.c linenumber=1563 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1566 hts_log /src/htslib/hts.c linenumber=1572 extend_ref /src/htslib/cram/cram_encode.c linenumber=1627 hts_log /src/htslib/hts.c linenumber=1940 hts_log /src/htslib/hts.c linenumber=1944 pthread_mutex_lock linenumber=1947 pthread_mutex_unlock linenumber=1951 pthread_mutex_lock linenumber=1955 pthread_mutex_unlock linenumber=1957 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=1976 pthread_mutex_lock linenumber=2977 cram_ref_decr_locked /src/htslib/cram/cram_io.c linenumber=2978 __assert_fail linenumber=2962 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2968 pthread_mutex_unlock linenumber=2979 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1978 hts_log /src/htslib/hts.c linenumber=1979 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1983 process_one_read /src/htslib/cram/cram_encode.c linenumber=1995 bam_aux_get /src/htslib/sam.c linenumber=3296 bam_aux_get /src/htslib/sam.c linenumber=3305 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3312 kh_init_m_i2i /src/htslib/cram/cram_structs.h linenumber=65 kh_put_m_i2i /src/htslib/cram/cram_structs.h linenumber=70 kh_resize_m_i2i /src/htslib/cram/cram_structs.h linenumber=64 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3314 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3334 block_grow /src/htslib/cram/cram_io.h linenumber=3350 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=3351 nibble2base /src/htslib/cram/../sam_internal.h linenumber=3356 hts_log /src/htslib/hts.c linenumber=3369 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3378 hts_log /src/htslib/hts.c linenumber=3413 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3426 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=3427 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=261 cram_add_substitution /src/htslib/cram/cram_encode.c linenumber=3490 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2527 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2534 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2535 block_append_char /src/htslib/cram/cram_io.h linenumber=2536 block_grow /src/htslib/cram/cram_io.h linenumber=262 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2538 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2493 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2501 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2504 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2509 cram_add_bases /src/htslib/cram/cram_encode.c linenumber=3503 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2554 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3509 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2565 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2566 block_append_char /src/htslib/cram/cram_io.h linenumber=2567 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2568 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3518 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3534 kputc_ /src/htslib/cram/../htslib/kstring.h linenumber=3536 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=270 kputsn /src/htslib/cram/../htslib/kstring.h linenumber=3537 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=246 cram_add_deletion /src/htslib/cram/cram_encode.c linenumber=3543 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2595 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2596 cram_add_skip /src/htslib/cram/cram_encode.c linenumber=3550 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2651 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2652 cram_add_insertion /src/htslib/cram/cram_encode.c linenumber=3557 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2673 block_append /src/htslib/cram/cram_io.h linenumber=2679 block_grow /src/htslib/cram/cram_io.h linenumber=249 block_append_char /src/htslib/cram/cram_io.h linenumber=2683 block_append_char /src/htslib/cram/cram_io.h linenumber=2685 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2687 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3562 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2581 block_append_char /src/htslib/cram/cram_io.h linenumber=2582 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2583 cram_add_softclip /src/htslib/cram/cram_encode.c linenumber=3571 block_append /src/htslib/cram/cram_io.h linenumber=2608 block_append_char /src/htslib/cram/cram_io.h linenumber=2609 block_append /src/htslib/cram/cram_io.h linenumber=2616 block_append_char /src/htslib/cram/cram_io.h linenumber=2620 block_append_char /src/htslib/cram/cram_io.h linenumber=2622 cram_add_feature 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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=1621 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 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1377 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1399 hts_pack 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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=1653 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 realloc linenumber=86 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=1863 pthread_mutex_unlock linenumber=1998 pthread_mutex_unlock linenumber=2010 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2011 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2019 hts_log /src/htslib/hts.c linenumber=2019 pthread_mutex_lock linenumber=2022 pthread_mutex_unlock linenumber=2026 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2027 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2045 hts_log /src/htslib/hts.c linenumber=2048 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2063 hts_log /src/htslib/hts.c linenumber=2063 pthread_mutex_lock linenumber=843 pthread_mutex_unlock linenumber=847 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=850 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=857 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=862 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=867 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=870 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=874 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=879 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=884 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=887 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=906 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=912 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=929 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=947 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1150 cram_free_block /src/htslib/cram/cram_io.c linenumber=1161 cram_encode_slice_header /src/htslib/cram/cram_encode.c linenumber=1172 cram_new_block /src/htslib/cram/cram_io.c linenumber=509 hts_malloc_pse /src/htslib/cram/../htslib/hts_alloc.h linenumber=515 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=173 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=174 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=175 hts_malloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=176 cram_free_block /src/htslib/cram/cram_io.c linenumber=517 hts_log /src/htslib/hts.c linenumber=523 cram_free_block /src/htslib/cram/cram_io.c linenumber=524 __assert_fail linenumber=547 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=2384 cram_new_block /src/htslib/cram/cram_io.c linenumber=87 cram_new_block /src/htslib/cram/cram_io.c linenumber=88 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=107 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=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=111 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=113 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=118 kh_init_map /src/htslib/cram/cram_structs.h linenumber=128 calloc linenumber=83 kh_put_map /src/htslib/cram/cram_structs.h linenumber=131 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=136 kh_put_map /src/htslib/cram/cram_structs.h linenumber=140 kh_put_map /src/htslib/cram/cram_structs.h linenumber=144 kh_put_map /src/htslib/cram/cram_structs.h linenumber=150 kh_put_map /src/htslib/cram/cram_structs.h linenumber=154 kh_put_map /src/htslib/cram/cram_structs.h linenumber=158 kh_put_map /src/htslib/cram/cram_structs.h linenumber=164 block_append /src/htslib/cram/cram_io.h linenumber=188 block_append_char /src/htslib/cram/cram_io.h linenumber=198 sub_idx /src/htslib/cram/cram_encode.c linenumber=211 sub_idx /src/htslib/cram/cram_encode.c linenumber=212 sub_idx /src/htslib/cram/cram_encode.c linenumber=213 sub_idx /src/htslib/cram/cram_encode.c linenumber=214 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 block_append /src/htslib/cram/cram_io.h linenumber=235 block_append /src/htslib/cram/cram_io.h linenumber=241 hts_log /src/htslib/hts.c linenumber=248 block_append /src/htslib/cram/cram_io.h linenumber=257 block_append /src/htslib/cram/cram_io.h linenumber=458 block_append /src/htslib/cram/cram_io.h linenumber=484 hts_log /src/htslib/hts.c linenumber=486 cram_free_block /src/htslib/cram/cram_io.c linenumber=490 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2391 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2460 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2468 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=3884 htell /src/htslib/cram/../htslib/hfile.h linenumber=3833 cram_write_container /src/htslib/cram/cram_io.c linenumber=3836 itf8_put /src/htslib/cram/cram_io.c linenumber=3776 crc32 linenumber=3804 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=3812 htell /src/htslib/cram/../htslib/hfile.h linenumber=3839 cram_write_block /src/htslib/cram/cram_io.c linenumber=3842 __assert_fail linenumber=1277 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1279 hputc2 /src/htslib/hfile.c linenumber=268 flush_buffer /src/htslib/hfile.c linenumber=403 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1280 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1284 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1289 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1292 __assert_fail linenumber=1297 crc32 linenumber=1309 crc32 linenumber=1312 crc32 linenumber=1314 int32_encode /src/htslib/cram/cram_io.c linenumber=1317 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=784 htell /src/htslib/cram/../htslib/hfile.h linenumber=3846 cram_write_block /src/htslib/cram/cram_io.c linenumber=3851 cram_write_block /src/htslib/cram/cram_io.c linenumber=3855 htell /src/htslib/cram/../htslib/hfile.h linenumber=3859 cram_index_slice /src/htslib/cram/cram_index.c linenumber=3863 hts_log /src/htslib/hts.c linenumber=710 cram_index_build_multiref /src/htslib/cram/cram_index.c linenumber=716 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=648 cram_dependent_data_series /src/htslib/cram/cram_decode.c linenumber=2376 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=615 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=621 hts_calloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=628 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=689 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=2338 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=2339 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=705 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=735 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=751 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=780 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=826 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2397 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2398 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2399 strcmp linenumber=2411 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2419 hts_log /src/htslib/hts.c linenumber=2429 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2434 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=2437 hts_log /src/htslib/hts.c linenumber=2443 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2454 hts_log /src/htslib/hts.c linenumber=2463 pthread_mutex_lock linenumber=2468 pthread_mutex_lock linenumber=2469 pthread_mutex_unlock linenumber=2475 pthread_mutex_unlock linenumber=2476 memcmp linenumber=2495 hts_log /src/htslib/hts.c linenumber=2505 hts_log /src/htslib/hts.c linenumber=2513 hts_md5_init /src/htslib/md5.c linenumber=2518 hts_md5_update /src/htslib/md5.c linenumber=2523 hts_md5_final /src/htslib/md5.c linenumber=2524 hts_md5_destroy /src/htslib/md5.c linenumber=2525 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2527 hts_md5_init /src/htslib/md5.c linenumber=2529 hts_md5_update /src/htslib/md5.c linenumber=2531 hts_md5_final /src/htslib/md5.c linenumber=2532 hts_md5_destroy /src/htslib/md5.c linenumber=2533 memcmp linenumber=2539 sam_hdr_tid2name /src/htslib/header.c linenumber=2541 hts_log /src/htslib/hts.c linenumber=2543 md5_print /src/htslib/cram/cram_decode.c linenumber=2545 hts_log /src/htslib/hts.c linenumber=2545 md5_print /src/htslib/cram/cram_decode.c linenumber=2546 hts_log /src/htslib/hts.c linenumber=2546 sam_hdr_find_tag_id /src/htslib/header.c linenumber=2548 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2294 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2299 sam_hrecs_find_key /src/htslib/header.c linenumber=2303 kputsn /src/htslib/./htslib/kstring.h linenumber=2308 hts_log /src/htslib/hts.c linenumber=2549 hts_log /src/htslib/hts.c linenumber=2550 ks_free /src/htslib/cram/../htslib/kstring.h linenumber=2551 ks_initialize /src/htslib/cram/../htslib/kstring.h linenumber=238 pthread_mutex_lock linenumber=2557 pthread_mutex_lock linenumber=2558 calloc linenumber=2559 pthread_mutex_unlock linenumber=2560 pthread_mutex_unlock linenumber=2561 hts_log /src/htslib/hts.c linenumber=2619 pthread_mutex_lock linenumber=2630 pthread_mutex_unlock linenumber=2632 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2635 pthread_mutex_lock linenumber=2644 pthread_mutex_unlock linenumber=2649 pthread_mutex_lock linenumber=2651 pthread_mutex_unlock linenumber=2653 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2656 pthread_mutex_lock linenumber=2661 pthread_mutex_lock linenumber=2662 pthread_mutex_unlock linenumber=2664 pthread_mutex_unlock linenumber=2665 hts_log /src/htslib/hts.c linenumber=2676 hts_log /src/htslib/hts.c linenumber=2687 pthread_mutex_lock linenumber=2704 pthread_mutex_unlock linenumber=2706 hts_log /src/htslib/hts.c linenumber=2799 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2825 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2853 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2862 cram_decode_aux_1_0 /src/htslib/cram/cram_decode.c linenumber=2889 map_find /src/htslib/cram/cram_decode.c linenumber=1960 block_append /src/htslib/cram/cram_io.h linenumber=1963 cram_decode_aux /src/htslib/cram/cram_decode.c linenumber=2891 strlen linenumber=2020 map_find /src/htslib/cram/cram_decode.c linenumber=2048 block_append /src/htslib/cram/cram_io.h linenumber=2052 aux_ele_size /src/htslib/cram/cram_decode.c linenumber=2061 hts_log /src/htslib/hts.c linenumber=2086 block_resize /src/htslib/cram/cram_io.h linenumber=2897 block_resize /src/htslib/cram/cram_io.h linenumber=2905 hts_log /src/htslib/hts.c linenumber=2915 cram_decode_seq /src/htslib/cram/cram_decode.c linenumber=2922 block_append /src/htslib/cram/cram_io.h linenumber=1123 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1154 hts_log /src/htslib/hts.c linenumber=1204 memchr linenumber=1234 add_md_char /src/htslib/cram/cram_decode.c linenumber=1240 block_append_uint /src/htslib/cram/cram_io.h linenumber=1075 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=1076 block_append_uint /src/htslib/cram/cram_io.h linenumber=1369 add_md_char /src/htslib/cram/cram_decode.c linenumber=1381 block_append_uint /src/htslib/cram/cram_io.h linenumber=1410 block_append_char /src/htslib/cram/cram_io.h linenumber=1413 block_append /src/htslib/cram/cram_io.h linenumber=1414 block_append_char /src/htslib/cram/cram_io.h linenumber=1424 block_append /src/htslib/cram/cram_io.h linenumber=1425 block_append_uint /src/htslib/cram/cram_io.h linenumber=1428 block_append_uint /src/htslib/cram/cram_io.h linenumber=1507 block_append_uint /src/htslib/cram/cram_io.h linenumber=1511 block_append_char /src/htslib/cram/cram_io.h linenumber=1520 block_append_uint /src/htslib/cram/cram_io.h linenumber=1585 