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=5292 cram_read_file_def /src/htslib/cram/cram_io.c linenumber=5312 hread /src/htslib/cram/../htslib/hfile.h linenumber=4667 memcmp linenumber=4672 hts_log /src/htslib/hts.c linenumber=4678 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5318 cram_init_varint /src/htslib/cram/cram_io.c linenumber=5250 cram_read_SAM_hdr /src/htslib/cram/cram_io.c linenumber=5320 int32_decode /src/htslib/cram/cram_io.c linenumber=4725 hread /src/htslib/cram/../htslib/hfile.h linenumber=1008 hread /src/htslib/cram/../htslib/hfile.h linenumber=4737 cram_read_container /src/htslib/cram/cram_io.c linenumber=4745 int32_decode /src/htslib/cram/cram_io.c linenumber=3807 crc32 linenumber=3818 calloc linenumber=3878 __errno_location linenumber=3884 cram_free_container /src/htslib/cram/cram_io.c linenumber=3885 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=3719 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=4365 cram_free_block /src/htslib/cram/cram_io.c linenumber=4395 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4397 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4399 cram_free_block /src/htslib/cram/cram_io.c linenumber=3722 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3728 cram_free_block /src/htslib/cram/cram_io.c linenumber=4426 cram_free_block /src/htslib/cram/cram_io.c linenumber=4435 cram_free_block /src/htslib/cram/cram_io.c linenumber=4446 cram_free_slice_header /src/htslib/cram/cram_io.c linenumber=4453 cram_free_block /src/htslib/cram/cram_io.c linenumber=4456 cram_free_block /src/htslib/cram/cram_io.c linenumber=4459 cram_free_block /src/htslib/cram/cram_io.c linenumber=4462 cram_free_block /src/htslib/cram/cram_io.c linenumber=4465 cram_free_block /src/htslib/cram/cram_io.c linenumber=4468 cram_free_block /src/htslib/cram/cram_io.c linenumber=4471 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4486 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4489 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4491 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3737 cram_stats_free /src/htslib/cram/cram_stats.c linenumber=3742 kh_destroy_m_i2i /src/htslib/cram/cram_structs.h linenumber=226 cram_free_block /src/htslib/cram/cram_io.c linenumber=3764 cram_free_block /src/htslib/cram/cram_io.c linenumber=3765 kh_destroy_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3770 free_bam_list /src/htslib/cram/cram_io.c linenumber=3777 bam_destroy1 /src/htslib/sam.c linenumber=3700 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=473 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=475 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=483 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3889 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=3890 cram_free_container /src/htslib/cram/cram_io.c linenumber=3891 cram_free_container /src/htslib/cram/cram_io.c linenumber=3896 int32_decode /src/htslib/cram/cram_io.c linenumber=3904 cram_free_container /src/htslib/cram/cram_io.c linenumber=3905 hts_log /src/htslib/hts.c linenumber=3917 cram_free_container /src/htslib/cram/cram_io.c linenumber=3918 cram_free_container /src/htslib/cram/cram_io.c linenumber=4757 cram_read_block /src/htslib/cram/cram_io.c linenumber=4761 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1424 hts_log /src/htslib/hts.c linenumber=1426 crc32 linenumber=1429 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1430 crc32 linenumber=1431 hread /src/htslib/cram/../htslib/hfile.h linenumber=1446 hread /src/htslib/cram/../htslib/hfile.h linenumber=1458 int32_decode /src/htslib/cram/cram_io.c linenumber=1466 cram_free_container /src/htslib/cram/cram_io.c linenumber=4762 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=4765 crc32 linenumber=1587 hts_log /src/htslib/hts.c linenumber=1590 __assert_fail linenumber=1600 zlib_mem_inflate /src/htslib/cram/cram_io.c linenumber=1608 inflateInit2_ linenumber=1181 hts_log /src/htslib/hts.c linenumber=1183 inflate linenumber=1194 hts_log /src/htslib/hts.c linenumber=1199 inflateEnd linenumber=1201 realloc linenumber=1207 inflateEnd linenumber=1210 inflateEnd linenumber=1215 BZ2_bzBuffToBuffDecompress linenumber=1627 lzma_mem_inflate /src/htslib/cram/cram_io.c linenumber=1648 lzma_easy_decoder_memusage linenumber=1321 lzma_stream_decoder linenumber=1321 realloc linenumber=1331 lzma_code linenumber=1339 hts_log /src/htslib/hts.c linenumber=1341 lzma_code linenumber=1352 hts_log /src/htslib/hts.c linenumber=1354 realloc linenumber=1358 lzma_end linenumber=1363 lzma_end linenumber=1368 rans_uncompress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1669 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=1687 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=1700 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=1719 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=1738 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=4766 cram_free_block /src/htslib/cram/cram_io.c linenumber=4767 int32_get_blk /src/htslib/cram/cram_io.c linenumber=4777 cram_free_container /src/htslib/cram/cram_io.c linenumber=4780 cram_free_block /src/htslib/cram/cram_io.c linenumber=4781 cram_free_container /src/htslib/cram/cram_io.c linenumber=4785 cram_free_block /src/htslib/cram/cram_io.c linenumber=4786 cram_free_block /src/htslib/cram/cram_io.c linenumber=4791 cram_read_block /src/htslib/cram/cram_io.c linenumber=4795 cram_free_container /src/htslib/cram/cram_io.c linenumber=4796 cram_free_block /src/htslib/cram/cram_io.c linenumber=4804 cram_free_container /src/htslib/cram/cram_io.c linenumber=4811 hread /src/htslib/cram/../htslib/hfile.h linenumber=4816 cram_free_container /src/htslib/cram/cram_io.c linenumber=4817 cram_free_container /src/htslib/cram/cram_io.c linenumber=4825 sam_hdr_init /src/htslib/sam.c linenumber=4829 calloc linenumber=111 sam_hdr_add_lines /src/htslib/header.c linenumber=4835 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=4837 sam_hrecs_free /src/htslib/header.c linenumber=137 kh_destroy_s2i /src/htslib/hts.c linenumber=139 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5321 calloc linenumber=5327 strncpy linenumber=5340 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5343 strrchr linenumber=5348 strdup linenumber=5348 refs_create /src/htslib/cram/cram_io.c linenumber=5356 calloc linenumber=2469 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2476 kh_init_refs /src/htslib/cram/cram_structs.h linenumber=2484 calloc linenumber=686 pthread_mutex_init linenumber=2487 refs_free /src/htslib/cram/cram_io.c linenumber=2492 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2438 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2450 mfclose /src/htslib/cram/mFILE.c linenumber=2420 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=2454 bgzf_close /src/htslib/bgzf.c linenumber=2461 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=2363 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=2463 pthread_mutex_init linenumber=5392 pthread_mutex_init linenumber=5393 pthread_mutex_init linenumber=5394 pthread_mutex_init linenumber=5395 cram_new_metrics /src/htslib/cram/cram_io.c linenumber=5398 calloc linenumber=2329 kh_init_m_metrics /src/htslib/cram/cram_structs.h linenumber=5403 calloc linenumber=308 refs_from_header /src/htslib/cram/cram_io.c linenumber=5413 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2782 hts_realloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=2792 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2806 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=686 strcmp linenumber=686 calloc linenumber=2811 string_dup /src/htslib/cram/string_alloc.c linenumber=2817 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2822 sam_hrecs_find_key /src/htslib/header.c linenumber=2823 string_dup /src/htslib/cram/string_alloc.c linenumber=2824 sam_hrecs_find_key /src/htslib/header.c linenumber=2826 strtoll linenumber=2828 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2835 kh_resize_refs /src/htslib/cram/cram_structs.h linenumber=686 realloc linenumber=686 cram_set_option /src/htslib/cram/cram_io.c linenumber=1585 cram_set_voption /src/htslib/cram/cram_io.c linenumber=5681 __errno_location linenumber=5698 strdup linenumber=5710 refs_free /src/htslib/cram/cram_io.c linenumber=5786 cram_seek_to_refpos /src/htslib/cram/cram_index.c linenumber=5793 cram_index_query /src/htslib/cram/cram_index.c linenumber=582 cram_seek /src/htslib/cram/cram_io.c linenumber=583 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5434 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3640 pthread_mutex_lock linenumber=262 pthread_mutex_unlock linenumber=264 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3641 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=3644 cram_free_container /src/htslib/cram/cram_io.c linenumber=3653 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3657 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3658 cram_free_container /src/htslib/cram/cram_io.c linenumber=3673 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3677 cram_free_container /src/htslib/cram/cram_io.c linenumber=3687 hseek /src/htslib/hfile.c linenumber=5436 pthread_mutex_lock linenumber=591 pthread_mutex_unlock linenumber=599 cram_free_container /src/htslib/cram/cram_io.c linenumber=602 cram_free_container /src/htslib/cram/cram_io.c linenumber=604 pthread_mutex_lock linenumber=616 pthread_mutex_unlock linenumber=618 pthread_mutex_lock linenumber=5794 pthread_mutex_unlock linenumber=5799 pthread_mutex_lock linenumber=5805 pthread_mutex_unlock linenumber=5818 cram_load_reference /src/htslib/cram/cram_io.c linenumber=5823 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3603 strlen linenumber=2547 refs_create /src/htslib/cram/cram_io.c linenumber=2553 bgzf_close /src/htslib/bgzf.c linenumber=2557 strstr linenumber=2562 string_ndup /src/htslib/cram/string_alloc.c linenumber=2564 snprintf linenumber=2567 strcmp linenumber=2570 string_ndup /src/htslib/cram/string_alloc.c linenumber=2572 snprintf linenumber=2575 string_dup /src/htslib/cram/string_alloc.c linenumber=2578 snprintf linenumber=2580 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=2584 strncmp linenumber=2507 hisremote /src/htslib/hfile.c linenumber=2510 find_scheme_handler /src/htslib/hfile.c linenumber=1347 snprintf linenumber=2513 access linenumber=2514 fai_build /src/htslib/faidx.c