block_append_char /src/htslib/cram/cram_io.h linenumber=1592 hts_log /src/htslib/hts.c linenumber=1691 hts_log /src/htslib/hts.c linenumber=1706 memchr linenumber=1735 add_md_char /src/htslib/cram/cram_decode.c linenumber=1746 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1767 block_append_uint /src/htslib/cram/cram_io.h linenumber=1791 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1797 block_append_char /src/htslib/cram/cram_io.h linenumber=1834 block_append /src/htslib/cram/cram_io.h linenumber=1886 hts_log /src/htslib/hts.c linenumber=1905 pthread_mutex_lock linenumber=2974 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2979 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2984 pthread_mutex_unlock linenumber=2986 cram_decode_slice_xref /src/htslib/cram/cram_decode.c linenumber=2989 hts_log /src/htslib/hts.c linenumber=2233 cram_free_block /src/htslib/cram/cram_io.c linenumber=2996 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3010 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3011 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3012 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3013 bulk_cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3024 pthread_mutex_lock linenumber=2308 pthread_mutex_unlock linenumber=2313 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2319 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=2328 calloc linenumber=2333 calloc linenumber=2338 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=2345 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=2350 strlen linenumber=3139 append_uint64 /src/htslib/cram/cram_io.h linenumber=3144 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=3148 bam_set1 /src/htslib/sam.c linenumber=3183 bam_cigar2rqlens /src/htslib/sam.c linenumber=555 hts_log /src/htslib/hts.c linenumber=563 __errno_location linenumber=564 hts_log /src/htslib/hts.c linenumber=568 __errno_location linenumber=569 hts_log /src/htslib/hts.c linenumber=573 __errno_location linenumber=574 hts_log /src/htslib/hts.c linenumber=578 __errno_location linenumber=579 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 subtract_check_underflow /src/htslib/sam.c linenumber=587 subtract_check_underflow /src/htslib/sam.c linenumber=588 hts_log /src/htslib/hts.c linenumber=590 __errno_location linenumber=591 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=597 realloc_bam_data /src/htslib/./sam_internal.h linenumber=597 sam_realloc_bam_data /src/htslib/sam.c linenumber=50 __errno_location linenumber=446 __errno_location linenumber=451 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=455 realloc linenumber=456 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=462 bam_set_mempolicy /src/htslib/./htslib/sam.h linenumber=462 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=604 strncpy linenumber=616 bam_tag2cigar /src/htslib/sam.c linenumber=3214 bam_aux_get /src/htslib/sam.c linenumber=698 __errno_location linenumber=699 __errno_location linenumber=701 __errno_location linenumber=702 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=713 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=723 __errno_location linenumber=57 sam_realloc_bam_data /src/htslib/sam.c linenumber=61 bam_endpos /src/htslib/sam.c linenumber=734 bam_cigar2rlen /src/htslib/sam.c linenumber=677 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=734 hts_log /src/htslib/hts.c linenumber=736 pthread_mutex_lock linenumber=3031 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3034 pthread_mutex_unlock linenumber=3037 snprintf linenumber=671 strlen linenumber=675 bgzf_write /src/htslib/bgzf.c linenumber=675 hwrite /src/htslib/./htslib/hfile.h linenumber=2010 __assert_fail linenumber=2015 lazy_flush /src/htslib/bgzf.c linenumber=2025 mt_queue /src/htslib/bgzf.c linenumber=1932 bgzf_flush /src/htslib/bgzf.c linenumber=1934 snprintf linenumber=685 strlen linenumber=689 bgzf_write /src/htslib/bgzf.c linenumber=689 snprintf linenumber=718 strlen linenumber=722 bgzf_write /src/htslib/bgzf.c linenumber=722 __errno_location linenumber=4044 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=4045 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=844 cram_flush_thread /src/htslib/cram/cram_io.c linenumber=4045 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=3896 hts_log /src/htslib/hts.c linenumber=3897 __errno_location linenumber=4046 cram_flush_result /src/htslib/cram/cram_io.c linenumber=4047 hts_tpool_next_result /src/htslib/thread_pool.c linenumber=3912 pthread_mutex_lock linenumber=206 hts_tpool_next_result_locked /src/htslib/thread_pool.c linenumber=207 pthread_mutex_unlock linenumber=208 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3913 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3917 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=3925 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3932 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3941 cram_free_container /src/htslib/cram/cram_io.c linenumber=3954 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3959 cram_free_container /src/htslib/cram/cram_io.c linenumber=3966 hts_usleep /src/htslib/cram/../hts_internal.h linenumber=4052 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5287 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=5290 cram_flush_result /src/htslib/cram/cram_io.c linenumber=5292 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=5300 pthread_mutex_destroy linenumber=5303 pthread_mutex_destroy linenumber=5304 pthread_mutex_destroy linenumber=5305 pthread_mutex_destroy linenumber=5306 cram_write_eof_block /src/htslib/cram/cram_io.c linenumber=5310 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=5231 cram_write_container /src/htslib/cram/cram_io.c linenumber=5236 cram_write_block /src/htslib/cram/cram_io.c linenumber=5237 cram_close /src/htslib/cram/cram_io.c linenumber=5238 free_bam_list /src/htslib/cram/cram_io.c linenumber=5316 hclose /src/htslib/hfile.c linenumber=5320 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5324 sam_hdr_destroy /src/htslib/sam.c linenumber=5327 cram_free_container /src/htslib/cram/cram_io.c linenumber=5332 cram_free_container /src/htslib/cram/cram_io.c linenumber=5335 refs_free /src/htslib/cram/cram_io.c linenumber=5338 kh_destroy_m_metrics /src/htslib/cram/cram_structs.h linenumber=5354 cram_index_free /src/htslib/cram/cram_index.c linenumber=5358 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=384 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=371 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=5361 bgzf_close /src/htslib/bgzf.c linenumber=5364 cram_free_block /src/htslib/cram/cram_io.c linenumber=5239 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=5243 cram_free_block /src/htslib/cram/cram_io.c linenumber=5244 sam_state_destroy /src/htslib/sam.c linenumber=1677 fastq_state_destroy /src/htslib/sam.c linenumber=1680 kh_destroy_tag /src/htslib/sam.c linenumber=3790 ks_free /src/htslib/./htslib/kstring.h linenumber=3791 ks_initialize /src/htslib/./htslib/kstring.h linenumber=238 ks_free /src/htslib/./htslib/kstring.h linenumber=3792 ks_free /src/htslib/./htslib/kstring.h linenumber=3793 regfree linenumber=3794 bgzf_close /src/htslib/bgzf.c linenumber=1683 hclose /src/htslib/hfile.c linenumber=1685 hts_idx_close_otf_fp /src/htslib/hts.c linenumber=1698 need_idx_ugly_delay_hack /src/htslib/hts.c linenumber=2916 idx_write_uint64 /src/htslib/hts.c linenumber=2918 ed_is_big /src/htslib/./htslib/hts.h linenumber=2737 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2737 bgzf_write /src/htslib/bgzf.c linenumber=2738 bgzf_close /src/htslib/bgzf.c linenumber=2920 __errno_location linenumber=1701 sam_hdr_destroy /src/htslib/sam.c linenumber=1702 hts_idx_destroy /src/htslib/hts.c linenumber=1703 cram_index_free /src/htslib/cram/cram_index.c linenumber=2698 kh_destroy_bin /src/htslib/hts.c linenumber=2710 hts_filter_free /src/htslib/hts_expr.c linenumber=1704 __errno_location linenumber=1709 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=993 strncpy linenumber=901 strchr linenumber=903 strchr linenumber=931 strchr linenumber=937 strstr linenumber=942 strdup linenumber=944 hopen /src/htslib/hfile.c linenumber=950 hts_hopen /src/htslib/hts.c linenumber=953 hts_opt_apply /src/htslib/hts.c linenumber=967 __errno_location linenumber=969 __errno_location linenumber=970 __errno_location linenumber=973 __errno_location linenumber=982 strerror linenumber=982 hts_log /src/htslib/hts.c linenumber=982 hclose_abruptly /src/htslib/hfile.c linenumber=987 abort linenumber=69 sam_hdr_read /src/htslib/sam.c linenumber=86 __errno_location linenumber=1912 bam_hdr_read /src/htslib/sam.c linenumber=1918 bgzf_check_EOF /src/htslib/bgzf.c linenumber=240 pthread_mutex_lock linenumber=2138 pthread_cond_signal linenumber=2144 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=2145 pthread_mutex_unlock linenumber=2149 pthread_cond_wait linenumber=2152 pthread_cond_signal linenumber=2157 abort linenumber=2162 pthread_mutex_unlock linenumber=2167 bgzf_check_EOF_common /src/htslib/bgzf.c linenumber=2169 htell /src/htslib/./htslib/hfile.h linenumber=1547 hseek /src/htslib/hfile.c linenumber=1548 __errno_location linenumber=1549 hclearerr /src/htslib/./htslib/hfile.h linenumber=1549 __errno_location linenumber=1556 hclearerr /src/htslib/./htslib/hfile.h linenumber=1556 hread /src/htslib/./htslib/hfile.h linenumber=1560 hseek /src/htslib/hfile.c linenumber=1561 memcmp linenumber=1562 perror linenumber=242 hts_log /src/htslib/hts.c linenumber=244 bgzf_read /src/htslib/bgzf.c linenumber=247 memcmp linenumber=248 hts_log /src/htslib/hts.c linenumber=249 sam_hdr_init /src/htslib/sam.c linenumber=252 bgzf_read /src/htslib/bgzf.c linenumber=256 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=258 bgzf_read /src/htslib/bgzf.c linenumber=268 bgzf_read /src/htslib/bgzf.c linenumber=271 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=273 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=1588 calloc linenumber=283 calloc linenumber=285 bgzf_read /src/htslib/bgzf.c linenumber=294 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=296 bgzf_read /src/htslib/bgzf.c linenumber=303 realloc linenumber=311 bgzf_read /src/htslib/bgzf.c linenumber=317 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=319 hts_log /src/htslib/hts.c linenumber=331 hts_log /src/htslib/hts.c linenumber=336 sam_hdr_destroy /src/htslib/sam.c linenumber=341 sam_hdr_sanitise /src/htslib/sam.c linenumber=1918 sam_hdr_destroy /src/htslib/sam.c linenumber=1846 hts_log /src/htslib/hts.c linenumber=1858 hts_log /src/htslib/hts.c linenumber=1863 hts_log /src/htslib/hts.c linenumber=1867 sam_hdr_destroy /src/htslib/sam.c linenumber=1868 realloc linenumber=1872 sam_hdr_destroy /src/htslib/sam.c linenumber=1874 sam_hdr_dup /src/htslib/sam.c linenumber=1922 sam_hdr_init /src/htslib/sam.c linenumber=175 calloc linenumber=184 calloc linenumber=186 strdup linenumber=192 sam_hdr_dup_sdict /src/htslib/sam.c linenumber=199 kh_init_s2i /src/htslib/hts.c linenumber=149 kh_get_s2i /src/htslib/hts.c linenumber=157 kh_put_s2i /src/htslib/hts.c linenumber=159 kh_destroy_s2i /src/htslib/hts.c linenumber=161 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=205 kputsn /src/htslib/./htslib/kstring.h linenumber=2381 sam_hrecs_rebuild_lines /src/htslib/header.c linenumber=2383 kputsn /src/htslib/./htslib/kstring.h linenumber=763 build_header_line /src/htslib/header.c linenumber=767 kputc_ /src/htslib/./htslib/kstring.h linenumber=749 kputsn /src/htslib/./htslib/kstring.h linenumber=750 kputc_ /src/htslib/./htslib/kstring.h linenumber=752 kputsn /src/htslib/./htslib/kstring.h linenumber=753 kputc /src/htslib/./htslib/kstring.h linenumber=769 ks_release /src/htslib/./htslib/kstring.h linenumber=206 ks_release /src/htslib/./htslib/kstring.h linenumber=211 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=213 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=217 sam_hdr_destroy /src/htslib/sam.c linenumber=227 sam_hdr_sanitise /src/htslib/sam.c linenumber=1922 sam_hdr_create /src/htslib/sam.c linenumber=1926 sam_hdr_init /src/htslib/sam.c linenumber=1891 sam_hdr_build_from_sam_file /src/htslib/header.c linenumber=1895 sam_hrecs_new /src/htslib/header.c linenumber=1360 hts_getline /src/htslib/hts.c linenumber=1369 hts_log /src/htslib/hts.c linenumber=2040 abort linenumber=2041 kgetline2 /src/htslib/kstring.c linenumber=2047 ks_resize /src/htslib/./htslib/kstring.h linenumber=322 hgetln_wrapper /src/htslib/hts.c linenumber=2047 hgetln /src/htslib/./htslib/hfile.h linenumber=2033 herrno /src/htslib/./htslib/hfile.h linenumber=2049 __errno_location linenumber=2049 bgzf_getline /src/htslib/bgzf.c linenumber=2055 bgzf_read_block /src/htslib/bgzf.c linenumber=2325 memchr linenumber=2332 ks_expand /src/htslib/./htslib/kstring.h linenumber=2338 bgzf_htell /src/htslib/bgzf.c linenumber=2343 abort linenumber=2059 isalpha_c /src/htslib/./textutils_internal.h linenumber=1377 sam_hrecs_error /src/htslib/header.c linenumber=1378 strncmp linenumber=1383 kputc /src/htslib/./htslib/kstring.h linenumber=1386 valid_sam_header_type /src/htslib/header.c linenumber=1389 hts_log /src/htslib/hts.c linenumber=1390 warn_if_known_stderr /src/htslib/header.c linenumber=1391 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1395 TYPEKEY /src/htslib/./header.h linenumber=1400 kputsn /src/htslib/./htslib/kstring.h linenumber=1406 kputc /src/htslib/./htslib/kstring.h linenumber=1409 bgzf_peek /src/htslib/bgzf.c linenumber=1413 bgzf_read_block /src/htslib/bgzf.c linenumber=1298 hts_log /src/htslib/hts.c linenumber=1299 hpeek /src/htslib/hfile.c linenumber=1416 strstr linenumber=1434 hopen /src/htslib/hfile.c linenumber=1438 khgetline /src/htslib/hfile.c linenumber=1443 kgetline /src/htslib/kstring.c linenumber=310 ks_resize /src/htslib/./htslib/kstring.h linenumber=277 strlen linenumber=281 hgets_wrapper /src/htslib/hfile.c linenumber=310 hgets /src/htslib/hfile.c linenumber=303 strchr linenumber=1444 strtoll linenumber=1452 kputs /src/htslib/./htslib/kstring.h linenumber=1454 kputsn /src/htslib/./htslib/kstring.h linenumber=1455 kputs /src/htslib/./htslib/kstring.h linenumber=1456 kputll /src/htslib/./htslib/kstring.h linenumber=1457 kputc /src/htslib/./htslib/kstring.h linenumber=1458 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1462 ks_free /src/htslib/./htslib/kstring.h linenumber=1474 hclose /src/htslib/hfile.c linenumber=1475 hts_log /src/htslib/hts.c linenumber=1476 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1486 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1490 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1504 kputsn /src/htslib/./htslib/kstring.h linenumber=1510 ks_release /src/htslib/./htslib/kstring.h linenumber=1512 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1514 ks_free /src/htslib/./htslib/kstring.h linenumber=1520 sam_hdr_destroy /src/htslib/sam.c linenumber=1896 sam_hdr_destroy /src/htslib/sam.c linenumber=1901 sam_hdr_sanitise /src/htslib/sam.c linenumber=1902 sam_hdr_init /src/htslib/sam.c linenumber=1931 __errno_location linenumber=1934 __errno_location linenumber=1938 sam_hdr_incr_ref /src/htslib/header.c linenumber=1945 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=2151 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2173 sam_hdr_write /src/htslib/sam.c linenumber=99 __errno_location linenumber=1953 bam_hdr_write /src/htslib/sam.c linenumber=1963 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=356 hts_log /src/htslib/hts.c linenumber=358 hts_log /src/htslib/hts.c linenumber=362 hts_log /src/htslib/hts.c linenumber=363 hts_log /src/htslib/hts.c linenumber=369 hts_log /src/htslib/hts.c linenumber=372 hts_log /src/htslib/hts.c linenumber=373 bgzf_write /src/htslib/bgzf.c linenumber=379 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=382 bgzf_write /src/htslib/bgzf.c linenumber=383 bgzf_write /src/htslib/bgzf.c linenumber=385 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=387 bgzf_write /src/htslib/bgzf.c linenumber=388 bgzf_write /src/htslib/bgzf.c linenumber=390 bgzf_write /src/htslib/bgzf.c linenumber=392 bgzf_write /src/htslib/bgzf.c linenumber=394 strlen linenumber=400 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=402 bgzf_write /src/htslib/bgzf.c linenumber=403 bgzf_write /src/htslib/bgzf.c linenumber=405 bgzf_write /src/htslib/bgzf.c linenumber=407 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=409 bgzf_write /src/htslib/bgzf.c linenumber=410 bgzf_write /src/htslib/bgzf.c linenumber=412 bgzf_flush /src/htslib/bgzf.c linenumber=415 cram_set_header2 /src/htslib/cram/cram_io.c linenumber=1968 sam_hdr_destroy /src/htslib/sam.c linenumber=2621 sam_hdr_dup /src/htslib/sam.c linenumber=2622 refs_from_header /src/htslib/cram/cram_io.c linenumber=2626 cram_load_reference /src/htslib/cram/cram_io.c linenumber=1970 cram_write_SAM_hdr /src/htslib/cram/cram_io.c linenumber=1971 cram_write_file_def /src/htslib/cram/cram_io.c linenumber=4640 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4438 sam_hrecs_find_rg /src/htslib/header.c linenumber=4646 sam_hdr_add_line /src/htslib/header.c linenumber=4647 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1701 sam_hrecs_vadd /src/htslib/header.c linenumber=1707 rebuild_target_arrays /src/htslib/header.c linenumber=1711 redact_header_text /src/htslib/header.c linenumber=1715 refs_from_header /src/htslib/cram/cram_io.c linenumber=4652 refs2id /src/htslib/cram/cram_io.c linenumber=4654 sam_hrecs_find_type_id /src/htslib/header.c linenumber=4664 sam_hrecs_find_key /src/htslib/header.c linenumber=4667 cram_get_ref /src/htslib/cram/cram_io.c linenumber=4679 hts_log /src/htslib/hts.c linenumber=4683 hts_log /src/htslib/hts.c linenumber=4685 hts_log /src/htslib/hts.c linenumber=4686 pthread_mutex_lock linenumber=4688 pthread_mutex_unlock linenumber=4692 hts_md5_init /src/htslib/md5.c linenumber=4698 hts_md5_update /src/htslib/md5.c linenumber=4702 hts_md5_final /src/htslib/md5.c linenumber=4713 hts_md5_destroy /src/htslib/md5.c linenumber=4714 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=4715 hts_md5_hex /src/htslib/md5.c linenumber=4717 sam_hdr_update_line /src/htslib/header.c linenumber=4719 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1917 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1923 check_for_name_update /src/htslib/header.c linenumber=1932 TYPEKEY /src/htslib/./header.h linenumber=1879 TYPEKEY /src/htslib/./header.h linenumber=1881 TYPEKEY /src/htslib/./header.h linenumber=1883 sam_hrecs_find_key /src/htslib/header.c linenumber=1892 __assert_fail linenumber=1895 strcmp linenumber=1901 strcmp linenumber=1902 kh_get_m_s2i /src/htslib/./header.h linenumber=1903 hts_log /src/htslib/hts.c linenumber=1936 TYPEKEY /src/htslib/./header.h linenumber=1940 hts_log /src/htslib/hts.c linenumber=1942 sam_hrecs_vupdate /src/htslib/header.c linenumber=1946 kh_get_m_s2i /src/htslib/./header.h linenumber=1957 sam_hrecs_find_key /src/htslib/header.c linenumber=1958 __assert_fail linenumber=1960 __assert_fail linenumber=1961 __assert_fail linenumber=1962 kh_del_m_s2i /src/htslib/./header.h linenumber=1964 kh_put_m_s2i /src/htslib/./header.h linenumber=1965 hts_log /src/htslib/hts.c linenumber=1967 TYPEKEY /src/htslib/./header.h linenumber=1973 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1973 rebuild_target_arrays /src/htslib/header.c linenumber=1976 redact_header_text /src/htslib/header.c linenumber=1979 full_path /src/htslib/cram/cram_io.c linenumber=4725 strlen linenumber=4594 hisremote /src/htslib/hfile.c linenumber=4595 hts_log /src/htslib/hts.c linenumber=4597 strncpy linenumber=4600 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=4606 strncpy linenumber=4608 getcwd linenumber=4614 strlen linenumber=4615 strncpy linenumber=4616 snprintf linenumber=4621 sam_hdr_update_line /src/htslib/header.c linenumber=4726 sam_hdr_length /src/htslib/header.c linenumber=4733 sam_hdr_rebuild /src/htslib/header.c linenumber=1580 rebuild_target_arrays /src/htslib/header.c linenumber=1614 hts_log /src/htslib/hts.c linenumber=1615 sam_hdr_link_pg /src/htslib/header.c linenumber=1624 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2477 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2486 calloc linenumber=2490 __assert_fail linenumber=2501 kh_get_m_s2i /src/htslib/./header.h linenumber=2511 hts_log /src/htslib/hts.c linenumber=2514 hts_log /src/htslib/hts.c linenumber=2521 redact_header_text /src/htslib/header.c linenumber=2550 hts_log /src/htslib/hts.c linenumber=1625 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1630 ks_free /src/htslib/./htslib/kstring.h linenumber=1631 ks_len /src/htslib/./htslib/kstring.h linenumber=1640 ks_release /src/htslib/./htslib/kstring.h linenumber=1641 hts_log /src/htslib/hts.c linenumber=4735 int32_encode /src/htslib/cram/cram_io.c linenumber=4739 sam_hdr_str /src/htslib/header.c linenumber=4743 sam_hdr_rebuild /src/htslib/header.c linenumber=1587 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4743 cram_new_block /src/htslib/cram/cram_io.c linenumber=4747 cram_new_container /src/htslib/cram/cram_io.c linenumber=4748 calloc linenumber=3401 calloc linenumber=3429 cram_new_compression_header /src/htslib/cram/cram_io.c linenumber=3433 calloc linenumber=4069 cram_new_block /src/htslib/cram/cram_io.c linenumber=4073 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4078 cram_free_block /src/htslib/cram/cram_io.c linenumber=4079 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4084 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4085 cram_free_block /src/htslib/cram/cram_io.c linenumber=4086 cram_stats_create /src/htslib/cram/cram_stats.c linenumber=3438 calloc linenumber=50 kh_init_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3442 calloc linenumber=380 cram_free_block /src/htslib/cram/cram_io.c linenumber=4754 cram_free_container /src/htslib/cram/cram_io.c linenumber=4755 int32_put_blk /src/htslib/cram/cram_io.c linenumber=4759 block_append /src/htslib/cram/cram_io.h linenumber=815 sam_hdr_str /src/htslib/header.c linenumber=4762 block_append /src/htslib/cram/cram_io.h linenumber=4762 cram_compress_block /src/htslib/cram/cram_io.c linenumber=4767 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=2086 cram_free_block /src/htslib/cram/cram_io.c linenumber=4779 cram_free_container /src/htslib/cram/cram_io.c linenumber=4780 calloc linenumber=4807 cram_free_block /src/htslib/cram/cram_io.c linenumber=4808 cram_free_container /src/htslib/cram/cram_io.c linenumber=4809 block_append /src/htslib/cram/cram_io.h linenumber=4812 cram_write_container /src/htslib/cram/cram_io.c linenumber=4817 cram_free_block /src/htslib/cram/cram_io.c linenumber=4818 cram_free_container /src/htslib/cram/cram_io.c linenumber=4819 cram_write_block /src/htslib/cram/cram_io.c linenumber=4823 cram_free_block /src/htslib/cram/cram_io.c linenumber=4824 cram_free_container /src/htslib/cram/cram_io.c linenumber=4825 block_resize /src/htslib/cram/cram_io.h linenumber=4830 cram_write_block /src/htslib/cram/cram_io.c linenumber=4835 cram_free_block /src/htslib/cram/cram_io.c linenumber=4836 cram_free_container /src/htslib/cram/cram_io.c linenumber=4837 cram_free_block /src/htslib/cram/cram_io.c linenumber=4842 cram_free_container /src/htslib/cram/cram_io.c linenumber=4843 hflush /src/htslib/hfile.c linenumber=4846 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1989 strstr linenumber=1997 bgzf_write /src/htslib/bgzf.c linenumber=2005 hwrite /src/htslib/./htslib/hfile.h linenumber=2007 kputsn /src/htslib/./htslib/kstring.h linenumber=2017 kputs /src/htslib/./htslib/kstring.h linenumber=2018 kputsn /src/htslib/./htslib/kstring.h linenumber=2019 kputw /src/htslib/./htslib/kstring.h linenumber=2020 kputc /src/htslib/./htslib/kstring.h linenumber=2021 bgzf_write /src/htslib/bgzf.c linenumber=2026 hwrite /src/htslib/./htslib/hfile.h linenumber=2028 bgzf_flush /src/htslib/bgzf.c linenumber=2035 hflush /src/htslib/hfile.c linenumber=2037 sam_hdr_dup /src/htslib/sam.c linenumber=2055 sam_hdr_destroy /src/htslib/sam.c linenumber=2056 bam_init1 /src/htslib/sam.c linenumber=102 calloc linenumber=435 sam_read1 /src/htslib/sam.c linenumber=106 sam_read1_bam /src/htslib/sam.c linenumber=4255 bam_read1 /src/htslib/sam.c linenumber=4117 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=796 bgzf_read /src/htslib/bgzf.c linenumber=168 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=801 bgzf_read /src/htslib/bgzf.c linenumber=809 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=813 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=814 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=819 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=822 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=823 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=824 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=825 realloc_bam_data /src/htslib/./sam_internal.h linenumber=832 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=835 fixup_missing_qname_nul /src/htslib/sam.c linenumber=837 realloc_bam_data /src/htslib/./sam_internal.h linenumber=775 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=842 swap_data /src/htslib/sam.c linenumber=844 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=762 bam_tag2cigar /src/htslib/sam.c linenumber=845 bam_cigar2rqlens /src/htslib/sam.c linenumber=851 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=853 hts_log /src/htslib/hts.c linenumber=856 __errno_location linenumber=4121 sam_read1_cram /src/htslib/sam.c linenumber=4259 cram_get_bam_seq /src/htslib/cram/cram_decode.c linenumber=4130 cram_get_seq /src/htslib/cram/cram_decode.c linenumber=3647 pthread_mutex_lock linenumber=3579 pthread_mutex_unlock linenumber=3582 cram_next_slice /src/htslib/cram/cram_decode.c linenumber=3585 cram_first_slice /src/htslib/cram/cram_decode.c linenumber=3293 cram_free_container /src/htslib/cram/cram_io.c linenumber=3236 cram_read_container /src/htslib/cram/cram_io.c linenumber=3238 cram_seek /src/htslib/cram/cram_io.c linenumber=3254 cram_free_container /src/htslib/cram/cram_io.c linenumber=3256 cram_read_container /src/htslib/cram/cram_io.c linenumber=3258 cram_read_block /src/htslib/cram/cram_io.c linenumber=3269 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3274 calloc linenumber=149 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=157 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=178 kh_init_map /src/htslib/cram/cram_structs.h linenumber=186 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=194 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=213 kh_put_map /src/htslib/cram/cram_structs.h linenumber=226 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=228 kh_put_map /src/htslib/cram/cram_structs.h linenumber=238 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=240 kh_put_map /src/htslib/cram/cram_structs.h linenumber=250 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=252 kh_put_map /src/htslib/cram/cram_structs.h linenumber=262 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=264 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=274 kh_put_map /src/htslib/cram/cram_structs.h linenumber=305 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=307 cram_decode_TD /src/htslib/cram/cram_decode.c linenumber=314 cram_new_block /src/htslib/cram/cram_io.c linenumber=80 hts_log /src/htslib/hts.c linenumber=84 cram_free_block /src/htslib/cram/cram_io.c linenumber=85 cram_free_block /src/htslib/cram/cram_io.c linenumber=95 cram_free_block /src/htslib/cram/cram_io.c linenumber=100 block_append /src/htslib/cram/cram_io.h linenumber=104 block_append_char /src/htslib/cram/cram_io.h linenumber=109 calloc linenumber=122 cram_free_block /src/htslib/cram/cram_io.c linenumber=123 cram_free_block /src/htslib/cram/cram_io.c linenumber=137 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=316 kh_put_map /src/htslib/cram/cram_structs.h linenumber=323 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=325 hts_log /src/htslib/hts.c linenumber=333 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=340 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=357 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=371 hts_log /src/htslib/hts.c linenumber=454 hts_log /src/htslib/hts.c linenumber=459 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=463 cram_encoding2str /src/htslib/cram/cram_codecs.c linenumber=2264 hts_log /src/htslib/hts.c linenumber=2264 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=466 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=476 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=489 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=504 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=519 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=521 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=532 sam_hrecs_sort_order /src/htslib/header.c linenumber=3278 TYPEKEY /src/htslib/./header.h linenumber=3135 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3135 strcmp linenumber=3141 strcmp linenumber=3143 strcmp linenumber=3145 strcmp linenumber=3147 hts_log /src/htslib/hts.c linenumber=3148 pthread_mutex_lock linenumber=3279 pthread_mutex_unlock linenumber=3281 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3300 cram_free_container /src/htslib/cram/cram_io.c linenumber=3311 cram_read_container /src/htslib/cram/cram_io.c linenumber=3344 cram_free_container /src/htslib/cram/cram_io.c linenumber=3357 cram_free_container /src/htslib/cram/cram_io.c linenumber=3370 cram_free_container /src/htslib/cram/cram_io.c linenumber=3379 cram_free_container /src/htslib/cram/cram_io.c linenumber=3392 hseek /src/htslib/hfile.c linenumber=3395 cram_read_block /src/htslib/cram/cram_io.c linenumber=3405 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3411 sam_hrecs_sort_order /src/htslib/header.c linenumber=3416 pthread_mutex_lock linenumber=3417 pthread_mutex_unlock linenumber=3419 cram_free_container /src/htslib/cram/cram_io.c linenumber=3430 cram_read_slice /src/htslib/cram/cram_io.c linenumber=3435 cram_read_block /src/htslib/cram/cram_io.c linenumber=4310 calloc linenumber=4311 cram_decode_slice_header /src/htslib/cram/cram_decode.c linenumber=4321 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=959 calloc linenumber=969 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1003 cram_content_type2str /src/htslib/cram/cram_io.c linenumber=4326 hts_log /src/htslib/hts.c linenumber=4326 hts_log /src/htslib/hts.c linenumber=4332 calloc linenumber=4336 cram_read_block /src/htslib/cram/cram_io.c linenumber=4341 calloc linenumber=4352 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4366 cram_new_block /src/htslib/cram/cram_io.c linenumber=4369 cram_new_block /src/htslib/cram/cram_io.c linenumber=4370 cram_new_block /src/htslib/cram/cram_io.c linenumber=4371 cram_new_block /src/htslib/cram/cram_io.c linenumber=4372 cram_new_block /src/htslib/cram/cram_io.c linenumber=4373 cram_new_block /src/htslib/cram/cram_io.c linenumber=4374 cram_free_block /src/htslib/cram/cram_io.c linenumber=4385 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4388 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3450 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3459 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3468 cram_decode_slice_mt /src/htslib/cram/cram_decode.c linenumber=3480 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3068 hts_tpool_process_sz /src/htslib/thread_pool.c linenumber=3078 pthread_mutex_lock linenumber=307 pthread_mutex_unlock linenumber=309 __errno_location linenumber=3080 __errno_location linenumber=3081 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=3082 cram_decode_slice_thread /src/htslib/cram/cram_decode.c linenumber=3082 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3054 __errno_location linenumber=3085 __errno_location linenumber=3091 hts_log /src/htslib/hts.c linenumber=3481 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3482 hts_tpool_process_len /src/htslib/thread_pool.c linenumber=3503 pthread_mutex_lock linenumber=293 pthread_mutex_unlock linenumber=295 hts_tpool_process_qsize /src/htslib/thread_pool.c linenumber=3504 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3515 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3520 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3522 hts_log /src/htslib/hts.c linenumber=3523 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3527 hts_log /src/htslib/hts.c linenumber=3532 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3534 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3538 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3610 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3617 