linenumber=2515 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=2349 calloc linenumber=2350 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=2288 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=2293 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=2429 __errno_location linenumber=2430 get_name_suffix /src/htslib/bgzf.c linenumber=2436 strlen linenumber=2381 snprintf linenumber=2384 hopen /src/htslib/hfile.c linenumber=2441 bgzf_index_dump_hfile /src/htslib/bgzf.c linenumber=2447 hts_log /src/htslib/hts.c linenumber=2397 __errno_location linenumber=2398 bgzf_flush /src/htslib/bgzf.c linenumber=2402 hwrite_uint64 /src/htslib/bgzf.c linenumber=2408 ed_is_big /src/htslib/./htslib/hts.h linenumber=2374 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2374 hwrite /src/htslib/./htslib/hfile.h linenumber=2375 hwrite_uint64 /src/htslib/bgzf.c linenumber=2412 hwrite_uint64 /src/htslib/bgzf.c linenumber=2413 __errno_location linenumber=2418 strerror linenumber=2418 hts_log /src/htslib/hts.c linenumber=2418 hclose /src/htslib/hfile.c linenumber=2449 __errno_location linenumber=2461 strerror linenumber=2461 hts_log /src/htslib/hts.c linenumber=2461 hclose_abruptly /src/htslib/hfile.c linenumber=2463 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=2519 perror linenumber=2520 bgzf_index_load /src/htslib/bgzf.c linenumber=2524 get_name_suffix /src/htslib/bgzf.c linenumber=2516 hopen /src/htslib/hfile.c linenumber=2521 bgzf_index_load_hfile /src/htslib/bgzf.c linenumber=2527 calloc linenumber=2477 hread_uint64 /src/htslib/bgzf.c linenumber=2480 hread /src/htslib/./htslib/hfile.h linenumber=2470 ed_is_big /src/htslib/./htslib/hts.h linenumber=2471 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2471 hread_uint64 /src/htslib/bgzf.c linenumber=2493 hread_uint64 /src/htslib/bgzf.c linenumber=2494 __errno_location linenumber=2500 strerror linenumber=2500 hts_log /src/htslib/hts.c linenumber=2500 hclose /src/htslib/hfile.c linenumber=2529 __errno_location linenumber=2540 strerror linenumber=2540 hts_log /src/htslib/hts.c linenumber=2540 hclose_abruptly /src/htslib/hfile.c linenumber=2542 hts_log /src/htslib/hts.c linenumber=2525 bgzf_close /src/htslib/bgzf.c linenumber=2526 hts_log /src/htslib/hts.c linenumber=2585 hopen /src/htslib/hfile.c linenumber=2589 hts_log /src/htslib/hts.c linenumber=2590 perror linenumber=2592 hgets /src/htslib/hfile.c linenumber=2595 __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=2605 string_dup /src/htslib/cram/string_alloc.c linenumber=2608 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2611 strtoll linenumber=2613 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2616 strtoll linenumber=2618 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2621 strtol linenumber=2623 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2626 strtol linenumber=2628 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2639 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2665 hclose /src/htslib/hfile.c linenumber=2677 hclose_abruptly /src/htslib/hfile.c linenumber=2683 refs_free /src/htslib/cram/cram_io.c linenumber=2686 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3608 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2705 strcmp linenumber=2717 __assert_fail linenumber=2717 hts_log /src/htslib/hts.c linenumber=2721 refs_free /src/htslib/cram/cram_io.c linenumber=3614 refs_create /src/htslib/cram/cram_io.c linenumber=3615 refs_from_header /src/htslib/cram/cram_io.c linenumber=3617 refs2id /src/htslib/cram/cram_io.c linenumber=3622 calloc linenumber=2747 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2753 hts_log /src/htslib/hts.c linenumber=2757 __isoc99_sscanf linenumber=5828 hts_log /src/htslib/hts.c linenumber=5829 hts_log /src/htslib/hts.c linenumber=5836 __errno_location linenumber=5837 hts_log /src/htslib/hts.c linenumber=5842 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5855 hts_tpool_init /src/htslib/thread_pool.c linenumber=5869 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=5872 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=5886 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5885 hts_log /src/htslib/hts.c linenumber=5952 __errno_location linenumber=5953 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=3753 sam_set_thread_pool /src/htslib/sam.c linenumber=3756 sam_state_create /src/htslib/sam.c linenumber=3725 calloc linenumber=3057 pthread_mutex_init linenumber=3729 pthread_mutex_init linenumber=3730 pthread_cond_init linenumber=3731 hts_tpool_size /src/htslib/thread_pool.c linenumber=3735 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=3736 sam_state_destroy /src/htslib/sam.c linenumber=3738 pthread_mutex_lock linenumber=3103 pthread_cond_signal linenumber=3106 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3109 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3116 pthread_mutex_unlock linenumber=3117 hts_usleep /src/htslib/./hts_internal.h linenumber=3118 pthread_mutex_lock linenumber=3119 pthread_mutex_unlock linenumber=3122 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3128 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=832 sam_format_worker /src/htslib/sam.c linenumber=3128 pthread_mutex_lock linenumber=3662 pthread_mutex_unlock linenumber=3667 calloc linenumber=3670 sam_state_err /src/htslib/sam.c linenumber=3672 pthread_mutex_lock linenumber=3071 pthread_mutex_unlock linenumber=3074 sam_format1_append /src/htslib/sam.c linenumber=3684 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4334 __errno_location linenumber=279 ks_resize /src/htslib/./htslib/kstring.h linenumber=280 kputc_ /src/htslib/./htslib/kstring.h linenumber=4335 ks_resize /src/htslib/./htslib/kstring.h linenumber=270 kputw /src/htslib/./htslib/kstring.h linenumber=4336 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=4336 kputs /src/htslib/./htslib/kstring.h linenumber=4338 kputc_ /src/htslib/./htslib/kstring.h linenumber=4339 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4340 kputll /src/htslib/./htslib/kstring.h linenumber=4341 ks_resize /src/htslib/./htslib/kstring.h linenumber=388 kputuw /src/htslib/./htslib/kstring.h linenumber=398 kputc_ /src/htslib/./htslib/kstring.h linenumber=4341 kputw /src/htslib/./htslib/kstring.h linenumber=4342 kputc_ /src/htslib/./htslib/kstring.h linenumber=4342 kputw /src/htslib/./htslib/kstring.h linenumber=4346 kputc_ /src/htslib/./htslib/kstring.h linenumber=4347 kputc_ /src/htslib/./htslib/kstring.h linenumber=4349 kputc_ /src/htslib/./htslib/kstring.h linenumber=4350 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4351 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4352 kputs /src/htslib/./htslib/kstring.h linenumber=4354 kputc_ /src/htslib/./htslib/kstring.h linenumber=4355 kputll /src/htslib/./htslib/kstring.h linenumber=4357 kputc_ /src/htslib/./htslib/kstring.h linenumber=4357 kputll /src/htslib/./htslib/kstring.h linenumber=4358 kputc_ /src/htslib/./htslib/kstring.h linenumber=4358 ks_resize /src/htslib/./htslib/kstring.h linenumber=4361 nibble2base /src/htslib/./sam_internal.h linenumber=4365 add33 /src/htslib/sam.c linenumber=4375 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4381 kputc_ /src/htslib/./htslib/kstring.h linenumber=4387 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4388 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=4391 hts_log /src/htslib/hts.c linenumber=4397 __errno_location linenumber=4399 hts_log /src/htslib/hts.c linenumber=4403 __errno_location linenumber=4404 __errno_location linenumber=3685 sam_state_err /src/htslib/sam.c linenumber=3685 kputc /src/htslib/./htslib/kstring.h linenumber=3688 pthread_mutex_lock linenumber=3691 pthread_mutex_unlock linenumber=3705 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3132 pthread_mutex_lock linenumber=3133 pthread_mutex_unlock linenumber=3135 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3137 hts_usleep /src/htslib/./hts_internal.h linenumber=3138 pthread_mutex_lock linenumber=3139 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=3142 pthread_mutex_unlock linenumber=3144 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3147 pthread_join linenumber=3152 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=3158 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3161 pthread_mutex_destroy linenumber=3164 pthread_mutex_destroy linenumber=3165 pthread_cond_destroy linenumber=3166 sam_free_sp_bams /src/htslib/sam.c linenumber=3181 sam_free_sp_bams /src/htslib/sam.c linenumber=3186 bam_hdr_destroy /src/htslib/./htslib/sam.h linenumber=3192 sam_hdr_destroy /src/htslib/sam.c linenumber=401 bgzf_thread_pool /src/htslib/bgzf.c linenumber=3743 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=3759 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=3823 calloc linenumber=3789 strcpy linenumber=3792 regcomp linenumber=3796 strcmp linenumber=3843 kh_init_tag /src/htslib/sam.c linenumber=3845 calloc linenumber=63 strlen linenumber=3848 hts_log /src/htslib/hts.c linenumber=3852 kh_put_tag /src/htslib/sam.c linenumber=3856 kh_resize_tag /src/htslib/sam.c linenumber=63 realloc linenumber=63 strncpy linenumber=3868 strcmp linenumber=3878 __ctype_b_loc linenumber=3882 isalnum_c /src/htslib/./textutils_internal.h linenumber=3882 strncpy linenumber=3887 hts_log /src/htslib/hts.c linenumber=3901 regfree linenumber=3911 regcomp linenumber=3912 hts_log /src/htslib/hts.c linenumber=3913 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=5567 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=5569 pthread_mutex_lock linenumber=4288 reset_metrics /src/htslib/cram/cram_io.c linenumber=4291 pthread_mutex_unlock linenumber=4256 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=4257 pthread_mutex_lock linenumber=4258 pthread_mutex_unlock linenumber=4294 cram_flush_container /src/htslib/cram/cram_io.c linenumber=4297 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=4145 pthread_mutex_lock linenumber=1868 hts_log /src/htslib/hts.c linenumber=1871 hts_log /src/htslib/hts.c linenumber=1876 pthread_mutex_unlock linenumber=1879 pthread_mutex_lock linenumber=1883 pthread_mutex_unlock linenumber=1885 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1897 pthread_mutex_lock linenumber=3425 hts_log /src/htslib/hts.c linenumber=3440 pthread_mutex_unlock linenumber=3441 pthread_mutex_lock linenumber=3458 hts_log /src/htslib/hts.c linenumber=3461 cram_populate_ref /src/htslib/cram/cram_io.c linenumber=3463 getenv linenumber=2980 getenv linenumber=2985 hts_log /src/htslib/hts.c linenumber=2989 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2994 sam_hrecs_find_key /src/htslib/header.c linenumber=2997 hts_log /src/htslib/hts.c linenumber=3000 expand_cache_path /src/htslib/cram/cram_io.c linenumber=3005 strchr linenumber=2891 strncpy linenumber=2893 strlen linenumber=2898 strcpy linenumber=2900 strtol linenumber=2909 strlen linenumber=2910 strncpy linenumber=2913 strlen linenumber=2932 strcpy linenumber=2934 strlen linenumber=2938 strcpy linenumber=2942 stat linenumber=3006 stat linenumber=3027 bgzf_open /src/htslib/bgzf.c linenumber=3029 string_dup /src/htslib/cram/string_alloc.c linenumber=3033 bgzf_close /src/htslib/bgzf.c linenumber=3036 open_path_mfile /src/htslib/cram/open_trace_file.c linenumber=3052 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=3054 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=3072 strstr linenumber=3075 strncmp linenumber=3076 hts_log /src/htslib/hts.c linenumber=3078 strncmp linenumber=3082 bgzf_close /src/htslib/bgzf.c linenumber=3087 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3091 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3093 bgzf_close /src/htslib/bgzf.c linenumber=3097 refs2id /src/htslib/cram/cram_io.c linenumber=3105 expand_cache_path /src/htslib/cram/cram_io.c linenumber=3118 hts_log /src/htslib/hts.c linenumber=3121 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=3122 strrchr linenumber=2950 is_directory /src/htslib/cram/cram_io.c linenumber=2955 stat linenumber=2877 mkdir linenumber=2960 chmod linenumber=2961 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2966 mkdir linenumber=2967 chmod linenumber=2968 hts_open_tmpfile /src/htslib/hts.c linenumber=3124 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=3126 hts_md5_init /src/htslib/md5.c linenumber=3138 hts_md5_reset /src/htslib/md5.c linenumber=329 hclose_abruptly /src/htslib/hfile.c linenumber=3139 unlink linenumber=3140 hts_md5_update /src/htslib/md5.c linenumber=3144 body /src/htslib/md5.c linenumber=260 body /src/htslib/md5.c linenumber=264 hts_md5_final /src/htslib/md5.c linenumber=3145 body /src/htslib/md5.c linenumber=283 body /src/htslib/md5.c linenumber=300 hts_md5_destroy /src/htslib/md5.c linenumber=3146 hts_md5_hex /src/htslib/md5.c linenumber=3147 strncmp linenumber=3149 hts_log /src/htslib/hts.c linenumber=3150 hclose_abruptly /src/htslib/hfile.c linenumber=3151 unlink linenumber=3152 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=3157 hclose /src/htslib/hfile.c linenumber=3158 chmod linenumber=3159 rename linenumber=3160 __errno_location linenumber=3161 strerror linenumber=3161 hts_log /src/htslib/hts.c linenumber=3161 unlink linenumber=3163 hts_log /src/htslib/hts.c linenumber=3464 hts_log /src/htslib/hts.c linenumber=3466 pthread_mutex_unlock linenumber=3467 pthread_mutex_unlock linenumber=3468 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3473 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3505 cram_ref_load /src/htslib/cram/cram_io.c linenumber=3508 __assert_fail linenumber=3334 __assert_fail linenumber=3344 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3348 strcmp linenumber=3356 bgzf_close /src/htslib/bgzf.c linenumber=3358 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3361 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3367 bgzf_useek /src/htslib/bgzf.c linenumber=3256 hseek /src/htslib/hfile.c linenumber=2562 bgzf_read_block /src/htslib/bgzf.c linenumber=2570 bgzf_seek_common /src/htslib/bgzf.c linenumber=2595 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=2598 __assert_fail linenumber=2610 perror linenumber=3257 bgzf_read /src/htslib/bgzf.c linenumber=3265 __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=3266 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3283 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3288 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3297 hts_log /src/htslib/hts.c linenumber=3304 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=3311 toupper linenumber=180 pthread_mutex_unlock linenumber=3509 pthread_mutex_unlock linenumber=3510 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3518 pthread_mutex_unlock linenumber=3534 pthread_mutex_unlock linenumber=3535 pthread_mutex_unlock linenumber=3555 pthread_mutex_unlock linenumber=3556 strcmp linenumber=3561 bgzf_close /src/htslib/bgzf.c linenumber=3563 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3566 pthread_mutex_unlock linenumber=3567 pthread_mutex_unlock linenumber=3568 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3573 pthread_mutex_unlock linenumber=3574 pthread_mutex_unlock linenumber=3575 pthread_mutex_unlock linenumber=3588 pthread_mutex_unlock linenumber=3589 hts_log /src/htslib/hts.c linenumber=1901 hts_log /src/htslib/hts.c linenumber=1903 pthread_mutex_lock linenumber=1905 pthread_mutex_unlock linenumber=1908 hts_log /src/htslib/hts.c linenumber=1913 hts_log /src/htslib/hts.c linenumber=1916 hts_log /src/htslib/hts.c linenumber=1917 hts_log /src/htslib/hts.c linenumber=1920 pthread_mutex_lock linenumber=1922 pthread_mutex_unlock linenumber=1924 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1927 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1809 sam_hrecs_find_key /src/htslib/header.c linenumber=1814 hts_md5_init /src/htslib/md5.c linenumber=1825 hts_md5_update /src/htslib/md5.c linenumber=1827 hts_md5_final /src/htslib/md5.c linenumber=1828 hts_md5_destroy /src/htslib/md5.c linenumber=1829 hts_md5_hex /src/htslib/md5.c linenumber=1830 strcmp linenumber=1833 hts_log /src/htslib/hts.c linenumber=1834 hts_log /src/htslib/hts.c linenumber=1836 cram_ref_incr /src/htslib/cram/cram_io.c linenumber=1960 pthread_mutex_lock linenumber=3186 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3187 pthread_mutex_unlock linenumber=3188 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1967 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1968 hts_log /src/htslib/hts.c linenumber=1971 __assert_fail linenumber=1986 lossy_read_names /src/htslib/cram/cram_encode.c linenumber=1990 kh_init_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1355 calloc linenumber=55 expected_template_count /src/htslib/cram/cram_encode.c linenumber=1373 bam_aux_get /src/htslib/sam.c linenumber=1308 bam_aux_first /src/htslib/sam.c linenumber=4847 __errno_location linenumber=4825 skip_aux /src/htslib/sam.c linenumber=4850 aux_type2size /src/htslib/sam.c linenumber=4800 memchr linenumber=4804 aux_type2size /src/htslib/sam.c linenumber=4808 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=4809 bam_aux_next /src/htslib/sam.c linenumber=4847 skip_aux /src/htslib/sam.c linenumber=4832 __errno_location linenumber=4834 hts_log /src/htslib/hts.c linenumber=4838 __errno_location linenumber=4840 hts_log /src/htslib/hts.c linenumber=4861 __errno_location linenumber=4863 bam_data_end /src/htslib/cram/cram_encode.c linenumber=1310 bam_aux2i_end /src/htslib/cram/cram_encode.c linenumber=1310 __errno_location linenumber=1262 __errno_location linenumber=1268 __errno_location linenumber=1274 le_to_i16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1277 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=241 __errno_location linenumber=1280 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1283 __errno_location linenumber=1286 le_to_i32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1289 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=252 __errno_location linenumber=1292 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1295 __errno_location linenumber=1297 bam_aux_get /src/htslib/sam.c linenumber=1315 kh_put_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1376 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=1408 kh_destroy_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1421 cram_generate_reference /src/htslib/cram/cram_encode.c linenumber=2001 extend_ref /src/htslib/cram/cram_encode.c linenumber=1748 realloc linenumber=1531 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1536 hts_log /src/htslib/hts.c linenumber=1759 cram_add_to_ref /src/htslib/cram/cram_encode.c linenumber=1763 bam_aux_get /src/htslib/sam.c linenumber=1666 cram_add_to_ref_MD /src/htslib/cram/cram_encode.c linenumber=1670 bam_cigar2rlen /src/htslib/sam.c linenumber=1566 extend_ref /src/htslib/cram/cram_encode.c linenumber=1570 __ctype_b_loc linenumber=1580 hts_str2uint /src/htslib/cram/../textutils_internal.h linenumber=1583 extend_ref /src/htslib/cram/cram_encode.c linenumber=1585 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1590 hts_log /src/htslib/hts.c linenumber=1597 __ctype_b_loc linenumber=1616 extend_ref /src/htslib/cram/cram_encode.c linenumber=1617 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1620 hts_log /src/htslib/hts.c linenumber=1626 extend_ref /src/htslib/cram/cram_encode.c linenumber=1634 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1637 hts_log /src/htslib/hts.c linenumber=1643 extend_ref /src/htslib/cram/cram_encode.c linenumber=1698 hts_log /src/htslib/hts.c linenumber=2011 hts_log /src/htslib/hts.c linenumber=2015 pthread_mutex_lock linenumber=2018 pthread_mutex_unlock linenumber=2022 pthread_mutex_lock linenumber=2026 pthread_mutex_unlock linenumber=2028 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2047 pthread_mutex_lock linenumber=3216 cram_ref_decr_locked /src/htslib/cram/cram_io.c linenumber=3217 __assert_fail linenumber=3201 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3207 pthread_mutex_unlock linenumber=3218 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2049 hts_log /src/htslib/hts.c linenumber=2050 validate_md5 /src/htslib/cram/cram_encode.c linenumber=2054 process_one_read /src/htslib/cram/cram_encode.c linenumber=2066 bam_aux_get /src/htslib/sam.c linenumber=3410 bam_aux_get /src/htslib/sam.c linenumber=3419 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3426 kh_init_m_i2i /src/htslib/cram/cram_structs.h linenumber=65 calloc linenumber=64 kh_put_m_i2i /src/htslib/cram/cram_structs.h linenumber=70 kh_resize_m_i2i /src/htslib/cram/cram_structs.h linenumber=64 realloc linenumber=64 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3428 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3448 block_grow /src/htslib/cram/cram_io.h linenumber=3464 