bam_get_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3653 bam_copy1 /src/htslib/sam.c linenumber=3657 realloc_bam_data /src/htslib/./sam_internal.h linenumber=490 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3664 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3670 cram_eof /src/htslib/cram/cram_io.c linenumber=4132 sam_read1_sam /src/htslib/sam.c linenumber=4263 sam_parse1 /src/htslib/sam.c linenumber=4143 strchr linenumber=2699 hts_log /src/htslib/hts.c linenumber=2701 hts_log /src/htslib/hts.c linenumber=2702 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2704 parse_sam_flag /src/htslib/sam.c linenumber=2714 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2483 strtoul linenumber=2489 strchr linenumber=2718 strcmp linenumber=2719 hts_log /src/htslib/hts.c linenumber=2720 bam_name2id /src/htslib/./htslib/sam.h linenumber=2721 sam_hdr_name2tid /src/htslib/header.c linenumber=780 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2401 kh_get_m_s2i /src/htslib/./header.h linenumber=2409 hts_log /src/htslib/hts.c linenumber=2722 hts_strprint /src/htslib/textutils.c linenumber=2723 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=2723 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2727 hts_log /src/htslib/hts.c linenumber=2730 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2736 bam_parse_cigar /src/htslib/sam.c linenumber=2742 hts_log /src/htslib/hts.c linenumber=2916 read_ncigar /src/htslib/sam.c linenumber=2921 isdigit_c /src/htslib/./textutils_internal.h linenumber=2830 hts_log /src/htslib/hts.c linenumber=2832 hts_log /src/htslib/hts.c linenumber=2836 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2929 hts_log /src/htslib/hts.c linenumber=2930 parse_cigar /src/htslib/sam.c linenumber=2942 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2856 hts_log /src/htslib/hts.c linenumber=2858 hts_log /src/htslib/hts.c linenumber=2862 hts_log /src/htslib/hts.c linenumber=2868 bam_cigar2rlen /src/htslib/sam.c linenumber=2747 strchr linenumber=2752 hts_log /src/htslib/hts.c linenumber=2755 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2757 strchr linenumber=2759 strcmp linenumber=2760 strcmp linenumber=2762 bam_name2id /src/htslib/./htslib/sam.h linenumber=2765 hts_log /src/htslib/hts.c linenumber=2766 hts_strprint /src/htslib/textutils.c linenumber=2767 hts_log /src/htslib/hts.c linenumber=2767 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2770 hts_log /src/htslib/hts.c linenumber=2773 hts_str2int /src/htslib/./textutils_internal.h linenumber=2777 hts_log /src/htslib/hts.c linenumber=2779 strchr linenumber=2781 strcmp linenumber=2782 hts_log /src/htslib/hts.c linenumber=2783 bam_cigar2qlen /src/htslib/sam.c linenumber=2785 hts_log /src/htslib/hts.c linenumber=2786 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2788 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2797 hts_log /src/htslib/hts.c linenumber=2803 hts_log /src/htslib/hts.c linenumber=2807 aux_parse /src/htslib/sam.c linenumber=2812 hts_log /src/htslib/hts.c linenumber=2538 isspace_c /src/htslib/./textutils_internal.h linenumber=2542 hts_log /src/htslib/hts.c linenumber=2542 isspace_c /src/htslib/./textutils_internal.h linenumber=2545 isspace_c /src/htslib/./textutils_internal.h linenumber=2547 kh_get_tag /src/htslib/sam.c linenumber=2554 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2562 isspace_c /src/htslib/./textutils_internal.h linenumber=2566 hts_log /src/htslib/hts.c linenumber=2566 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2569 hts_str2int /src/htslib/./textutils_internal.h linenumber=2576 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2582 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=275 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2586 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=283 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2590 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2596 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2600 strtod linenumber=2606 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2606 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=345 strtod linenumber=2610 double_to_le /src/htslib/./htslib/hts_endian.h linenumber=2610 u64_to_le /src/htslib/./htslib/hts_endian.h linenumber=359 strchr linenumber=2613 strlen linenumber=2614 isspace_c /src/htslib/./textutils_internal.h linenumber=2615 hts_log /src/htslib/hts.c linenumber=2615 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2618 isspace_c /src/htslib/./textutils_internal.h linenumber=2625 hts_log /src/htslib/hts.c linenumber=2625 sam_parse_B_vals /src/htslib/sam.c linenumber=2628 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2478 hts_log /src/htslib/hts.c linenumber=2358 aux_type2size /src/htslib/sam.c linenumber=2368 hts_log /src/htslib/hts.c linenumber=2370 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2387 hts_log /src/htslib/hts.c linenumber=2388 sam_parse_Bc_vals /src/htslib/sam.c linenumber=2401 grow_B_array /src/htslib/sam.c linenumber=2232 __errno_location linenumber=2207 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2212 hts_log /src/htslib/hts.c linenumber=2213 hts_str2int /src/htslib/./textutils_internal.h linenumber=2235 sam_parse_BC_vals /src/htslib/sam.c linenumber=2404 grow_B_array /src/htslib/sam.c linenumber=2246 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2250 sam_parse_Bs_vals /src/htslib/sam.c linenumber=2407 grow_B_array /src/htslib/sam.c linenumber=2266 hts_str2int /src/htslib/./textutils_internal.h linenumber=2269 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2269 sam_parse_BS_vals /src/htslib/sam.c linenumber=2410 grow_B_array /src/htslib/sam.c linenumber=2281 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2285 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2285 sam_parse_Bi_vals /src/htslib/sam.c linenumber=2413 grow_B_array /src/htslib/sam.c linenumber=2302 hts_str2int /src/htslib/./textutils_internal.h linenumber=2305 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2305 sam_parse_BI_vals /src/htslib/sam.c linenumber=2416 grow_B_array /src/htslib/sam.c linenumber=2317 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2321 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2321 sam_parse_Bf_vals /src/htslib/sam.c linenumber=2419 grow_B_array /src/htslib/sam.c linenumber=2338 strtod linenumber=2341 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2341 hts_log /src/htslib/hts.c linenumber=2424 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2427 hts_str2int /src/htslib/./textutils_internal.h linenumber=2441 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2450 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2452 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2454 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2458 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2460 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2462 hts_log /src/htslib/hts.c linenumber=2467 isspace_c /src/htslib/./textutils_internal.h linenumber=2630 hts_strprint /src/htslib/textutils.c linenumber=2630 hts_log /src/htslib/hts.c linenumber=2630 isspace_c /src/htslib/./textutils_internal.h linenumber=2636 hts_log /src/htslib/hts.c linenumber=2636 bam_tag2cigar /src/htslib/sam.c linenumber=2815 sam_state_destroy /src/htslib/sam.c linenumber=4154 __errno_location linenumber=4155 bgzf_seek /src/htslib/bgzf.c linenumber=4158 bgzf_seek_common /src/htslib/bgzf.c linenumber=2259 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=4169 pthread_create linenumber=4173 sam_dispatcher_read /src/htslib/sam.c linenumber=4173 ks_resize /src/htslib/./htslib/kstring.h linenumber=3317 pthread_mutex_lock linenumber=3322 pthread_cond_signal linenumber=3326 pthread_mutex_unlock linenumber=3327 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3328 pthread_mutex_unlock linenumber=3334 pthread_mutex_lock linenumber=3336 pthread_mutex_unlock linenumber=3342 calloc linenumber=3346 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3350 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3361 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=320 hts_prod_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=321 hts_realloc /src/htslib/./htslib/hts_alloc.h linenumber=322 bgzf_read /src/htslib/bgzf.c linenumber=3374 hread /src/htslib/./htslib/hfile.h linenumber=3376 __errno_location linenumber=3378 sam_state_err /src/htslib/sam.c linenumber=3378 hts_realloc_pse /src/htslib/./htslib/hts_alloc.h linenumber=3395 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=348 hts_prod_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=349 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=350 hts_realloc /src/htslib/./htslib/hts_alloc.h linenumber=351 __assert_fail linenumber=3400 __assert_fail linenumber=3401 __assert_fail linenumber=3402 ks_resize /src/htslib/./htslib/kstring.h linenumber=3408 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=3420 sam_parse_worker /src/htslib/sam.c linenumber=3420 pthread_mutex_lock linenumber=3207 pthread_mutex_unlock linenumber=3212 calloc linenumber=3215 calloc linenumber=3220 sam_state_err /src/htslib/sam.c linenumber=3222 sam_state_err /src/htslib/sam.c linenumber=3233 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3243 sam_state_err /src/htslib/sam.c linenumber=3246 strchr linenumber=3262 sam_parse1 /src/htslib/sam.c linenumber=3274 __errno_location linenumber=3275 sam_state_err /src/htslib/sam.c linenumber=3275 cleanup_sp_lines /src/htslib/sam.c linenumber=3276 __assert_fail linenumber=3188 sam_free_sp_bams /src/htslib/sam.c linenumber=3191 pthread_mutex_lock linenumber=3285 pthread_mutex_unlock linenumber=3288 sam_free_sp_bams /src/htslib/sam.c linenumber=3292 cleanup_sp_lines /src/htslib/sam.c linenumber=3420 cleanup_sp_bams /src/htslib/sam.c linenumber=3420 sam_free_sp_bams /src/htslib/sam.c linenumber=3302 pthread_mutex_lock linenumber=3423 pthread_mutex_unlock linenumber=3425 pthread_mutex_unlock linenumber=3430 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3434 sam_parse_eof /src/htslib/sam.c linenumber=3434 pthread_mutex_lock linenumber=3440 pthread_cond_wait linenumber=3442 pthread_cond_signal linenumber=3445 pthread_mutex_unlock linenumber=3446 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3447 pthread_mutex_unlock linenumber=3451 pthread_mutex_lock linenumber=3457 pthread_cond_signal linenumber=3459 pthread_mutex_unlock linenumber=3460 pthread_mutex_lock linenumber=3463 pthread_mutex_unlock linenumber=3466 __errno_location linenumber=3473 sam_state_err /src/htslib/sam.c linenumber=3473 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3474 hts_log /src/htslib/hts.c linenumber=4180 __errno_location linenumber=4188 pthread_mutex_lock linenumber=4192 pthread_mutex_unlock linenumber=4194 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=4198 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4201 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4202 pthread_mutex_lock linenumber=4205 pthread_mutex_unlock linenumber=4207 bam_copy1 /src/htslib/sam.c linenumber=4212 pthread_mutex_lock linenumber=4215 pthread_mutex_unlock linenumber=4218 hts_getline /src/htslib/hts.c linenumber=4231 sam_parse1 /src/htslib/sam.c linenumber=4234 hts_log /src/htslib/hts.c linenumber=4237 fastq_state_init /src/htslib/sam.c linenumber=4270 fastq_parse1 /src/htslib/sam.c linenumber=4275 hts_getline /src/htslib/hts.c linenumber=3928 strpbrk linenumber=3944 isspace_c /src/htslib/./textutils_internal.h linenumber=3956 isspace_c /src/htslib/./textutils_internal.h linenumber=3964 hts_getline /src/htslib/hts.c linenumber=3972 kputsn /src/htslib/./htslib/kstring.h linenumber=3978 hts_getline /src/htslib/hts.c linenumber=3987 kputsn /src/htslib/./htslib/kstring.h linenumber=3991 isdigit_c /src/htslib/./textutils_internal.h linenumber=4004 regexec linenumber=4018 hts_log /src/htslib/hts.c linenumber=4023 isalpha_c /src/htslib/./textutils_internal.h linenumber=4031 bam_set1 /src/htslib/sam.c linenumber=4051 bam_aux_append /src/htslib/sam.c linenumber=4063 __assert_fail linenumber=4746 realloc_bam_data /src/htslib/./sam_internal.h linenumber=4750 __errno_location linenumber=4770 isdigit_c /src/htslib/./textutils_internal.h linenumber=4075 strtol linenumber=4076 isdigit_c /src/htslib/./textutils_internal.h linenumber=4090 isspace_c /src/htslib/./textutils_internal.h linenumber=4093 bam_aux_append /src/htslib/sam.c linenumber=4102 aux_parse /src/htslib/sam.c linenumber=4109 __errno_location linenumber=4279 __errno_location linenumber=4283 sam_passes_filter /src/htslib/sam.c linenumber=4288 hts_filter_eval2 /src/htslib/hts_expr.c linenumber=1542 ks_free /src/htslib/./htslib/kstring.h linenumber=924 hts_filter_eval_ /src/htslib/hts_expr.c linenumber=927 expression /src/htslib/hts_expr.c linenumber=882 and_expr /src/htslib/hts_expr.c linenumber=847 eq_expr /src/htslib/hts_expr.c linenumber=798 cmp_expr /src/htslib/hts_expr.c linenumber=699 bitor_expr /src/htslib/hts_expr.c linenumber=626 bitxor_expr /src/htslib/hts_expr.c linenumber=588 bitand_expr /src/htslib/hts_expr.c linenumber=553 add_expr /src/htslib/hts_expr.c linenumber=518 mul_expr /src/htslib/hts_expr.c linenumber=473 unary_expr /src/htslib/hts_expr.c linenumber=426 ws /src/htslib/hts_expr.c linenumber=368 simple_expr /src/htslib/hts_expr.c linenumber=370 ws /src/htslib/hts_expr.c linenumber=288 expression /src/htslib/hts_expr.c linenumber=290 ws /src/htslib/hts_expr.c linenumber=291 fprintf linenumber=293 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=303 __ctype_b_loc linenumber=365 strtod linenumber=386 strtod linenumber=409 ks_clear /src/htslib/./htslib/kstring.h linenumber=321 kputsn /src/htslib/./htslib/kstring.h linenumber=321 func_expr /src/htslib/hts_expr.c linenumber=348 strncmp linenumber=160 expression /src/htslib/hts_expr.c linenumber=161 expr_func_avg /src/htslib/hts_expr.c linenumber=162 strncmp linenumber=167 expression /src/htslib/hts_expr.c linenumber=168 ws /src/htslib/hts_expr.c linenumber=173 expression /src/htslib/hts_expr.c linenumber=173 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=175 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=72 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=179 ks_free /src/htslib/./htslib/kstring.h linenumber=85 strncmp linenumber=185 expression /src/htslib/hts_expr.c linenumber=186 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=188 strncmp linenumber=190 expression /src/htslib/hts_expr.c linenumber=191 exp linenumber=193 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=196 ks_clear /src/htslib/./htslib/kstring.h linenumber=77 strncmp linenumber=202 expression /src/htslib/hts_expr.c linenumber=203 expr_func_length /src/htslib/hts_expr.c linenumber=204 strncmp linenumber=205 expression /src/htslib/hts_expr.c linenumber=206 log linenumber=208 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=211 strncmp linenumber=216 expression /src/htslib/hts_expr.c linenumber=217 expr_func_min /src/htslib/hts_expr.c linenumber=218 strncmp linenumber=219 expression /src/htslib/hts_expr.c linenumber=220 expr_func_max /src/htslib/hts_expr.c linenumber=221 strncmp linenumber=226 expression /src/htslib/hts_expr.c linenumber=227 ws /src/htslib/hts_expr.c linenumber=234 expression /src/htslib/hts_expr.c linenumber=234 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=235 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=236 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=238 pow linenumber=242 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=243 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=248 strncmp linenumber=253 expression /src/htslib/hts_expr.c linenumber=254 sqrt linenumber=256 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=259 ws /src/htslib/hts_expr.c linenumber=267 fprintf linenumber=269 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=371 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=372 unary_expr /src/htslib/hts_expr.c linenumber=380 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=384 unary_expr /src/htslib/hts_expr.c linenumber=397 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=398 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=399 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=402 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=403 simple_expr /src/htslib/hts_expr.c linenumber=410 ws /src/htslib/hts_expr.c linenumber=432 unary_expr /src/htslib/hts_expr.c linenumber=434 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=435 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=436 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=438 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=451 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=455 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=459 ws /src/htslib/hts_expr.c linenumber=479 mul_expr /src/htslib/hts_expr.c linenumber=482 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=483 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=486 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=499 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=506 ws /src/htslib/hts_expr.c linenumber=523 add_expr /src/htslib/hts_expr.c linenumber=525 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=526 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=529 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=539 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=541 ws /src/htslib/hts_expr.c linenumber=558 bitand_expr /src/htslib/hts_expr.c linenumber=560 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=561 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=564 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=574 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=576 ws /src/htslib/hts_expr.c linenumber=593 bitxor_expr /src/htslib/hts_expr.c linenumber=595 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=596 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=599 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=609 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=611 ws /src/htslib/hts_expr.c linenumber=628 cmp_expr /src/htslib/hts_expr.c linenumber=634 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=635 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=636 strcmp linenumber=640 cmp_expr /src/htslib/hts_expr.c linenumber=646 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=647 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=648 strcmp linenumber=652 cmp_expr /src/htslib/hts_expr.c linenumber=658 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=659 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=660 strcmp linenumber=664 cmp_expr /src/htslib/hts_expr.c linenumber=670 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=671 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=672 strcmp linenumber=676 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=682 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=683 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=684 ws /src/htslib/hts_expr.c linenumber=701 eq_expr /src/htslib/hts_expr.c linenumber=711 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=714 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=715 strcmp linenumber=718 eq_expr /src/htslib/hts_expr.c linenumber=726 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=729 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=730 strcmp linenumber=733 eq_expr /src/htslib/hts_expr.c linenumber=742 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=744 regcomp linenumber=758 regerror linenumber=761 fprintf linenumber=762 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=763 regexec linenumber=769 regfree linenumber=773 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=783 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=784 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=785 ws /src/htslib/hts_expr.c linenumber=802 eq_expr /src/htslib/hts_expr.c linenumber=804 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=805 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=806 eq_expr /src/htslib/hts_expr.c linenumber=815 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=816 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=818 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=820 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=823 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=825 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=828 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=839 ws /src/htslib/hts_expr.c linenumber=885 fprintf linenumber=886 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=897 bam_sym_lookup /src/htslib/sam.c linenumber=1542 memcmp linenumber=1221 ks_clear /src/htslib/./htslib/kstring.h linenumber=1224 kputw /src/htslib/./htslib/kstring.h linenumber=1229 kputc_ /src/htslib/./htslib/kstring.h linenumber=1230 kputs /src/htslib/./htslib/kstring.h linenumber=1232 kputs /src/htslib/./htslib/kstring.h linenumber=1234 memcmp linenumber=1241 bam_endpos /src/htslib/sam.c linenumber=1243 memcmp linenumber=1249 memcmp linenumber=1256 memcmp linenumber=1260 memcmp linenumber=1264 memcmp linenumber=1268 memcmp linenumber=1272 memcmp linenumber=1276 memcmp linenumber=1280 memcmp linenumber=1284 memcmp linenumber=1288 memcmp linenumber=1292 memcmp linenumber=1296 memcmp linenumber=1300 hts_log /src/htslib/hts.c linenumber=1305 memcmp linenumber=1313 memcmp linenumber=1333 bam_get_library /src/htslib/sam.c linenumber=1336 bam_aux_get /src/htslib/sam.c linenumber=1180 sam_hdr_find_tag_id /src/htslib/header.c linenumber=1187 ks_clear /src/htslib/./htslib/kstring.h linenumber=1337 kputs /src/htslib/./htslib/kstring.h linenumber=1337 memcmp linenumber=1343 memcmp linenumber=1347 memcmp linenumber=1351 sam_hdr_tid2name /src/htslib/header.c linenumber=1354 ks_clear /src/htslib/./htslib/kstring.h linenumber=1355 kputs /src/htslib/./htslib/kstring.h linenumber=1355 memcmp linenumber=1357 memcmp linenumber=1365 memcmp linenumber=1373 memcmp linenumber=1377 memcmp linenumber=1385 bam_cigar2qlen /src/htslib/sam.c linenumber=1387 memcmp linenumber=1389 ks_clear /src/htslib/./htslib/kstring.h linenumber=1392 kputs /src/htslib/./htslib/kstring.h linenumber=1392 memcmp linenumber=1394 ks_clear /src/htslib/./htslib/kstring.h linenumber=1396 ks_resize /src/htslib/./htslib/kstring.h linenumber=1397 memcmp linenumber=1407 bam_cigar2rlen /src/htslib/sam.c linenumber=1409 memcmp linenumber=1411 sam_hdr_tid2name /src/htslib/header.c linenumber=1414 ks_clear /src/htslib/./htslib/kstring.h linenumber=1415 kputs /src/htslib/./htslib/kstring.h linenumber=1415 memcmp linenumber=1417 sam_hdr_tid2name /src/htslib/header.c linenumber=1420 ks_clear /src/htslib/./htslib/kstring.h linenumber=1421 kputs /src/htslib/./htslib/kstring.h linenumber=1421 memcmp linenumber=1423 memcmp linenumber=1431 ks_clear /src/htslib/./htslib/kstring.h linenumber=1433 ks_resize /src/htslib/./htslib/kstring.h linenumber=1434 nibble2base /src/htslib/./sam_internal.h linenumber=1436 memcmp linenumber=1441 memcmp linenumber=1472 bam_aux_get /src/htslib/sam.c linenumber=1484 ks_clear /src/htslib/./htslib/kstring.h linenumber=1492 kputs /src/htslib/./htslib/kstring.h linenumber=1492 ks_clear /src/htslib/./htslib/kstring.h linenumber=1497 kputsn /src/htslib/./htslib/kstring.h linenumber=1497 bam_aux2i /src/htslib/sam.c linenumber=1504 get_int_aux_val /src/htslib/sam.c linenumber=5102 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=5086 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=5088 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=5089 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=5090 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=5091 __errno_location linenumber=5093 bam_aux2f /src/htslib/sam.c linenumber=1510 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=5109 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=5110 get_int_aux_val /src/htslib/sam.c linenumber=5111 hts_log /src/htslib/hts.c linenumber=1514 hts_log /src/htslib/hts.c linenumber=1543 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1544 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1549 sam_write1 /src/htslib/sam.c linenumber=107 bam_write_idx1 /src/htslib/sam.c linenumber=4542 bam_write1 /src/htslib/sam.c linenumber=940 hts_log /src/htslib/hts.c linenumber=871 __errno_location linenumber=872 hts_log /src/htslib/hts.c linenumber=879 bgzf_flush_try /src/htslib/bgzf.c linenumber=891 lazy_flush /src/htslib/bgzf.c linenumber=2000 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=893 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=895 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=895 bgzf_write /src/htslib/bgzf.c linenumber=198 swap_data /src/htslib/sam.c linenumber=896 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=898 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=900 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=901 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=903 bam_cigar2rlen /src/htslib/sam.c linenumber=907 hts_log /src/htslib/hts.c linenumber=911 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=920 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=921 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=922 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=923 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=924 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=925 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=926 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=927 swap_data /src/htslib/sam.c linenumber=929 bgzf_flush_try /src/htslib/bgzf.c linenumber=943 hts_idx_amend_last /src/htslib/hts.c linenumber=946 bam_write1 /src/htslib/sam.c linenumber=948 bam_endpos /src/htslib/sam.c linenumber=952 bgzf_idx_push /src/htslib/bgzf.c linenumber=952 hts_idx_push /src/htslib/hts.c linenumber=195 hts_idx_check_range /src/htslib/hts.c linenumber=2564 hts_idx_maxpos /src/htslib/hts.c linenumber=2542 hts_bin_maxpos /src/htslib/./htslib/hts.h linenumber=2537 hts_log /src/htslib/hts.c linenumber=2547 idx_format_name /src/htslib/hts.c linenumber=2552 hts_log /src/htslib/hts.c linenumber=2552 __errno_location linenumber=2556 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2571 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2575 hts_log /src/htslib/hts.c linenumber=2588 hts_log /src/htslib/hts.c linenumber=2593 hts_log /src/htslib/hts.c linenumber=2599 hts_log /src/htslib/hts.c linenumber=2604 kh_init_bin /src/htslib/hts.c linenumber=2609 calloc linenumber=2243 insert_to_l /src/htslib/hts.c linenumber=2614 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2359 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2618 insert_to_b /src/htslib/hts.c linenumber=2621 kh_put_bin /src/htslib/hts.c linenumber=2326 kh_resize_bin /src/htslib/hts.c linenumber=2243 realloc linenumber=2243 calloc linenumber=2331 kh_del_bin /src/htslib/hts.c linenumber=2333 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2338 insert_to_b /src/htslib/hts.c linenumber=2626 insert_to_b /src/htslib/hts.c linenumber=2628 hts_idx_check_range /src/htslib/hts.c linenumber=198 pthread_mutex_lock linenumber=201 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=208 pthread_mutex_unlock linenumber=209 pthread_mutex_unlock linenumber=224 sam_hdr_tid2name /src/htslib/header.c linenumber=953 sam_hdr_tid2len /src/htslib/header.c linenumber=953 kh_get_s2i /src/htslib/hts.c linenumber=2443 hts_log /src/htslib/hts.c linenumber=953 cram_put_bam_seq /src/htslib/cram/cram_encode.c linenumber=4545 cram_new_container /src/htslib/cram/cram_io.c linenumber=3934 pthread_mutex_lock linenumber=3940 pthread_mutex_unlock linenumber=3943 hts_log /src/htslib/hts.c linenumber=3968 pthread_mutex_lock linenumber=3971 hts_log /src/htslib/hts.c linenumber=3974 pthread_mutex_unlock linenumber=3976 cram_next_container /src/htslib/cram/cram_encode.c linenumber=3985 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=3193 hts_log /src/htslib/hts.c linenumber=3199 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=3204 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3210 cram_free_container /src/htslib/cram/cram_io.c linenumber=3218 cram_new_container /src/htslib/cram/cram_io.c linenumber=3221 pthread_mutex_lock linenumber=3226 pthread_mutex_unlock linenumber=3230 cram_new_slice /src/htslib/cram/cram_io.c linenumber=3238 calloc linenumber=4248 calloc linenumber=4252 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4260 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4262 cram_new_block /src/htslib/cram/cram_io.c linenumber=4265 cram_new_block /src/htslib/cram/cram_io.c linenumber=4266 cram_new_block /src/htslib/cram/cram_io.c linenumber=4267 cram_new_block /src/htslib/cram/cram_io.c linenumber=4268 cram_new_block /src/htslib/cram/cram_io.c linenumber=4269 cram_new_block /src/htslib/cram/cram_io.c linenumber=4270 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4281 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4282 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4283 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4293 pthread_mutex_lock linenumber=4017 hts_log /src/htslib/hts.c linenumber=4019 pthread_mutex_lock linenumber=4033 calloc linenumber=4034 pthread_mutex_unlock linenumber=4035 pthread_mutex_lock linenumber=4049 calloc linenumber=4050 pthread_mutex_unlock linenumber=4051 pthread_mutex_lock linenumber=4055 pthread_mutex_unlock linenumber=4058 pthread_mutex_lock linenumber=4068 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4073 pthread_mutex_unlock linenumber=4076 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4082 calloc linenumber=4090 pthread_mutex_unlock linenumber=4093 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4098 pthread_mutex_unlock linenumber=4100 bam_copy1 /src/htslib/sam.c linenumber=4107 bam_cigar2qlen /src/htslib/sam.c linenumber=4117 hts_log /src/htslib/hts.c linenumber=4119 pthread_create linenumber=4568 sam_dispatcher_write /src/htslib/sam.c linenumber=4568 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3487 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3488 sam_state_err /src/htslib/sam.c linenumber=3490 bgzf_flush_try /src/htslib/bgzf.c linenumber=3505 bgzf_write /src/htslib/bgzf.c linenumber=3507 hwrite /src/htslib/./htslib/hfile.h linenumber=3510 bam_endpos /src/htslib/sam.c linenumber=3517 bgzf_idx_push /src/htslib/bgzf.c linenumber=3516 __errno_location linenumber=3520 sam_state_err /src/htslib/sam.c linenumber=3520 sam_hdr_tid2name /src/htslib/header.c linenumber=3521 sam_hdr_tid2len /src/htslib/header.c linenumber=3521 hts_log /src/htslib/hts.c linenumber=3521 bam_endpos /src/htslib/sam.c linenumber=3526 hts_idx_push /src/htslib/hts.c linenumber=3526 __errno_location linenumber=3528 sam_state_err /src/htslib/sam.c linenumber=3528 sam_hdr_tid2name /src/htslib/header.c linenumber=3529 sam_hdr_tid2len /src/htslib/header.c linenumber=3529 hts_log /src/htslib/hts.c linenumber=3529 __assert_fail linenumber=3536 pthread_mutex_lock linenumber=3539 pthread_mutex_unlock linenumber=3543 bgzf_write /src/htslib/bgzf.c linenumber=3590 bgzf_flush_try /src/htslib/bgzf.c linenumber=3598 bgzf_write /src/htslib/bgzf.c linenumber=3603 hwrite /src/htslib/./htslib/hfile.h linenumber=3610 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3615 pthread_mutex_lock linenumber=3618 pthread_mutex_unlock linenumber=3621 sam_state_err /src/htslib/sam.c linenumber=3624 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3625 __errno_location linenumber=3629 sam_state_err /src/htslib/sam.c linenumber=3629 hts_log /src/htslib/hts.c linenumber=4575 pthread_mutex_lock linenumber=4582 pthread_mutex_unlock linenumber=4589 pthread_mutex_unlock linenumber=4591 calloc linenumber=4592 calloc linenumber=4593 bam_copy1 /src/htslib/sam.c linenumber=4606 pthread_mutex_lock linenumber=4613 pthread_mutex_unlock linenumber=4615 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=4618 sam_format_worker /src/htslib/sam.c linenumber=4618 cleanup_sp_bams /src/htslib/sam.c linenumber=4618 cleanup_sp_lines /src/htslib/sam.c linenumber=4618 pthread_mutex_unlock linenumber=4621 pthread_mutex_unlock linenumber=4624 sam_format1 /src/htslib/sam.c linenumber=4633 sam_format1_append /src/htslib/sam.c linenumber=4390 kputc /src/htslib/./htslib/kstring.h linenumber=4634 bgzf_flush_try /src/htslib/bgzf.c linenumber=4636 bgzf_write /src/htslib/bgzf.c linenumber=4638 hwrite /src/htslib/./htslib/hfile.h linenumber=4640 bam_endpos /src/htslib/sam.c linenumber=4645 bgzf_idx_push /src/htslib/bgzf.c linenumber=4645 sam_hdr_tid2name /src/htslib/header.c linenumber=4647 sam_hdr_tid2len /src/htslib/header.c linenumber=4647 hts_log /src/htslib/hts.c