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=3465 nibble2base /src/htslib/cram/../sam_internal.h linenumber=3470 hts_log /src/htslib/hts.c linenumber=3483 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3491 hts_log /src/htslib/hts.c linenumber=3525 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3538 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=3539 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=261 cram_add_substitution /src/htslib/cram/cram_encode.c linenumber=3602 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2615 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2622 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2623 block_append_char /src/htslib/cram/cram_io.h linenumber=2624 block_grow /src/htslib/cram/cram_io.h linenumber=262 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2626 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2582 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2589 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2592 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2597 cram_add_bases /src/htslib/cram/cram_encode.c linenumber=3615 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2642 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3621 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2653 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2654 block_append_char /src/htslib/cram/cram_io.h linenumber=2655 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2656 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3630 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3646 kputc_ /src/htslib/cram/../htslib/kstring.h linenumber=3648 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=270 kputsn /src/htslib/cram/../htslib/kstring.h linenumber=3649 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=246 cram_add_deletion /src/htslib/cram/cram_encode.c linenumber=3655 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2683 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2684 cram_add_skip /src/htslib/cram/cram_encode.c linenumber=3662 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2739 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2740 cram_add_insertion /src/htslib/cram/cram_encode.c linenumber=3669 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2761 block_append /src/htslib/cram/cram_io.h linenumber=2767 block_grow /src/htslib/cram/cram_io.h linenumber=249 block_append_char /src/htslib/cram/cram_io.h linenumber=2771 block_append_char /src/htslib/cram/cram_io.h linenumber=2773 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2775 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3674 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2669 block_append_char /src/htslib/cram/cram_io.h linenumber=2670 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2671 cram_add_softclip /src/htslib/cram/cram_encode.c linenumber=3683 block_append /src/htslib/cram/cram_io.h linenumber=2696 block_append_char /src/htslib/cram/cram_io.h linenumber=2697 block_append /src/htslib/cram/cram_io.h linenumber=2704 block_append_char /src/htslib/cram/cram_io.h linenumber=2708 block_append_char /src/htslib/cram/cram_io.h linenumber=2710 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2717 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3692 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3696 cram_add_hardclip /src/htslib/cram/cram_encode.c linenumber=3705 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2729 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2730 cram_add_pad /src/htslib/cram/cram_encode.c linenumber=3710 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2749 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2750 hts_log /src/htslib/hts.c linenumber=3715 hts_log /src/htslib/hts.c linenumber=3720 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3726 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3730 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3739 cram_encode_aux /src/htslib/cram/cram_encode.c linenumber=3747 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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 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/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 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/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=2102 pthread_mutex_unlock linenumber=2237 pthread_mutex_unlock linenumber=2249 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2250 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2258 hts_log /src/htslib/hts.c linenumber=2258 pthread_mutex_lock linenumber=2261 pthread_mutex_unlock linenumber=2265 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2266 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2284 hts_log /src/htslib/hts.c linenumber=2287 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2302 hts_log /src/htslib/hts.c linenumber=2302 pthread_mutex_lock linenumber=878 pthread_mutex_unlock linenumber=882 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=885 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=892 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=897 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=902 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=905 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=909 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=914 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=919 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=922 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=926 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=931 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=941 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=947 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=964 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=982 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1219 cram_free_block /src/htslib/cram/cram_io.c linenumber=1229 cram_encode_slice_header /src/htslib/cram/cram_encode.c linenumber=1240 cram_new_block /src/htslib/cram/cram_io.c linenumber=515 hts_malloc_pse /src/htslib/cram/../htslib/hts_alloc.h linenumber=521 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=523 hts_log /src/htslib/hts.c linenumber=533 cram_free_block /src/htslib/cram/cram_io.c linenumber=534 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=2474 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=625 block_append /src/htslib/cram/cram_io.h linenumber=626 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=163 kh_put_map /src/htslib/cram/cram_structs.h linenumber=170 block_append /src/htslib/cram/cram_io.h linenumber=194 block_append_char /src/htslib/cram/cram_io.h linenumber=204 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=220 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=225 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=230 sub_idx /src/htslib/cram/cram_encode.c linenumber=232 sub_idx /src/htslib/cram/cram_encode.c linenumber=233 sub_idx /src/htslib/cram/cram_encode.c linenumber=234 sub_idx /src/htslib/cram/cram_encode.c linenumber=235 sub_idx /src/htslib/cram/cram_encode.c linenumber=237 sub_idx /src/htslib/cram/cram_encode.c linenumber=238 sub_idx /src/htslib/cram/cram_encode.c linenumber=239 sub_idx /src/htslib/cram/cram_encode.c linenumber=240 block_append /src/htslib/cram/cram_io.h linenumber=241 block_append /src/htslib/cram/cram_io.h linenumber=247 hts_log /src/htslib/hts.c linenumber=254 block_append /src/htslib/cram/cram_io.h linenumber=263 block_append /src/htslib/cram/cram_io.h linenumber=464 block_append /src/htslib/cram/cram_io.h linenumber=490 hts_log /src/htslib/hts.c linenumber=492 cram_free_block /src/htslib/cram/cram_io.c linenumber=496 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2481 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2550 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2558 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=4148 htell /src/htslib/cram/../htslib/hfile.h linenumber=4097 cram_write_container /src/htslib/cram/cram_io.c linenumber=4100 itf8_put /src/htslib/cram/cram_io.c linenumber=4035 crc32 linenumber=4068 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4076 htell /src/htslib/cram/../htslib/hfile.h linenumber=4103 cram_write_block /src/htslib/cram/cram_io.c linenumber=4106 __assert_fail linenumber=1516 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1518 hputc2 /src/htslib/hfile.c linenumber=268 flush_buffer /src/htslib/hfile.c linenumber=403 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1519 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1523 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1528 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1531 __assert_fail linenumber=1536 crc32 linenumber=1548 crc32 linenumber=1551 crc32 linenumber=1553 int32_encode /src/htslib/cram/cram_io.c linenumber=1556 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1023 htell /src/htslib/cram/../htslib/hfile.h linenumber=4110 cram_write_block /src/htslib/cram/cram_io.c linenumber=4115 cram_write_block /src/htslib/cram/cram_io.c linenumber=4119 htell /src/htslib/cram/../htslib/hfile.h linenumber=4123 cram_index_slice /src/htslib/cram/cram_index.c linenumber=4127 hts_log /src/htslib/hts.c linenumber=707 cram_index_build_multiref /src/htslib/cram/cram_index.c linenumber=713 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=645 cram_dependent_data_series /src/htslib/cram/cram_decode.c linenumber=2361 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=620 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=626 hts_calloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=633 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=694 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=4000 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=4001 hts_log /src/htslib/hts.c linenumber=4013 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=710 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=740 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=756 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=785 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=831 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2382 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2383 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2384 strcmp linenumber=2396 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2404 hts_log /src/htslib/hts.c linenumber=2417 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2422 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=2425 hts_log /src/htslib/hts.c linenumber=2431 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2442 hts_log /src/htslib/hts.c linenumber=2451 pthread_mutex_lock linenumber=2456 pthread_mutex_lock linenumber=2457 pthread_mutex_unlock linenumber=2463 pthread_mutex_unlock linenumber=2464 hts_log /src/htslib/hts.c linenumber=2470 memcmp linenumber=2483 hts_log /src/htslib/hts.c linenumber=2493 hts_log /src/htslib/hts.c linenumber=2501 hts_md5_init /src/htslib/md5.c linenumber=2506 hts_md5_update /src/htslib/md5.c linenumber=2511 hts_md5_final /src/htslib/md5.c linenumber=2512 hts_md5_destroy /src/htslib/md5.c linenumber=2513 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2515 hts_md5_init /src/htslib/md5.c linenumber=2517 hts_md5_update /src/htslib/md5.c linenumber=2519 hts_md5_final /src/htslib/md5.c linenumber=2520 hts_md5_destroy /src/htslib/md5.c linenumber=2521 memcmp linenumber=2527 sam_hdr_tid2name /src/htslib/header.c linenumber=2529 hts_log /src/htslib/hts.c linenumber=2531 md5_print /src/htslib/cram/cram_decode.c linenumber=2533 hts_log /src/htslib/hts.c linenumber=2533 md5_print /src/htslib/cram/cram_decode.c linenumber=2534 hts_log /src/htslib/hts.c linenumber=2534 sam_hdr_find_tag_id /src/htslib/header.c linenumber=2536 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=2537 hts_log /src/htslib/hts.c linenumber=2538 ks_free /src/htslib/cram/../htslib/kstring.h linenumber=2539 ks_initialize /src/htslib/cram/../htslib/kstring.h linenumber=238 pthread_mutex_lock linenumber=2545 pthread_mutex_lock linenumber=2546 calloc linenumber=2547 pthread_mutex_unlock linenumber=2548 pthread_mutex_unlock linenumber=2549 hts_log /src/htslib/hts.c linenumber=2607 pthread_mutex_lock linenumber=2618 pthread_mutex_unlock linenumber=2620 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2623 pthread_mutex_lock linenumber=2632 pthread_mutex_unlock linenumber=2637 pthread_mutex_lock linenumber=2639 pthread_mutex_unlock linenumber=2641 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2644 pthread_mutex_lock linenumber=2649 pthread_mutex_lock linenumber=2650 pthread_mutex_unlock linenumber=2652 pthread_mutex_unlock linenumber=2653 hts_log /src/htslib/hts.c linenumber=2664 hts_log /src/htslib/hts.c linenumber=2675 pthread_mutex_lock linenumber=2698 pthread_mutex_unlock linenumber=2700 hts_log /src/htslib/hts.c linenumber=2793 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2823 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2851 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2860 cram_decode_aux_1_0 /src/htslib/cram/cram_decode.c linenumber=2886 map_find /src/htslib/cram/cram_decode.c linenumber=1972 block_append /src/htslib/cram/cram_io.h linenumber=1975 cram_decode_aux /src/htslib/cram/cram_decode.c linenumber=2888 strlen linenumber=2031 sam_hdr_line_name /src/htslib/header.c linenumber=2068 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2244 hts_log /src/htslib/hts.c linenumber=2255 hts_log /src/htslib/hts.c linenumber=2263 hts_log /src/htslib/hts.c linenumber=2271 hts_log /src/htslib/hts.c linenumber=2275 strlen linenumber=2072 block_append /src/htslib/cram/cram_io.h linenumber=2074 block_append /src/htslib/cram/cram_io.h linenumber=2075 block_append_char /src/htslib/cram/cram_io.h linenumber=2076 block_append /src/htslib/cram/cram_io.h linenumber=2085 map_find /src/htslib/cram/cram_decode.c linenumber=2090 block_append /src/htslib/cram/cram_io.h linenumber=2094 aux_ele_size /src/htslib/cram/cram_decode.c linenumber=2103 hts_log /src/htslib/hts.c linenumber=2129 block_resize /src/htslib/cram/cram_io.h linenumber=2894 block_resize /src/htslib/cram/cram_io.h linenumber=2902 hts_log /src/htslib/hts.c linenumber=2912 cram_decode_seq /src/htslib/cram/cram_decode.c linenumber=2919 block_append /src/htslib/cram/cram_io.h linenumber=1135 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1166 hts_log /src/htslib/hts.c linenumber=1191 hts_log /src/htslib/hts.c linenumber=1205 hts_log /src/htslib/hts.c linenumber=1216 memchr linenumber=1246 add_md_char /src/htslib/cram/cram_decode.c linenumber=1252 block_append_uint /src/htslib/cram/cram_io.h linenumber=1083 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=1084 block_append_uint /src/htslib/cram/cram_io.h linenumber=1381 add_md_char /src/htslib/cram/cram_decode.c linenumber=1393 block_append_uint /src/htslib/cram/cram_io.h linenumber=1422 block_append_char /src/htslib/cram/cram_io.h linenumber=1425 block_append /src/htslib/cram/cram_io.h linenumber=1426 block_append_char /src/htslib/cram/cram_io.h linenumber=1436 block_append /src/htslib/cram/cram_io.h linenumber=1437 block_append_uint /src/htslib/cram/cram_io.h linenumber=1440 block_append_uint /src/htslib/cram/cram_io.h linenumber=1519 block_append_uint /src/htslib/cram/cram_io.h linenumber=1523 block_append_char /src/htslib/cram/cram_io.h linenumber=1532 block_append_uint /src/htslib/cram/cram_io.h linenumber=1597 block_append_char /src/htslib/cram/cram_io.h linenumber=1604 hts_log /src/htslib/hts.c linenumber=1703 hts_log /src/htslib/hts.c linenumber=1718 memchr linenumber=1747 add_md_char /src/htslib/cram/cram_decode.c linenumber=1758 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1779 block_append_uint /src/htslib/cram/cram_io.h linenumber=1803 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1809 block_append_char /src/htslib/cram/cram_io.h linenumber=1846 block_append /src/htslib/cram/cram_io.h linenumber=1898 pthread_mutex_lock linenumber=2971 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2976 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2981 pthread_mutex_unlock linenumber=2983 cram_decode_slice_xref /src/htslib/cram/cram_decode.c linenumber=2986 hts_log /src/htslib/hts.c linenumber=2276 cram_free_block /src/htslib/cram/cram_io.c linenumber=2993 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3007 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3008 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3009 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3010 pthread_mutex_lock linenumber=3017 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3020 pthread_mutex_unlock linenumber=3023 hts_log /src/htslib/hts.c linenumber=655 snprintf linenumber=668 strlen linenumber=672 bgzf_write /src/htslib/bgzf.c linenumber=672 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=682 strlen linenumber=686 bgzf_write /src/htslib/bgzf.c linenumber=686 snprintf linenumber=715 strlen linenumber=719 bgzf_write /src/htslib/bgzf.c linenumber=719 __errno_location linenumber=4308 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=4309 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=844 cram_flush_thread /src/htslib/cram/cram_io.c linenumber=4309 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=4160 hts_log /src/htslib/hts.c linenumber=4161 __errno_location linenumber=4310 cram_flush_result /src/htslib/cram/cram_io.c linenumber=4311 hts_tpool_next_result /src/htslib/thread_pool.c linenumber=4176 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=4177 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4181 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=4189 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4196 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4205 cram_free_container /src/htslib/cram/cram_io.c linenumber=4218 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4223 cram_free_container /src/htslib/cram/cram_io.c linenumber=4230 hts_usleep /src/htslib/cram/../hts_internal.h linenumber=4316 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5574 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=5577 cram_flush_result /src/htslib/cram/cram_io.c linenumber=5579 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=5587 pthread_mutex_destroy linenumber=5590 pthread_mutex_destroy linenumber=5591 pthread_mutex_destroy linenumber=5592 pthread_mutex_destroy linenumber=5593 cram_write_eof_block /src/htslib/cram/cram_io.c linenumber=5597 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=5509 cram_write_container /src/htslib/cram/cram_io.c linenumber=5514 cram_write_block /src/htslib/cram/cram_io.c linenumber=5515 cram_close /src/htslib/cram/cram_io.c linenumber=5516 free_bam_list /src/htslib/cram/cram_io.c linenumber=5605 hclose /src/htslib/hfile.c linenumber=5609 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5613 sam_hdr_destroy /src/htslib/sam.c linenumber=5616 cram_free_container /src/htslib/cram/cram_io.c linenumber=5621 cram_free_container /src/htslib/cram/cram_io.c linenumber=5624 refs_free /src/htslib/cram/cram_io.c linenumber=5627 kh_destroy_m_metrics /src/htslib/cram/cram_structs.h linenumber=5643 cram_index_free /src/htslib/cram/cram_index.c linenumber=5647 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=381 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=368 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=5650 bgzf_close /src/htslib/bgzf.c linenumber=5653 cram_free_block /src/htslib/cram/cram_io.c linenumber=5517 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=5521 cram_free_block /src/htslib/cram/cram_io.c linenumber=5522 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=3808 ks_free /src/htslib/./htslib/kstring.h linenumber=3809 ks_initialize /src/htslib/./htslib/kstring.h linenumber=238 ks_free /src/htslib/./htslib/kstring.h linenumber=3810 ks_free /src/htslib/./htslib/kstring.h linenumber=3811 regfree linenumber=3812 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=1930 bam_hdr_read /src/htslib/sam.c linenumber=1936 bgzf_check_EOF /src/htslib/bgzf.c linenumber=239 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=241 hts_log /src/htslib/hts.c linenumber=243 bgzf_read /src/htslib/bgzf.c linenumber=246 memcmp linenumber=247 hts_log /src/htslib/hts.c linenumber=248 sam_hdr_init /src/htslib/sam.c linenumber=251 bgzf_read /src/htslib/bgzf.c linenumber=255 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=257 bgzf_read /src/htslib/bgzf.c linenumber=267 bgzf_read /src/htslib/bgzf.c linenumber=270 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=272 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=1588 calloc