linenumber=4647 bam_endpos /src/htslib/sam.c linenumber=4652 hts_idx_push /src/htslib/hts.c linenumber=4652 sam_hdr_tid2name /src/htslib/header.c linenumber=4654 sam_hdr_tid2len /src/htslib/header.c linenumber=4654 hts_log /src/htslib/hts.c linenumber=4654 fastq_state_init /src/htslib/sam.c linenumber=4669 fastq_format1 /src/htslib/sam.c linenumber=4674 kputc /src/htslib/./htslib/kstring.h linenumber=4403 kputs /src/htslib/./htslib/kstring.h linenumber=4403 bam_aux_get /src/htslib/sam.c linenumber=4425 kputc /src/htslib/./htslib/kstring.h linenumber=4427 isalpha_c /src/htslib/./textutils_internal.h linenumber=4430 toupper_c /src/htslib/./textutils_internal.h linenumber=4430 kputc /src/htslib/./htslib/kstring.h linenumber=4430 kputs /src/htslib/./htslib/kstring.h linenumber=4435 kputs /src/htslib/./htslib/kstring.h linenumber=4443 kputs /src/htslib/./htslib/kstring.h linenumber=4446 bam_aux_get /src/htslib/sam.c linenumber=4456 ksprintf /src/htslib/kstring.c linenumber=4457 isupper_c /src/htslib/./textutils_internal.h linenumber=4461 __ctype_b_loc linenumber=177 islower_c /src/htslib/./textutils_internal.h linenumber=4461 __ctype_b_loc linenumber=173 hts_log /src/htslib/hts.c linenumber=4462 strlen linenumber=4463 strlen linenumber=4471 isalpha_c /src/htslib/./textutils_internal.h linenumber=4474 islower_c /src/htslib/./textutils_internal.h linenumber=4476 toupper_c /src/htslib/./textutils_internal.h linenumber=4477 kh_get_tag /src/htslib/sam.c linenumber=4488 kputc_ /src/htslib/./htslib/kstring.h linenumber=4489 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4490 skip_aux /src/htslib/sam.c linenumber=4493 kputsn /src/htslib/./htslib/kstring.h linenumber=4496 ks_resize /src/htslib/./htslib/kstring.h linenumber=4499 kputc_ /src/htslib/./htslib/kstring.h linenumber=4500 kputc_ /src/htslib/./htslib/kstring.h linenumber=4506 kputc_ /src/htslib/./htslib/kstring.h linenumber=4509 kputsn /src/htslib/./htslib/kstring.h linenumber=4514 kputc_ /src/htslib/./htslib/kstring.h linenumber=4518 kputc_ /src/htslib/./htslib/kstring.h linenumber=4521 kputc_ /src/htslib/./htslib/kstring.h linenumber=4524 kputc /src/htslib/./htslib/kstring.h linenumber=4527 bgzf_flush_try /src/htslib/bgzf.c linenumber=4677 bgzf_write /src/htslib/bgzf.c linenumber=4679 hwrite /src/htslib/./htslib/hfile.h linenumber=4682 __errno_location linenumber=4689 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=1714 bcf_hdr_init /src/htslib/vcf.c linenumber=2602 calloc linenumber=1640 kh_init_vdict /src/htslib/vcf.c linenumber=1643 calloc linenumber=75 kh_resize_vdict /src/htslib/vcf.c linenumber=1646 realloc linenumber=75 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=75 calloc linenumber=1649 kh_init_hdict /src/htslib/vcf.c linenumber=1651 strchr linenumber=1659 bcf_hdr_append /src/htslib/vcf.c linenumber=1661 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1495 calloc linenumber=668 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=670 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=680 isalpha_c /src/htslib/./textutils_internal.h linenumber=697 isalnum_c /src/htslib/./textutils_internal.h linenumber=700 bcf_hrec_add_key /src/htslib/vcf.c linenumber=708 __assert_fail linenumber=445 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=446 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=449 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=453 is_escaped /src/htslib/vcf.c linenumber=728 hts_strprint /src/htslib/textutils.c linenumber=746 hts_log /src/htslib/hts.c linenumber=746 bcf_hrec_set_val /src/htslib/vcf.c linenumber=753 __errno_location linenumber=472 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=475 __errno_location linenumber=485 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=488 hts_log /src/htslib/hts.c linenumber=763 isspace_c /src/htslib/./textutils_internal.h linenumber=768 hts_strprint /src/htslib/textutils.c linenumber=771 hts_log /src/htslib/hts.c linenumber=771 bcf_hrec_destroy /src/htslib/vcf.c linenumber=781 hts_strprint /src/htslib/textutils.c linenumber=788 hts_log /src/htslib/hts.c linenumber=788 bcf_hrec_destroy /src/htslib/vcf.c linenumber=792 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1497 get_hdr_aux /src/htslib/vcf.c linenumber=1128 bcf_hrec_check /src/htslib/vcf.c linenumber=1133 bcf_hrec_set_type /src/htslib/vcf.c linenumber=600 strcmp linenumber=530 strcmp linenumber=531 strcmp linenumber=532 strcmp linenumber=533 bcf_hrec_find_key /src/htslib/vcf.c linenumber=604 strcasecmp linenumber=524 bcf_hrec_find_key /src/htslib/vcf.c linenumber=614 strcmp linenumber=617 bcf_hrec_find_key /src/htslib/vcf.c linenumber=625 hts_log /src/htslib/hts.c linenumber=636 hts_log /src/htslib/hts.c linenumber=640 hts_log /src/htslib/hts.c linenumber=644 bcf_hdr_register_hrec /src/htslib/vcf.c linenumber=1135 bcf_hrec_set_type /src/htslib/vcf.c linenumber=839 bcf_hrec_find_key /src/htslib/vcf.c linenumber=846 strtoll linenumber=850 bcf_hrec_find_key /src/htslib/vcf.c linenumber=854 strdup linenumber=856 kh_get_vdict /src/htslib/vcf.c linenumber=861 strcmp linenumber=75 kh_put_vdict /src/htslib/vcf.c linenumber=868 kh_resize_vdict /src/htslib/vcf.c linenumber=75 bcf_hrec_find_key /src/htslib/vcf.c linenumber=872 strtol linenumber=876 kh_del_vdict /src/htslib/vcf.c linenumber=880 hts_log /src/htslib/hts.c linenumber=883 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=892 hts_log /src/htslib/hts.c linenumber=806 __errno_location linenumber=808 hts_resize_array_ /src/htslib/hts.c linenumber=818 hts_log /src/htslib/hts.c linenumber=5117 __errno_location linenumber=5118 realloc linenumber=5122 __errno_location linenumber=5124 __errno_location linenumber=5125 strerror linenumber=5125 hts_log /src/htslib/hts.c linenumber=5125 __errno_location linenumber=5126 abort linenumber=5135 abort linenumber=5146 kh_del_vdict /src/htslib/vcf.c linenumber=894 hrec_add_idx /src/htslib/vcf.c linenumber=900 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=499 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=503 strdup linenumber=507 kputw /src/htslib/./htslib/kstring.h linenumber=511 strcmp linenumber=917 strcmp linenumber=918 strtol linenumber=921 hts_log /src/htslib/hts.c linenumber=924 strcmp linenumber=928 strcmp linenumber=930 strcmp linenumber=931 strcmp linenumber=932 strcmp linenumber=933 strcmp linenumber=934 hts_log /src/htslib/hts.c linenumber=937 strcmp linenumber=941 strcmp linenumber=944 strcmp linenumber=945 strcmp linenumber=946 strcmp linenumber=947 strcmp linenumber=948 strcmp linenumber=949 strcmp linenumber=950 strcmp linenumber=951 strcmp linenumber=952 __isoc99_sscanf linenumber=955 hts_log /src/htslib/hts.c linenumber=963 hts_log /src/htslib/hts.c linenumber=968 hts_log /src/htslib/hts.c linenumber=974 strdup linenumber=985 kh_get_vdict /src/htslib/vcf.c linenumber=989 hrec_add_idx /src/htslib/vcf.c linenumber=998 kh_put_vdict /src/htslib/vcf.c linenumber=1004 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=1013 kh_del_vdict /src/htslib/vcf.c linenumber=1014 hrec_add_idx /src/htslib/vcf.c linenumber=1019 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1142 ksprintf /src/htslib/kstring.c linenumber=1146 kh_get_hdict /src/htslib/vcf.c linenumber=1151 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1155 strcmp linenumber=1159 bcf_get_version /src/htslib/vcf.c linenumber=1160 get_hdr_aux /src/htslib/vcf.c linenumber=159 bcf_hdr_get_version /src/htslib/vcf.c linenumber=163 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=1599 ksprintf /src/htslib/kstring.c linenumber=1221 get_hdr_aux /src/htslib/vcf.c linenumber=1222 kh_get_hdict /src/htslib/vcf.c linenumber=1223 strcmp linenumber=1231 strcmp linenumber=1241 ksprintf /src/htslib/kstring.c linenumber=1244 get_hdr_aux /src/htslib/vcf.c linenumber=1245 kh_get_hdict /src/htslib/vcf.c linenumber=1246 strcmp linenumber=1254 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1255 strcmp linenumber=1256 kh_get_vdict /src/htslib/vcf.c linenumber=1261 hts_log /src/htslib/hts.c linenumber=1602 strstr linenumber=168 strchr linenumber=172 strtol linenumber=175 __errno_location linenumber=176 __errno_location linenumber=177 strtol linenumber=181 __errno_location linenumber=182 hts_log /src/htslib/hts.c linenumber=190 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1165 ksprintf /src/htslib/kstring.c linenumber=1167 kh_get_hdict /src/htslib/vcf.c linenumber=1172 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1176 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1184 bcf_hdr_unregister_hrec /src/htslib/vcf.c linenumber=1187 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1033 kh_get_vdict /src/htslib/vcf.c linenumber=1039 kh_put_hdict /src/htslib/vcf.c linenumber=1194 kh_resize_hdict /src/htslib/vcf.c linenumber=80 bcf_hdr_append /src/htslib/vcf.c linenumber=1663 kh_destroy_vdict /src/htslib/vcf.c linenumber=1670 hts_getline /src/htslib/hts.c linenumber=2608 hts_log /src/htslib/hts.c linenumber=2612 hopen /src/htslib/hfile.c linenumber=2617 khgetline /src/htslib/hfile.c linenumber=2622 strchr linenumber=2623 kputs /src/htslib/./htslib/kstring.h linenumber=2625 kputsn /src/htslib/./htslib/kstring.h linenumber=2626 kputs /src/htslib/./htslib/kstring.h linenumber=2627 atol linenumber=2628 kputl /src/htslib/./htslib/kstring.h linenumber=2628 kputll /src/htslib/./htslib/kstring.h linenumber=446 kputsn /src/htslib/./htslib/kstring.h linenumber=2629 hclose /src/htslib/hfile.c linenumber=2632 hts_log /src/htslib/hts.c linenumber=2633 kputsn /src/htslib/./htslib/kstring.h linenumber=2638 kputc /src/htslib/./htslib/kstring.h linenumber=2639 hts_log /src/htslib/hts.c linenumber=2645 bcf_hdr_parse /src/htslib/vcf.c linenumber=2648 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1417 strcasecmp linenumber=1418 hts_log /src/htslib/hts.c linenumber=1419 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1420 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1421 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1426 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1427 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1428 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1434 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1435 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1436 __assert_fail linenumber=1441 __errno_location linenumber=1444 strerror linenumber=1444 hts_log /src/htslib/hts.c linenumber=1444 strncmp linenumber=1459 strchr linenumber=1460 hts_strprint /src/htslib/textutils.c linenumber=1463 hts_log /src/htslib/hts.c linenumber=1463 hts_log /src/htslib/hts.c linenumber=1480 bcf_hdr_parse_sample_line /src/htslib/vcf.c linenumber=1484 strlen linenumber=290 strncmp linenumber=290 hts_log /src/htslib/hts.c linenumber=292 strlen linenumber=296 strncmp linenumber=298 hts_log /src/htslib/hts.c linenumber=300 bcf_hdr_add_sample_len /src/htslib/vcf.c linenumber=310 isspace_c /src/htslib/./textutils_internal.h linenumber=236 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=252 kh_put_vdict /src/htslib/vcf.c linenumber=259 hts_log /src/htslib/hts.c linenumber=268 bcf_hdr_sync /src/htslib/vcf.c linenumber=1486 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=328 get_hdr_aux /src/htslib/vcf.c linenumber=342 bcf_hdr_check_sanity /src/htslib/vcf.c linenumber=1488 bcf_get_version /src/htslib/vcf.c linenumber=1272 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1351 kh_get_vdict /src/htslib/vcf.c linenumber=4626 atoi linenumber=1357 hts_log /src/htslib/hts.c linenumber=1362 hts_log /src/htslib/hts.c linenumber=1367 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1378 atoi linenumber=1393 hts_log /src/htslib/hts.c linenumber=1398 hts_log /src/htslib/hts.c linenumber=1403 tbx_index_load3 /src/htslib/tbx.c linenumber=2651 index_load /src/htslib/tbx.c linenumber=642 calloc linenumber=599 hts_idx_load3 /src/htslib/hts.c linenumber=602 idx_find_and_load /src/htslib/hts.c linenumber=4995 strstr linenumber=4929 strdup linenumber=4933 __errno_location linenumber=4935 strerror linenumber=4935 hts_log /src/htslib/hts.c linenumber=4935 hts_idx_load3 /src/htslib/hts.c linenumber=4940 hisremote /src/htslib/hfile.c linenumber=4999 stat linenumber=5001 hts_log /src/htslib/hts.c linenumber=5004 idx_test_and_fetch /src/htslib/hts.c linenumber=5009 hisremote /src/htslib/hfile.c linenumber=4634 strncmp linenumber=4639 strcspn linenumber=4639 kputsn /src/htslib/./htslib/kstring.h linenumber=4646 access linenumber=4647 hopen /src/htslib/hfile.c linenumber=4656 hts_log /src/htslib/hts.c linenumber=4657 hts_detect_format2 /src/htslib/hts.c linenumber=4661 hts_log /src/htslib/hts.c linenumber=4662 hts_log /src/htslib/hts.c linenumber=4667 hts_open_tmpfile /src/htslib/hts.c linenumber=4672 hts_log /src/htslib/hts.c linenumber=4673 hts_log /src/htslib/hts.c linenumber=4676 calloc linenumber=4677 __errno_location linenumber=4679 strerror linenumber=4679 hts_log /src/htslib/hts.c linenumber=4679 hread /src/htslib/./htslib/hfile.h linenumber=4682 hwrite /src/htslib/./htslib/hfile.h linenumber=4683 __errno_location linenumber=4684 strerror linenumber=4684 hts_log /src/htslib/hts.c linenumber=4684 hts_log /src/htslib/hts.c linenumber=4692 hclose /src/htslib/hfile.c linenumber=4695 __errno_location linenumber=4696 strerror linenumber=4696 hts_log /src/htslib/hts.c linenumber=4696 rename linenumber=4701 __errno_location linenumber=4702 strerror linenumber=4702 hts_log /src/htslib/hts.c linenumber=4702 ks_clear /src/htslib/./htslib/kstring.h linenumber=4705 hclose /src/htslib/hfile.c linenumber=4714 hts_log /src/htslib/hts.c linenumber=4715 hopen /src/htslib/hfile.c linenumber=4723 hclose_abruptly /src/htslib/hfile.c linenumber=4724 strlen linenumber=4726 __errno_location linenumber=4731 hclose_abruptly /src/htslib/hfile.c linenumber=4732 hclose_abruptly /src/htslib/hfile.c linenumber=4733 unlink linenumber=4734 __errno_location linenumber=4737 strdup linenumber=5011 idx_read /src/htslib/hts.c linenumber=5019 bgzf_open /src/htslib/bgzf.c linenumber=2998 ed_is_big /src/htslib/./htslib/hts.h linenumber=3000 bgzf_read /src/htslib/bgzf.c linenumber=3001 memcmp linenumber=3003 bgzf_read /src/htslib/bgzf.c linenumber=3005 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3006 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3009 bgzf_read /src/htslib/bgzf.c linenumber=3010 bgzf_read /src/htslib/bgzf.c linenumber=3014 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3015 hts_idx_init /src/htslib/hts.c linenumber=3017 calloc linenumber=2410 calloc linenumber=2422 calloc linenumber=2424 idx_read_core /src/htslib/hts.c linenumber=3021 ed_is_big /src/htslib/./htslib/hts.h linenumber=2930 kh_init_bin /src/htslib/hts.c linenumber=2938 bgzf_read /src/htslib/bgzf.c linenumber=2939 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2940 bgzf_read /src/htslib/bgzf.c linenumber=2944 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2945 kh_put_bin /src/htslib/hts.c linenumber=2946 bgzf_read /src/htslib/bgzf.c linenumber=2951 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2952 bgzf_read /src/htslib/bgzf.c linenumber=2954 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2955 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2959 bgzf_read /src/htslib/bgzf.c linenumber=2961 swap_bins /src/htslib/hts.c linenumber=2962 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2745 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2746 bgzf_read /src/htslib/bgzf.c linenumber=2967 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2968 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2973 bgzf_read /src/htslib/bgzf.c linenumber=2975 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2976 update_loff /src/htslib/hts.c linenumber=2980 hts_bin_bot /src/htslib/./htslib/hts.h linenumber=2450 hts_bin_level /src/htslib/./htslib/hts.h linenumber=1552 bgzf_read /src/htslib/bgzf.c linenumber=2983 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2984 memcmp linenumber=3023 bgzf_read /src/htslib/bgzf.c linenumber=3027 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3028 hts_idx_init /src/htslib/hts.c linenumber=3030 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3031 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3034 bgzf_read /src/htslib/bgzf.c linenumber=3039 idx_read_core /src/htslib/hts.c linenumber=3042 memcmp linenumber=3044 bgzf_read /src/htslib/bgzf.c linenumber=3046 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3047 hts_idx_init /src/htslib/hts.c linenumber=3049 idx_read_core /src/htslib/hts.c linenumber=3050 __errno_location linenumber=3052 bgzf_close /src/htslib/bgzf.c linenumber=3054 bgzf_close /src/htslib/bgzf.c linenumber=3058 hts_idx_destroy /src/htslib/hts.c linenumber=3059 __errno_location linenumber=5021 strerror linenumber=5021 hts_log /src/htslib/hts.c linenumber=5021 hts_idx_check_local /src/htslib/hts.c linenumber=4945 hisremote /src/htslib/hfile.c linenumber=4772 strlen linenumber=4773 strncmp linenumber=4780 strncmp linenumber=4781 hts_log /src/htslib/hts.c linenumber=4791 strlen linenumber=4792 calloc linenumber=4793 strcpy linenumber=4799 stat linenumber=4800 strcpy linenumber=4806 stat linenumber=4807 strcpy linenumber=4816 stat linenumber=4817 strcpy linenumber=4823 stat linenumber=4824 strcpy linenumber=4832 stat linenumber=4833 strcpy linenumber=4839 stat linenumber=4840 strcpy linenumber=4848 stat linenumber=4849 strcpy linenumber=4855 stat linenumber=4856 strcpy linenumber=4865 strcmp linenumber=4867 strcmp linenumber=4868 strcpy linenumber=4869 stat linenumber=4870 strcpy linenumber=4875 stat linenumber=4877 hisremote /src/htslib/hfile.c linenumber=4945 idx_filename /src/htslib/hts.c linenumber=4947 haddextension /src/htslib/hfile.c linenumber=4894 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=4898 haddextension /src/htslib/hfile.c linenumber=4900 idx_test_and_fetch /src/htslib/hts.c linenumber=4904 idx_filename /src/htslib/hts.c linenumber=4950 idx_filename /src/htslib/hts.c linenumber=4951 idx_filename /src/htslib/hts.c linenumber=4956 idx_filename /src/htslib/hts.c linenumber=4959 idx_filename /src/htslib/hts.c linenumber=4960 hts_log /src/htslib/hts.c linenumber=4968 hts_idx_load3 /src/htslib/hts.c linenumber=4973 idx_read /src/htslib/hts.c linenumber=4975 hts_idx_get_meta /src/htslib/hts.c linenumber=608 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=611 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=612 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=613 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=614 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=615 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=616 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=617 get_tid /src/htslib/tbx.c linenumber=625 kh_init_s2i /src/htslib/hts.c linenumber=71 kh_put_s2i /src/htslib/hts.c linenumber=76 strdup linenumber=80 kh_del_s2i /src/htslib/hts.c linenumber=85 kh_get_s2i /src/htslib/hts.c linenumber=89 __errno_location linenumber=626 strerror linenumber=626 hts_log /src/htslib/hts.c linenumber=626 strlen linenumber=624 hts_log /src/htslib/hts.c linenumber=633 tbx_destroy /src/htslib/tbx.c linenumber=636 hts_idx_destroy /src/htslib/hts.c linenumber=562 kh_destroy_s2i /src/htslib/hts.c linenumber=563 tbx_seqnames /src/htslib/tbx.c linenumber=2655 calloc linenumber=661 calloc linenumber=664 __assert_fail linenumber=674 __assert_fail linenumber=679 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=2659 add_missing_contig_hrec /src/htslib/vcf.c linenumber=2661 calloc linenumber=2573 strdup linenumber=2577 bcf_hrec_add_key /src/htslib/vcf.c linenumber=2580 strlen linenumber=2581 bcf_hrec_set_val /src/htslib/vcf.c linenumber=2581 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=2583 __errno_location linenumber=2588 __errno_location linenumber=2589 strerror linenumber=2589 hts_log /src/htslib/hts.c linenumber=2589 bcf_hrec_destroy /src/htslib/vcf.c linenumber=2590 __errno_location linenumber=2591 bcf_hdr_sync /src/htslib/vcf.c linenumber=2665 tbx_destroy /src/htslib/tbx.c linenumber=2668 tbx_destroy /src/htslib/tbx.c linenumber=2674 bcf_hdr_destroy /src/htslib/vcf.c linenumber=2677 get_hdr_aux /src/htslib/vcf.c linenumber=1680 kh_destroy_hdict /src/htslib/vcf.c linenumber=1695 kh_destroy_vdict /src/htslib/vcf.c linenumber=1698 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1702 hts_log /src/htslib/hts.c linenumber=1716 __assert_fail linenumber=1720 bcf_hdr_init /src/htslib/vcf.c linenumber=1725 hts_log /src/htslib/hts.c linenumber=1727 bgzf_read /src/htslib/bgzf.c linenumber=1730 hts_log /src/htslib/hts.c linenumber=1732 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1733 strncmp linenumber=1736 strncmp linenumber=1738 hts_log /src/htslib/hts.c linenumber=1739 hts_log /src/htslib/hts.c linenumber=1741 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1742 bgzf_read /src/htslib/bgzf.c linenumber=1748 __errno_location linenumber=1750 __errno_location linenumber=1752 bgzf_read /src/htslib/bgzf.c linenumber=1756 bcf_hdr_parse /src/htslib/vcf.c linenumber=1758 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1761 get_hdr_aux /src/htslib/vcf.c linenumber=199 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1762 __assert_fail linenumber=53 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1762 bcf_hdr_decr_ref /src/htslib/vcf.c linenumber=216 get_hdr_aux /src/htslib/vcf.c linenumber=205 bcf_hdr_destroy /src/htslib/vcf.c linenumber=210 hts_log /src/htslib/hts.c linenumber=1766 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1768 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=1775 bcf_hdr_sync /src/htslib/vcf.c linenumber=1779 vcf_hdr_write /src/htslib/vcf.c linenumber=1784 bcf_hdr_format /src/htslib/vcf.c linenumber=2815 _bcf_hrec_format /src/htslib/vcf.c linenumber=2745 ksprintf /src/htslib/kstring.c linenumber=2719 strcmp linenumber=2723 kputc /src/htslib/./htslib/kstring.h linenumber=2724 ksprintf /src/htslib/kstring.c linenumber=2725 ksprintf /src/htslib/kstring.c linenumber=2728 ksprintf /src/htslib/kstring.c linenumber=2731 ksprintf /src/htslib/kstring.c linenumber=2747 ksprintf /src/htslib/kstring.c linenumber=2750 ksprintf /src/htslib/kstring.c linenumber=2752 ksprintf /src/htslib/kstring.c linenumber=2754 bgzf_write /src/htslib/bgzf.c linenumber=2822 bgzf_flush /src/htslib/bgzf.c linenumber=2823 hwrite /src/htslib/./htslib/hfile.h linenumber=2825 bcf_hdr_format /src/htslib/vcf.c linenumber=1791 kputc /src/htslib/./htslib/kstring.h linenumber=1795 bgzf_write /src/htslib/bgzf.c linenumber=1798 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1800 bgzf_write /src/htslib/bgzf.c linenumber=1801 bgzf_write /src/htslib/bgzf.c linenumber=1802 bgzf_flush /src/htslib/bgzf.c linenumber=1803 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1805 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1806 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1806 bcf_init /src/htslib/vcf.c linenumber=155 calloc linenumber=1819 bcf_read /src/htslib/vcf.c linenumber=159 vcf_read /src/htslib/vcf.c linenumber=2259 hts_getline /src/htslib/hts.c linenumber=4174 vcf_parse /src/htslib/vcf.c linenumber=4176 ks_resize /src/htslib/./htslib/kstring.h linenumber=4011 bcf_clear /src/htslib/vcf.c linenumber=4024 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=1843 kstrtok /src/htslib/kstring.c linenumber=4029 kh_get_vdict /src/htslib/vcf.c linenumber=4034 hts_log /src/htslib/hts.c linenumber=4036 fix_chromosome /src/htslib/vcf.c linenumber=4038 ksprintf /src/htslib/kstring.c linenumber=3752 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3754 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3756 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3757 bcf_hdr_sync /src/htslib/vcf.c linenumber=3758 kh_get_vdict /src/htslib/vcf.c linenumber=3759 hts_log /src/htslib/hts.c linenumber=4039 kstrtok /src/htslib/kstring.c linenumber=4047 hts_str2uint /src/htslib/./textutils_internal.h linenumber=4053 hts_log /src/htslib/hts.c linenumber=4055 hts_log /src/htslib/hts.c linenumber=4058 kstrtok /src/htslib/kstring.c linenumber=4067 memcmp linenumber=4071 bcf_enc_vchar /src/htslib/vcf.c linenumber=4071 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2973 ks_resize /src/htslib/./htslib/kstring.h linenumber=1576 ks_resize /src/htslib/./htslib/kstring.h linenumber=1584 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1596 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1600 kputsn /src/htslib/./htslib/kstring.h linenumber=2974 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=4072 kstrtok /src/htslib/kstring.c linenumber=4075 bcf_enc_vchar /src/htslib/vcf.c linenumber=4079 kstrtok /src/htslib/kstring.c linenumber=4083 memcmp linenumber=4087 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4091 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=4091 bcf_enc_vchar /src/htslib/vcf.c linenumber=4096 kstrtok /src/htslib/kstring.c linenumber=4105 memcmp linenumber=4109 atof linenumber=4109 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4110 kstrtok /src/htslib/kstring.c linenumber=4114 memcmp linenumber=4118 vcf_parse_filter /src/htslib/vcf.c linenumber=4119 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3776 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3778 hts_log /src/htslib/hts.c linenumber=3778 kstrtok /src/htslib/kstring.c linenumber=3785 kh_get_vdict /src/htslib/vcf.c linenumber=3787 hts_log /src/htslib/hts.c linenumber=3792 ksprintf /src/htslib/kstring.c linenumber=3795 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3796 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3798 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3799 bcf_hdr_sync /src/htslib/vcf.c linenumber=3800 kh_get_vdict /src/htslib/vcf.c linenumber=3801 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3804 hts_log /src/htslib/hts.c linenumber=3804 bcf_enc_vint /src/htslib/vcf.c linenumber=3813 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2840 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=2842 ks_resize /src/htslib/./htslib/kstring.h linenumber=1616 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1636 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1640 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2882 ks_resize /src/htslib/./htslib/kstring.h linenumber=2883 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2894 ks_resize /src/htslib/./htslib/kstring.h linenumber=2895 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2904 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2910 ks_resize /src/htslib/./htslib/kstring.h linenumber=2911 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2915 bcf_enc_vint /src/htslib/vcf.c linenumber=4122 kstrtok /src/htslib/kstring.c linenumber=4126 memcmp linenumber=4130 vcf_parse_info /src/htslib/vcf.c linenumber=4131 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3834 kh_get_vdict /src/htslib/vcf.c linenumber=3848 hts_log /src/htslib/hts.c linenumber=3851 ksprintf /src/htslib/kstring.c linenumber=3854 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3855 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3857 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3858 bcf_hdr_sync /src/htslib/vcf.c linenumber=3859 kh_get_vdict /src/htslib/vcf.c linenumber=3860 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3863 hts_log /src/htslib/hts.c linenumber=3863 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3870 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3872 bcf_enc_vchar /src/htslib/vcf.c linenumber=3874 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3882 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3884 hts_log /src/htslib/hts.c linenumber=3884 hts_str2int /src/htslib/./textutils_internal.h linenumber=3920 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3926 hts_log /src/htslib/hts.c linenumber=3926 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3945 bcf_enc_vint /src/htslib/vcf.c linenumber=3948 memcmp linenumber=3951 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3957 hts_log /src/htslib/hts.c linenumber=3957 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3967 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3969 bcf_enc_vfloat /src/htslib/vcf.c linenumber=3972 __assert_fail linenumber=2965 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2966 serialize_float_array /src/htslib/vcf.c linenumber=2967 ks_resize /src/htslib/./htslib/kstring.h linenumber=2951 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2955 kstrtok /src/htslib/kstring.c linenumber=4138 vcf_parse_format /src/htslib/vcf.c linenumber=4142 vcf_parse_format_empty1 /src/htslib/vcf.c linenumber=3698 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3143 hts_log /src/htslib/hts.c linenumber=3143 vcf_parse_format_dict2 /src/htslib/vcf.c linenumber=3702 kstrtok /src/htslib/kstring.c linenumber=3166 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3169 hts_log /src/htslib/hts.c linenumber=3169 kh_get_vdict /src/htslib/vcf.c linenumber=3175 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3179 hts_log /src/htslib/hts.c linenumber=3179 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3183 hts_log /src/htslib/hts.c linenumber=3183 ksprintf /src/htslib/kstring.c linenumber=3186 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3187 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3189 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3190 bcf_hdr_sync /src/htslib/vcf.c linenumber=3191 kh_get_vdict /src/htslib/vcf.c linenumber=3193 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3196 hts_log /src/htslib/hts.c linenumber=3196 vcf_parse_format_max3 /src/htslib/vcf.c linenumber=3723 hts_log /src/htslib/hts.c linenumber=3277 vcf_parse_format_alloc4 /src/htslib/vcf.c linenumber=3727 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3313 hts_log /src/htslib/hts.c linenumber=3313 align_mem /src/htslib/vcf.c linenumber=3318 kputsn /src/htslib/./htslib/kstring.h linenumber=3130 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3319 hts_log /src/htslib/hts.c linenumber=3319 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3329 hts_log /src/htslib/hts.c linenumber=3329 ks_resize /src/htslib/./htslib/kstring.h linenumber=3338 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3339 hts_log /src/htslib/hts.c linenumber=3339 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3364 hts_log /src/htslib/hts.c linenumber=3364 vcf_parse_format_fill5 /src/htslib/vcf.c linenumber=3731 bcf_get_version /src/htslib/vcf.c linenumber=3386 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3409 hts_log /src/htslib/hts.c linenumber=3409 hts_str2uint /src/htslib/./textutils_internal.h linenumber=3457 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3482 hts_log /src/htslib/hts.c linenumber=3482 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3486 hts_log /src/htslib/hts.c linenumber=3486 hts_str2int /src/htslib/./textutils_internal.h linenumber=3512 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3517 hts_log /src/htslib/hts.c linenumber=3517 isdigit_c /src/htslib/./textutils_internal.h linenumber=3538 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3539 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3543 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=3546 hts_log /src/htslib/hts.c linenumber=3546 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3556 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3558 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3560 hts_log /src/htslib/hts.c linenumber=3560 hts_strprint /src/htslib/textutils.c linenumber=3573 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3573 hts_log /src/htslib/hts.c linenumber=3573 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3608 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3609 vcf_parse_format_gt6 /src/htslib/vcf.c linenumber=3735 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3631 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3633 kputsn /src/htslib/./htslib/kstring.h linenumber=3634 bcf_enc_vint /src/htslib/vcf.c linenumber=3636 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3638 serialize_float_array /src/htslib/vcf.c linenumber=3639 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3642 hts_log /src/htslib/hts.c linenumber=3642 vcf_parse_format_check7 /src/htslib/vcf.c linenumber=3739 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3668 hts_log /src/htslib/hts.c linenumber=3668 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3675 hts_log /src/htslib/hts.c linenumber=3675 get_rlen /src/htslib/vcf.c linenumber=4148 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6454 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6465 strlen linenumber=186 memcmp linenumber=191 memcmp linenumber=192 memcmp linenumber=193 memcmp linenumber=194 strcmp linenumber=6469 strcmp linenumber=6470 strlen linenumber=6475 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6478 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=1708 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=1699 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=1666 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1669 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1672 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=1675 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=263 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6483 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6487 strncmp linenumber=6491 strncmp linenumber=6492 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6503 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6508 bcf_get_info /src/htslib/vcf.c linenumber=6513 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6061 bcf_get_info_id /src/htslib/vcf.c linenumber=6063 bcf_unpack /src/htslib/vcf.c linenumber=6080 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4250 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=3085 bcf_fmt_array /src/htslib/vcf.c linenumber=3086 kputc_ /src/htslib/./htslib/kstring.h linenumber=3042 memchr linenumber=3051 kputsn /src/htslib/./htslib/kstring.h linenumber=3052 kputc /src/htslib/./htslib/kstring.h linenumber=3055 le_to_i8 /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_i16 /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_i32 /src/htslib/./htslib/hts_endian.h linenumber=3073 kputc_ /src/htslib/./htslib/kstring.h linenumber=3073 kputc /src/htslib/./htslib/kstring.h linenumber=3073 kputw /src/htslib/./htslib/kstring.h linenumber=3073 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3074 kputc_ /src/htslib/./htslib/kstring.h linenumber=3074 kputc /src/htslib/./htslib/kstring.h linenumber=3074 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3074 kputd /src/htslib/kstring.c linenumber=3074 hts_log /src/htslib/hts.c linenumber=3075 exit linenumber=3075 kputc_ /src/htslib/./htslib/kstring.h linenumber=4252 hts_realloc_or_die /src/htslib/hts.c linenumber=4256 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4262 kputc_ /src/htslib/./htslib/kstring.h linenumber=4263 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4278 hts_realloc_or_die /src/htslib/hts.c linenumber=4279 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=4281 hts_realloc_or_die /src/htslib/hts.c linenumber=4288 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=4291 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4197 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4198 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=4210 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=4214 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=4218 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=4222 hts_realloc_or_die /src/htslib/hts.c linenumber=4296 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=4299 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4182 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4183 bcf_get_info /src/htslib/vcf.c linenumber=6514 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6517 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6519 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6525 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6532 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6541 bcf_get_fmt /src/htslib/vcf.c linenumber=6548 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6054 bcf_get_fmt_id /src/htslib/vcf.c linenumber=6056 bcf_unpack /src/htslib/vcf.c linenumber=6069 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6551 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=6553 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6558 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6588 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6592 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6596 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6600 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6632 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6636 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6640 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6644 bgzf_get_private_data /src/htslib/./bgzf_internal.h linenumber=2261 __assert_fail linenumber=68 bcf_read1_core /src/htslib/vcf.c linenumber=2262 bgzf_read /src/htslib/bgzf.c linenumber=1880 bcf_clear /src/htslib/vcf.c linenumber=1884 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1885 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1888 ks_resize /src/htslib/./htslib/kstring.h linenumber=1893 ks_resize /src/htslib/./htslib/kstring.h linenumber=1894 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1895 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1896 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1898 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1899 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1900 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1901 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1902 bgzf_read /src/htslib/bgzf.c linenumber=1909 bgzf_read /src/htslib/bgzf.c linenumber=1910 bcf_record_check /src/htslib/vcf.c linenumber=2263 bcf_get_version /src/htslib/vcf.c linenumber=2063 bcf_hdr_id2int /src/htslib/vcf.c linenumber=2064 hts_log /src/htslib/hts.c linenumber=2071 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2078 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=1961 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1931 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1934 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2080 get_type_name /src/htslib/vcf.c linenumber=2080 hts_log /src/htslib/hts.c linenumber=2080 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2089 hts_log /src/htslib/hts.c linenumber=2089 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2096 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2099 get_type_name /src/htslib/vcf.c linenumber=2099 hts_log /src/htslib/hts.c linenumber=2099 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2109 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2113 get_type_name /src/htslib/vcf.c linenumber=2113 hts_log /src/htslib/hts.c linenumber=2113 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=2120 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2125 hts_log /src/htslib/hts.c linenumber=2125 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2137 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2141 hts_log /src/htslib/hts.c linenumber=2141 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2144 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2148 get_type_name /src/htslib/vcf.c linenumber=2148 hts_log /src/htslib/hts.c linenumber=2148 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2162 bcf_record_check_err /src/htslib/vcf.c linenumber=2166 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2035 hts_log /src/htslib/hts.c linenumber=2035 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2169 bcf_record_check_err /src/htslib/vcf.c linenumber=2172 updatephasing /src/htslib/vcf.c linenumber=2177 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2192 hts_log /src/htslib/hts.c linenumber=2192 get_rlen /src/htslib/vcf.c linenumber=2198 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2207 hts_log /src/htslib/hts.c linenumber=2207 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2211 hts_log /src/htslib/hts.c linenumber=2211 bcf_subset_format /src/htslib/vcf.c linenumber=2265 hts_realloc_or_die /src/htslib/hts.c linenumber=2228 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=2233 bcf_write /src/htslib/vcf.c linenumber=160 bcf_hdr_sync /src/htslib/vcf.c linenumber=2514 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2518 vcf_write /src/htslib/vcf.c linenumber=2524 vcf_format /src/htslib/vcf.c linenumber=4592 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=4309 hts_log /src/htslib/hts.c linenumber=4311 __errno_location linenumber=4313 bcf_unpack /src/htslib/vcf.c linenumber=4317 get_hdr_aux /src/htslib/vcf.c linenumber=4328 calloc linenumber=4330 kputs /src/htslib/./htslib/kstring.h linenumber=4335 kputs /src/htslib/./htslib/kstring.h linenumber=4337 kputc_ /src/htslib/./htslib/kstring.h linenumber=4338 kputs /src/htslib/./htslib/kstring.h linenumber=4339 kputc_ /src/htslib/./htslib/kstring.h linenumber=4340 kputc_ /src/htslib/./htslib/kstring.h linenumber=4341 kputc_ /src/htslib/./htslib/kstring.h linenumber=4344 kputs /src/htslib/./htslib/kstring.h linenumber=4345 kputc_ /src/htslib/./htslib/kstring.h linenumber=4347 kputc_ /src/htslib/./htslib/kstring.h linenumber=4348 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4349 kputc_ /src/htslib/./htslib/kstring.h linenumber=4349 kputd /src/htslib/kstring.c linenumber=4350 kputc_ /src/htslib/./htslib/kstring.h linenumber=4351 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4357 hts_log /src/htslib/hts.c linenumber=4357 __errno_location linenumber=4359 kputc_ /src/htslib/./htslib/kstring.h linenumber=4362 strlen linenumber=4364 kputsn /src/htslib/./htslib/kstring.h linenumber=4365 kputc_ /src/htslib/./htslib/kstring.h linenumber=4367 kputc_ /src/htslib/./htslib/kstring.h linenumber=4369 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4389 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4390 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4406 hts_log /src/htslib/hts.c linenumber=4406 __errno_location linenumber=4411 strlen linenumber=4417 ks_resize /src/htslib/./htslib/kstring.h linenumber=4419 bcf_fmt_array /src/htslib/vcf.c linenumber=4436 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4441 kputc_ /src/htslib/./htslib/kstring.h linenumber=4442 kputd /src/htslib/kstring.c linenumber=4444 kputc_ /src/htslib/./htslib/kstring.h linenumber=4446 kputc_ /src/htslib/./htslib/kstring.h linenumber=4455 kputw /src/htslib/./htslib/kstring.h linenumber=4457 kputc_ /src/htslib/./htslib/kstring.h linenumber=4460 kputll /src/htslib/./htslib/kstring.h linenumber=4462 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4464 hts_log /src/htslib/hts.c linenumber=4464 __errno_location linenumber=4465 kputc_ /src/htslib/./htslib/kstring.h linenumber=4470 kputc_ /src/htslib/./htslib/kstring.h linenumber=4471 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=4490 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4500 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4501 kputc_ /src/htslib/./htslib/kstring.h linenumber=4507 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4514 hts_log /src/htslib/hts.c linenumber=4514 __errno_location linenumber=4515 strlen linenumber=4522 kputsn /src/htslib/./htslib/kstring.h linenumber=4524 kputsn /src/htslib/./htslib/kstring.h linenumber=4528 kputc_ /src/htslib/./htslib/kstring.h linenumber=4532 kputc_ /src/htslib/./htslib/kstring.h linenumber=4537 bcf_format_gt_v2 /src/htslib/vcf.c linenumber=4540 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6392 kputc /src/htslib/./htslib/kstring.h linenumber=6392 kputw /src/htslib/./htslib/kstring.h linenumber=6392 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6394 kputc /src/htslib/./htslib/kstring.h linenumber=6394 kputw /src/htslib/./htslib/kstring.h linenumber=6394 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6396 kputc /src/htslib/./htslib/kstring.h linenumber=6396 kputw /src/htslib/./htslib/kstring.h linenumber=6396 kputc /src/htslib/./htslib/kstring.h linenumber=6398 hts_log /src/htslib/hts.c linenumber=6399 get_hdr_aux /src/htslib/vcf.c linenumber=6403 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6413 ks_resize /src/htslib/./htslib/kstring.h linenumber=474 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6415 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6422 hts_log /src/htslib/hts.c linenumber=4541 __errno_location linenumber=4542 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4550 kputc_ /src/htslib/./htslib/kstring.h linenumber=2992 kputc_ /src/htslib/./htslib/kstring.h linenumber=2998 kputw /src/htslib/./htslib/kstring.h linenumber=2999 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3003 kputc_ /src/htslib/./htslib/kstring.h linenumber=3006 kputw /src/htslib/./htslib/kstring.h linenumber=3007 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3012 kputc_ /src/htslib/./htslib/kstring.h linenumber=3015 kputw /src/htslib/./htslib/kstring.h linenumber=3016 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3021 kputc_ /src/htslib/./htslib/kstring.h linenumber=3024 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3025 kputd /src/htslib/kstring.c linenumber=3025 hts_log /src/htslib/hts.c linenumber=3030 bcf_fmt_array /src/htslib/vcf.c linenumber=4552 kputc_ /src/htslib/./htslib/kstring.h linenumber=4558 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4560 bcf_fmt_array /src/htslib/vcf.c linenumber=4562 kputc_ /src/htslib/./htslib/kstring.h linenumber=4564 kputsn /src/htslib/./htslib/kstring.h linenumber=4571 kputc /src/htslib/./htslib/kstring.h linenumber=4573 bgzf_flush_try /src/htslib/bgzf.c linenumber=4595 hts_idx_amend_last /src/htslib/hts.c linenumber=4598 bgzf_write /src/htslib/bgzf.c linenumber=4599 hwrite /src/htslib/./htslib/hfile.h linenumber=4601 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4606 hts_idx_tbi_name /src/htslib/hts.c linenumber=4606 strlen linenumber=2657 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=2658 strcpy linenumber=2664 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=2668 u32_to_le /src/htslib/./cram/../htslib/hts_endian.h linenumber=2668 bgzf_idx_push /src/htslib/bgzf.c linenumber=4609 bcf_strerror /src/htslib/vcf.c linenumber=2533 add_desc_to_buffer /src/htslib/vcf.c linenumber=6340 strlen linenumber=6314 snprintf linenumber=6315 snprintf linenumber=6318 add_desc_to_buffer /src/htslib/vcf.c linenumber=6349 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2533 hts_log /src/htslib/hts.c linenumber=2533 bcf1_sync /src/htslib/vcf.c linenumber=2536 bcf1_sync_id /src/htslib/vcf.c linenumber=2343 strcmp linenumber=2282 strlen linenumber=2283 bcf_enc_vchar /src/htslib/vcf.c linenumber=2283 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2285 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2346 strlen linenumber=2293 bcf_enc_vchar /src/htslib/vcf.c linenumber=2293 strlen linenumber=2296 bcf1_sync_filter /src/htslib/vcf.c linenumber=2349 bcf_enc_vint /src/htslib/vcf.c linenumber=2303 bcf_enc_vint /src/htslib/vcf.c linenumber=2305 bcf1_sync_info /src/htslib/vcf.c linenumber=2352 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2322 bcf_unpack /src/htslib/vcf.c linenumber=2359 bcf1_sync_id /src/htslib/vcf.c linenumber=2366 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2368 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2374 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2377 strlen linenumber=2378 bcf1_sync_filter /src/htslib/vcf.c linenumber=2387 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2389 bcf_enc_vint /src/htslib/vcf.c linenumber=2391 bcf1_sync_info /src/htslib/vcf.c linenumber=2400 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2407 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2444 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2540 hts_log /src/htslib/hts.c linenumber=2540 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2546 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2547 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2548 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2549 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2550 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2551 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2552 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2553 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2554 bgzf_write /src/htslib/bgzf.c linenumber=2555 bgzf_write /src/htslib/bgzf.c linenumber=2556 bgzf_write /src/htslib/bgzf.c linenumber=2557 bgzf_idx_push /src/htslib/bgzf.c linenumber=2560 bcf_destroy /src/htslib/vcf.c linenumber=163 bcf_empty /src/htslib/vcf.c linenumber=1871 bcf_clear /src/htslib/vcf.c linenumber=1857 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 ====================================