linenumber=282 calloc linenumber=284 bgzf_read /src/htslib/bgzf.c linenumber=293 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=295 bgzf_read /src/htslib/bgzf.c linenumber=302 realloc linenumber=310 bgzf_read /src/htslib/bgzf.c linenumber=316 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=318 hts_log /src/htslib/hts.c linenumber=323 hts_log /src/htslib/hts.c linenumber=328 hts_log /src/htslib/hts.c linenumber=330 sam_hdr_destroy /src/htslib/sam.c linenumber=340 sam_hdr_sanitise /src/htslib/sam.c linenumber=1936 hts_log /src/htslib/hts.c linenumber=1863 sam_hdr_destroy /src/htslib/sam.c linenumber=1864 hts_log /src/htslib/hts.c linenumber=1881 hts_log /src/htslib/hts.c linenumber=1885 sam_hdr_destroy /src/htslib/sam.c linenumber=1886 realloc linenumber=1890 sam_hdr_destroy /src/htslib/sam.c linenumber=1892 sam_hdr_dup /src/htslib/sam.c linenumber=1940 sam_hdr_init /src/htslib/sam.c linenumber=174 calloc linenumber=183 calloc linenumber=185 strdup linenumber=191 sam_hdr_dup_sdict /src/htslib/sam.c linenumber=198 kh_init_s2i /src/htslib/hts.c linenumber=148 kh_get_s2i /src/htslib/hts.c linenumber=156 kh_put_s2i /src/htslib/hts.c linenumber=158 kh_destroy_s2i /src/htslib/hts.c linenumber=160 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=204 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=205 ks_release /src/htslib/./htslib/kstring.h linenumber=210 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=212 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=216 sam_hdr_destroy /src/htslib/sam.c linenumber=226 sam_hdr_sanitise /src/htslib/sam.c linenumber=1940 sam_hdr_create /src/htslib/sam.c linenumber=1944 sam_hdr_init /src/htslib/sam.c linenumber=1909 sam_hdr_build_from_sam_file /src/htslib/header.c linenumber=1913 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=2307 memchr linenumber=2314 ks_expand /src/htslib/./htslib/kstring.h linenumber=2320 bgzf_htell /src/htslib/bgzf.c linenumber=2325 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=1914 sam_hdr_destroy /src/htslib/sam.c linenumber=1919 sam_hdr_sanitise /src/htslib/sam.c linenumber=1920 sam_hdr_init /src/htslib/sam.c linenumber=1949 __errno_location linenumber=1952 __errno_location linenumber=1956 sam_hdr_incr_ref /src/htslib/header.c linenumber=1963 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=1971 bam_hdr_write /src/htslib/sam.c linenumber=1981 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=355 hts_log /src/htslib/hts.c linenumber=357 hts_log /src/htslib/hts.c linenumber=361 hts_log /src/htslib/hts.c linenumber=362 hts_log /src/htslib/hts.c linenumber=368 hts_log /src/htslib/hts.c linenumber=371 hts_log /src/htslib/hts.c linenumber=372 bgzf_write /src/htslib/bgzf.c linenumber=378 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=381 bgzf_write /src/htslib/bgzf.c linenumber=382 bgzf_write /src/htslib/bgzf.c linenumber=384 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=386 bgzf_write /src/htslib/bgzf.c linenumber=387 bgzf_write /src/htslib/bgzf.c linenumber=389 bgzf_write /src/htslib/bgzf.c linenumber=391 bgzf_write /src/htslib/bgzf.c linenumber=393 strlen linenumber=399 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=401 bgzf_write /src/htslib/bgzf.c linenumber=402 bgzf_write /src/htslib/bgzf.c linenumber=404 bgzf_write /src/htslib/bgzf.c linenumber=406 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=408 bgzf_write /src/htslib/bgzf.c linenumber=409 bgzf_write /src/htslib/bgzf.c linenumber=411 bgzf_flush /src/htslib/bgzf.c linenumber=414 cram_set_header2 /src/htslib/cram/cram_io.c linenumber=1986 sam_hdr_destroy /src/htslib/sam.c linenumber=2860 sam_hdr_dup /src/htslib/sam.c linenumber=2861 refs_from_header /src/htslib/cram/cram_io.c linenumber=2865 cram_load_reference /src/htslib/cram/cram_io.c linenumber=1988 cram_write_SAM_hdr /src/htslib/cram/cram_io.c linenumber=1989 cram_write_file_def /src/htslib/cram/cram_io.c linenumber=4899 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4697 sam_hrecs_find_rg /src/htslib/header.c linenumber=4905 sam_hdr_add_line /src/htslib/header.c linenumber=4906 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=4911 refs2id /src/htslib/cram/cram_io.c linenumber=4913 sam_hrecs_find_type_id /src/htslib/header.c linenumber=4923 sam_hrecs_find_key /src/htslib/header.c linenumber=4926 cram_get_ref /src/htslib/cram/cram_io.c linenumber=4938 hts_log /src/htslib/hts.c linenumber=4942 hts_log /src/htslib/hts.c linenumber=4944 hts_log /src/htslib/hts.c linenumber=4945 pthread_mutex_lock linenumber=4947 pthread_mutex_unlock linenumber=4951 hts_md5_init /src/htslib/md5.c linenumber=4957 hts_md5_update /src/htslib/md5.c linenumber=4961 hts_md5_final /src/htslib/md5.c linenumber=4972 hts_md5_destroy /src/htslib/md5.c linenumber=4973 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=4974 hts_md5_hex /src/htslib/md5.c linenumber=4976 sam_hdr_update_line /src/htslib/header.c linenumber=4978 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=4984 strlen linenumber=4853 hisremote /src/htslib/hfile.c linenumber=4854 hts_log /src/htslib/hts.c linenumber=4856 strncpy linenumber=4859 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=4865 strncpy linenumber=4867 getcwd linenumber=4873 strlen linenumber=4874 strncpy linenumber=4875 snprintf linenumber=4880 sam_hdr_update_line /src/htslib/header.c linenumber=4985 sam_hdr_length /src/htslib/header.c linenumber=4992 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=4994 int32_encode /src/htslib/cram/cram_io.c linenumber=4998 sam_hdr_str /src/htslib/header.c linenumber=5002 sam_hdr_rebuild /src/htslib/header.c linenumber=1587 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=5002 cram_new_block /src/htslib/cram/cram_io.c linenumber=5006 cram_new_container /src/htslib/cram/cram_io.c linenumber=5007 calloc linenumber=3640 calloc linenumber=3668 cram_new_compression_header /src/htslib/cram/cram_io.c linenumber=3672 calloc linenumber=4333 cram_new_block /src/htslib/cram/cram_io.c linenumber=4337 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4342 cram_free_block /src/htslib/cram/cram_io.c linenumber=4343 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4348 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4349 cram_free_block /src/htslib/cram/cram_io.c linenumber=4350 cram_stats_create /src/htslib/cram/cram_stats.c linenumber=3677 calloc linenumber=50 kh_init_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3681 calloc linenumber=394 cram_free_block /src/htslib/cram/cram_io.c linenumber=5013 cram_free_container /src/htslib/cram/cram_io.c linenumber=5014 int32_put_blk /src/htslib/cram/cram_io.c linenumber=5018 block_append /src/htslib/cram/cram_io.h linenumber=1054 sam_hdr_str /src/htslib/header.c linenumber=5021 block_append /src/htslib/cram/cram_io.h linenumber=5021 cram_compress_block /src/htslib/cram/cram_io.c linenumber=5026 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=2325 cram_free_block /src/htslib/cram/cram_io.c linenumber=5038 cram_free_container /src/htslib/cram/cram_io.c linenumber=5039 calloc linenumber=5066 cram_free_block /src/htslib/cram/cram_io.c linenumber=5067 cram_free_container /src/htslib/cram/cram_io.c linenumber=5068 block_append /src/htslib/cram/cram_io.h linenumber=5071 cram_write_container /src/htslib/cram/cram_io.c linenumber=5076 cram_free_block /src/htslib/cram/cram_io.c linenumber=5077 cram_free_container /src/htslib/cram/cram_io.c linenumber=5078 cram_write_block /src/htslib/cram/cram_io.c linenumber=5082 cram_free_block /src/htslib/cram/cram_io.c linenumber=5083 cram_free_container /src/htslib/cram/cram_io.c linenumber=5084 block_resize /src/htslib/cram/cram_io.h linenumber=5089 cram_write_block /src/htslib/cram/cram_io.c linenumber=5094 cram_free_block /src/htslib/cram/cram_io.c linenumber=5095 cram_free_container /src/htslib/cram/cram_io.c linenumber=5096 cram_free_block /src/htslib/cram/cram_io.c linenumber=5101 cram_free_container /src/htslib/cram/cram_io.c linenumber=5102 hflush /src/htslib/hfile.c linenumber=5105 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=2007 strstr linenumber=2015 bgzf_write /src/htslib/bgzf.c linenumber=2023 hwrite /src/htslib/./htslib/hfile.h linenumber=2025 kputsn /src/htslib/./htslib/kstring.h linenumber=2035 kputs /src/htslib/./htslib/kstring.h linenumber=2036 kputsn /src/htslib/./htslib/kstring.h linenumber=2037 kputw /src/htslib/./htslib/kstring.h linenumber=2038 kputc /src/htslib/./htslib/kstring.h linenumber=2039 bgzf_write /src/htslib/bgzf.c linenumber=2044 hwrite /src/htslib/./htslib/hfile.h linenumber=2046 bgzf_flush /src/htslib/bgzf.c linenumber=2053 hflush /src/htslib/hfile.c linenumber=2055 __errno_location linenumber=2067 sam_hdr_dup /src/htslib/sam.c linenumber=2073 sam_hdr_destroy /src/htslib/sam.c linenumber=2074 bam_init1 /src/htslib/sam.c linenumber=102 calloc linenumber=434 sam_read1 /src/htslib/sam.c linenumber=106 sam_read1_bam /src/htslib/sam.c linenumber=4276 bam_read1 /src/htslib/sam.c linenumber=4135 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=794 bgzf_read /src/htslib/bgzf.c linenumber=168 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=799 bgzf_read /src/htslib/bgzf.c linenumber=807 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=810 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=811 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=817 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=820 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=821 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=822 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=823 realloc_bam_data /src/htslib/./sam_internal.h linenumber=830 sam_realloc_bam_data /src/htslib/sam.c linenumber=50 __errno_location linenumber=445 __errno_location linenumber=450 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=454 realloc linenumber=455 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=461 bam_set_mempolicy /src/htslib/./htslib/sam.h linenumber=461 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=833 fixup_missing_qname_nul /src/htslib/sam.c linenumber=835 realloc_bam_data /src/htslib/./sam_internal.h linenumber=773 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=840 swap_data /src/htslib/sam.c linenumber=842 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=760 bam_tag2cigar /src/htslib/sam.c linenumber=843 bam_aux_get /src/htslib/sam.c linenumber=696 __errno_location linenumber=697 __errno_location linenumber=699 __errno_location linenumber=700 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=711 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=721 __errno_location linenumber=57 sam_realloc_bam_data /src/htslib/sam.c linenumber=61 bam_endpos /src/htslib/sam.c linenumber=732 bam_cigar2rlen /src/htslib/sam.c linenumber=676 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=732 hts_log /src/htslib/hts.c linenumber=734 bam_cigar2rqlens /src/htslib/sam.c linenumber=849 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=851 hts_log /src/htslib/hts.c linenumber=854 __errno_location linenumber=4139 sam_read1_cram /src/htslib/sam.c linenumber=4280 cram_get_bam_seq /src/htslib/cram/cram_decode.c linenumber=4148 cram_get_seq /src/htslib/cram/cram_decode.c linenumber=3621 cram_next_slice /src/htslib/cram/cram_decode.c linenumber=3559 cram_first_slice /src/htslib/cram/cram_decode.c linenumber=3275 cram_free_container /src/htslib/cram/cram_io.c linenumber=3218 cram_read_container /src/htslib/cram/cram_io.c linenumber=3220 cram_seek /src/htslib/cram/cram_io.c linenumber=3236 cram_free_container /src/htslib/cram/cram_io.c linenumber=3238 cram_read_container /src/htslib/cram/cram_io.c linenumber=3240 cram_read_block /src/htslib/cram/cram_io.c linenumber=3251 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3256 calloc linenumber=148 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=156 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=182 kh_init_map /src/htslib/cram/cram_structs.h linenumber=190 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=198 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=217 kh_put_map /src/htslib/cram/cram_structs.h linenumber=230 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=232 kh_put_map /src/htslib/cram/cram_structs.h linenumber=242 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=244 kh_put_map /src/htslib/cram/cram_structs.h linenumber=254 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=256 kh_put_map /src/htslib/cram/cram_structs.h linenumber=266 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=268 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=278 kh_put_map /src/htslib/cram/cram_structs.h linenumber=309 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=311 cram_decode_TD /src/htslib/cram/cram_decode.c linenumber=318 cram_new_block /src/htslib/cram/cram_io.c linenumber=79 hts_log /src/htslib/hts.c linenumber=83 cram_free_block /src/htslib/cram/cram_io.c linenumber=84 cram_free_block /src/htslib/cram/cram_io.c linenumber=94 cram_free_block /src/htslib/cram/cram_io.c linenumber=99 block_append /src/htslib/cram/cram_io.h linenumber=103 block_append_char /src/htslib/cram/cram_io.h linenumber=108 calloc linenumber=121 cram_free_block /src/htslib/cram/cram_io.c linenumber=122 cram_free_block /src/htslib/cram/cram_io.c linenumber=136 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=320 kh_put_map /src/htslib/cram/cram_structs.h linenumber=327 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=329 hts_log /src/htslib/hts.c linenumber=337 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=344 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=362 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=376 hts_log /src/htslib/hts.c linenumber=459 hts_log /src/htslib/hts.c linenumber=464 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=468 cram_encoding2str /src/htslib/cram/cram_codecs.c linenumber=3889 hts_log /src/htslib/hts.c linenumber=3889 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=471 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=481 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=494 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=509 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=524 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=526 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=537 sam_hrecs_sort_order /src/htslib/header.c linenumber=3260 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=3261 pthread_mutex_unlock linenumber=3263 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3282 cram_free_container /src/htslib/cram/cram_io.c linenumber=3293 cram_read_container /src/htslib/cram/cram_io.c linenumber=3326 cram_free_container /src/htslib/cram/cram_io.c linenumber=3339 cram_free_container /src/htslib/cram/cram_io.c linenumber=3352 cram_free_container /src/htslib/cram/cram_io.c linenumber=3361 cram_free_container /src/htslib/cram/cram_io.c linenumber=3374 hseek /src/htslib/hfile.c linenumber=3377 cram_read_block /src/htslib/cram/cram_io.c linenumber=3387 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3393 sam_hrecs_sort_order /src/htslib/header.c linenumber=3398 pthread_mutex_lock linenumber=3399 pthread_mutex_unlock linenumber=3401 cram_free_container /src/htslib/cram/cram_io.c linenumber=3412 cram_read_slice /src/htslib/cram/cram_io.c linenumber=3417 cram_read_block /src/htslib/cram/cram_io.c linenumber=4569 calloc linenumber=4570 cram_decode_slice_header /src/htslib/cram/cram_decode.c linenumber=4580 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=964 calloc linenumber=974 hts_log /src/htslib/hts.c linenumber=990 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1011 cram_content_type2str /src/htslib/cram/cram_io.c linenumber=4585 hts_log /src/htslib/hts.c linenumber=4585 hts_log /src/htslib/hts.c linenumber=4591 calloc linenumber=4595 cram_read_block /src/htslib/cram/cram_io.c linenumber=4600 calloc linenumber=4611 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4625 cram_new_block /src/htslib/cram/cram_io.c linenumber=4628 cram_new_block /src/htslib/cram/cram_io.c linenumber=4629 cram_new_block /src/htslib/cram/cram_io.c linenumber=4630 cram_new_block /src/htslib/cram/cram_io.c linenumber=4631 cram_new_block /src/htslib/cram/cram_io.c linenumber=4632 cram_new_block /src/htslib/cram/cram_io.c linenumber=4633 cram_free_block /src/htslib/cram/cram_io.c linenumber=4644 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4647 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3432 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3441 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3450 cram_decode_slice_mt /src/htslib/cram/cram_decode.c linenumber=3462 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3054 hts_tpool_process_sz /src/htslib/thread_pool.c linenumber=3064 pthread_mutex_lock linenumber=307 pthread_mutex_unlock linenumber=309 __errno_location linenumber=3066 __errno_location linenumber=3067 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=3068 cram_decode_slice_thread /src/htslib/cram/cram_decode.c linenumber=3068 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3040 __errno_location linenumber=3071 __errno_location linenumber=3077 hts_log /src/htslib/hts.c linenumber=3463 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3464 hts_tpool_process_len /src/htslib/thread_pool.c linenumber=3485 pthread_mutex_lock linenumber=293 pthread_mutex_unlock linenumber=295 hts_tpool_process_qsize /src/htslib/thread_pool.c linenumber=3486 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3497 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3502 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3504 hts_log /src/htslib/hts.c linenumber=3505 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3509 hts_log /src/htslib/hts.c linenumber=3514 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3516 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3520 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3584 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3591 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3627 strlen linenumber=3125 append_uint64 /src/htslib/cram/cram_io.h linenumber=3130 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=3134 bam_set1 /src/htslib/sam.c linenumber=3169 bam_cigar2rqlens /src/htslib/sam.c linenumber=554 hts_log /src/htslib/hts.c linenumber=562 __errno_location linenumber=563 hts_log /src/htslib/hts.c linenumber=567 __errno_location linenumber=568 hts_log /src/htslib/hts.c linenumber=572 __errno_location linenumber=573 hts_log /src/htslib/hts.c linenumber=577 __errno_location linenumber=578 subtract_check_underflow /src/htslib/sam.c linenumber=583 subtract_check_underflow /src/htslib/sam.c linenumber=584 subtract_check_underflow /src/htslib/sam.c linenumber=585 subtract_check_underflow /src/htslib/sam.c linenumber=586 subtract_check_underflow /src/htslib/sam.c linenumber=587 hts_log /src/htslib/hts.c linenumber=589 __errno_location linenumber=590 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=596 realloc_bam_data /src/htslib/./sam_internal.h linenumber=596 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=603 strncpy linenumber=615 cram_eof /src/htslib/cram/cram_io.c linenumber=4150 bam_tag2cigar /src/htslib/sam.c linenumber=4152 sam_read1_sam /src/htslib/sam.c linenumber=4284 sam_parse1 /src/htslib/sam.c linenumber=4164 strchr linenumber=2717 hts_log /src/htslib/hts.c linenumber=2719 hts_log /src/htslib/hts.c linenumber=2720 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2722 parse_sam_flag /src/htslib/sam.c linenumber=2732 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2501 strtoul linenumber=2507 strchr linenumber=2736 strcmp linenumber=2737 hts_log /src/htslib/hts.c linenumber=2738 bam_name2id /src/htslib/./htslib/sam.h linenumber=2739 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=2740 hts_strprint /src/htslib/textutils.c linenumber=2741 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=2741 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2745 hts_log /src/htslib/hts.c linenumber=2748 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2754 bam_parse_cigar /src/htslib/sam.c linenumber=2760 hts_log /src/htslib/hts.c linenumber=2934 read_ncigar /src/htslib/sam.c linenumber=2939 isdigit_c /src/htslib/./textutils_internal.h linenumber=2848 hts_log /src/htslib/hts.c linenumber=2850 hts_log /src/htslib/hts.c linenumber=2854 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2947 hts_log /src/htslib/hts.c linenumber=2948 parse_cigar /src/htslib/sam.c linenumber=2960 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2874 hts_log /src/htslib/hts.c linenumber=2876 hts_log /src/htslib/hts.c linenumber=2880 hts_log /src/htslib/hts.c linenumber=2886 bam_cigar2rlen /src/htslib/sam.c linenumber=2765 hts_log /src/htslib/hts.c linenumber=2768 strchr linenumber=2770 hts_log /src/htslib/hts.c linenumber=2773 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2775 strchr linenumber=2777 strcmp linenumber=2778 strcmp linenumber=2780 bam_name2id /src/htslib/./htslib/sam.h linenumber=2783 hts_log /src/htslib/hts.c linenumber=2784 hts_strprint /src/htslib/textutils.c linenumber=2785 hts_log /src/htslib/hts.c linenumber=2785 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2788 hts_log /src/htslib/hts.c linenumber=2791 hts_str2int /src/htslib/./textutils_internal.h linenumber=2795 hts_log /src/htslib/hts.c linenumber=2797 strchr linenumber=2799 strcmp linenumber=2800 hts_log /src/htslib/hts.c linenumber=2801 bam_cigar2qlen /src/htslib/sam.c linenumber=2803 hts_log /src/htslib/hts.c linenumber=2804 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2806 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2815 hts_log /src/htslib/hts.c linenumber=2821 hts_log /src/htslib/hts.c linenumber=2825 aux_parse /src/htslib/sam.c linenumber=2830 hts_log /src/htslib/hts.c linenumber=2556 isspace_c /src/htslib/./textutils_internal.h linenumber=2560 hts_log /src/htslib/hts.c linenumber=2560 isspace_c /src/htslib/./textutils_internal.h linenumber=2563 isspace_c /src/htslib/./textutils_internal.h linenumber=2565 kh_get_tag /src/htslib/sam.c linenumber=2572 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2580 isspace_c /src/htslib/./textutils_internal.h linenumber=2584 hts_log /src/htslib/hts.c linenumber=2584 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2587 hts_str2int /src/htslib/./textutils_internal.h linenumber=2594 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2600 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=275 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2604 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=283 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2608 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2614 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2618 strtod linenumber=2624 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2624 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=345 strtod linenumber=2628 double_to_le /src/htslib/./htslib/hts_endian.h linenumber=2628 u64_to_le /src/htslib/./htslib/hts_endian.h linenumber=359 strchr linenumber=2631 strlen linenumber=2632 isspace_c /src/htslib/./textutils_internal.h linenumber=2633 hts_log /src/htslib/hts.c linenumber=2633 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2636 isspace_c /src/htslib/./textutils_internal.h linenumber=2643 hts_log /src/htslib/hts.c linenumber=2643 sam_parse_B_vals /src/htslib/sam.c linenumber=2646 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2496 hts_log /src/htslib/hts.c linenumber=2376 aux_type2size /src/htslib/sam.c linenumber=2386 hts_log /src/htslib/hts.c linenumber=2388 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2405 hts_log /src/htslib/hts.c linenumber=2406 sam_parse_Bc_vals /src/htslib/sam.c linenumber=2419 grow_B_array /src/htslib/sam.c linenumber=2250 __errno_location linenumber=2225 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2230 hts_log /src/htslib/hts.c linenumber=2231 hts_str2int /src/htslib/./textutils_internal.h linenumber=2253 sam_parse_BC_vals /src/htslib/sam.c linenumber=2422 grow_B_array /src/htslib/sam.c linenumber=2264 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2268 sam_parse_Bs_vals /src/htslib/sam.c linenumber=2425 grow_B_array /src/htslib/sam.c linenumber=2284 hts_str2int /src/htslib/./textutils_internal.h linenumber=2287 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2287 sam_parse_BS_vals /src/htslib/sam.c linenumber=2428 grow_B_array /src/htslib/sam.c linenumber=2299 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2303 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2303 sam_parse_Bi_vals /src/htslib/sam.c linenumber=2431 grow_B_array /src/htslib/sam.c linenumber=2320 hts_str2int /src/htslib/./textutils_internal.h linenumber=2323 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2323 sam_parse_BI_vals /src/htslib/sam.c linenumber=2434 grow_B_array /src/htslib/sam.c linenumber=2335 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2339 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2339 sam_parse_Bf_vals /src/htslib/sam.c linenumber=2437 grow_B_array /src/htslib/sam.c linenumber=2356 strtod linenumber=2359 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2359 hts_log /src/htslib/hts.c linenumber=2442 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2445 hts_str2int /src/htslib/./textutils_internal.h linenumber=2459 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2468 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2470 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2472 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2476 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2478 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2480 hts_log /src/htslib/hts.c linenumber=2485 isspace_c /src/htslib/./textutils_internal.h linenumber=2648 hts_strprint /src/htslib/textutils.c linenumber=2648 hts_log /src/htslib/hts.c linenumber=2648 isspace_c /src/htslib/./textutils_internal.h linenumber=2654 hts_log /src/htslib/hts.c linenumber=2654 bam_tag2cigar /src/htslib/sam.c linenumber=2833 sam_state_destroy /src/htslib/sam.c linenumber=4175 __errno_location linenumber=4176 bgzf_seek /src/htslib/bgzf.c linenumber=4179 bgzf_seek_common /src/htslib/bgzf.c linenumber=2259 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=4190 pthread_create linenumber=4194 sam_dispatcher_read /src/htslib/sam.c linenumber=4194 ks_resize /src/htslib/./htslib/kstring.h linenumber=3335 pthread_mutex_lock linenumber=3340 pthread_cond_signal linenumber=3344 pthread_mutex_unlock linenumber=3345 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3346 pthread_mutex_unlock linenumber=3352 pthread_mutex_lock linenumber=3354 pthread_mutex_unlock linenumber=3360 calloc linenumber=3364 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3368 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3379 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=3392 hread /src/htslib/./htslib/hfile.h linenumber=3394 __errno_location linenumber=3396 sam_state_err /src/htslib/sam.c linenumber=3396 hts_realloc_pse /src/htslib/./htslib/hts_alloc.h linenumber=3413 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=3418 __assert_fail linenumber=3419 __assert_fail linenumber=3420 ks_resize /src/htslib/./htslib/kstring.h linenumber=3426 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=3438 sam_parse_worker /src/htslib/sam.c linenumber=3438 pthread_mutex_lock linenumber=3225 pthread_mutex_unlock linenumber=3230 calloc linenumber=3233 calloc linenumber=3238 sam_state_err /src/htslib/sam.c linenumber=3240 sam_state_err /src/htslib/sam.c linenumber=3251 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3261 sam_state_err /src/htslib/sam.c linenumber=3264 strchr linenumber=3280 sam_parse1 /src/htslib/sam.c linenumber=3292 __errno_location linenumber=3293 sam_state_err /src/htslib/sam.c linenumber=3293 cleanup_sp_lines /src/htslib/sam.c linenumber=3294 __assert_fail linenumber=3206 sam_free_sp_bams /src/htslib/sam.c linenumber=3209 pthread_mutex_lock linenumber=3303 pthread_mutex_unlock linenumber=3306 sam_free_sp_bams /src/htslib/sam.c linenumber=3310 cleanup_sp_lines /src/htslib/sam.c linenumber=3438 cleanup_sp_bams /src/htslib/sam.c linenumber=3438 sam_free_sp_bams /src/htslib/sam.c linenumber=3320 pthread_mutex_lock linenumber=3441 pthread_mutex_unlock linenumber=3443 pthread_mutex_unlock linenumber=3448 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3452 sam_parse_eof /src/htslib/sam.c linenumber=3452 pthread_cond_wait linenumber=3460 pthread_cond_signal linenumber=3463 pthread_mutex_unlock linenumber=3464 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3465 pthread_mutex_unlock linenumber=3469 pthread_mutex_lock linenumber=3475 pthread_cond_signal linenumber=3477 pthread_mutex_unlock linenumber=3478 pthread_mutex_lock linenumber=3481 pthread_mutex_unlock linenumber=3484 __errno_location linenumber=3491 sam_state_err /src/htslib/sam.c linenumber=3491 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3492 hts_log /src/htslib/hts.c linenumber=4201 __errno_location linenumber=4209 pthread_mutex_lock linenumber=4213 pthread_mutex_unlock linenumber=4215 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=4219 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4222 pthread_mutex_lock linenumber=4226 pthread_mutex_unlock linenumber=4228 bam_copy1 /src/htslib/sam.c linenumber=4233 realloc_bam_data /src/htslib/./sam_internal.h linenumber=489 pthread_mutex_lock linenumber=4236 pthread_mutex_unlock linenumber=4239 hts_getline /src/htslib/hts.c linenumber=4252 sam_parse1 /src/htslib/sam.c linenumber=4255 hts_log /src/htslib/hts.c linenumber=4258 fastq_state_init /src/htslib/sam.c linenumber=4291 fastq_parse1 /src/htslib/sam.c linenumber=4296 hts_getline /src/htslib/hts.c linenumber=3946 strpbrk linenumber=3962 isspace_c /src/htslib/./textutils_internal.h linenumber=3974 isspace_c /src/htslib/./textutils_internal.h linenumber=3982 hts_getline /src/htslib/hts.c linenumber=3990 kputsn /src/htslib/./htslib/kstring.h linenumber=3996 hts_getline /src/htslib/hts.c linenumber=4005 kputsn /src/htslib/./htslib/kstring.h linenumber=4009 isdigit_c /src/htslib/./textutils_internal.h linenumber=4022 regexec linenumber=4036 hts_log /src/htslib/hts.c linenumber=4041 isalpha_c /src/htslib/./textutils_internal.h linenumber=4049 bam_set1 /src/htslib/sam.c linenumber=4069 bam_aux_append /src/htslib/sam.c linenumber=4081 __assert_fail linenumber=4767 realloc_bam_data /src/htslib/./sam_internal.h linenumber=4771 __errno_location linenumber=4791 isdigit_c /src/htslib/./textutils_internal.h linenumber=4093 strtol linenumber=4094 isdigit_c /src/htslib/./textutils_internal.h linenumber=4108 isspace_c /src/htslib/./textutils_internal.h linenumber=4111 bam_aux_append /src/htslib/sam.c linenumber=4120 aux_parse /src/htslib/sam.c linenumber=4127 __errno_location linenumber=4300 __errno_location linenumber=4304 sam_passes_filter /src/htslib/sam.c linenumber=4309 hts_filter_eval2 /src/htslib/hts_expr.c linenumber=1540 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=1540 memcmp linenumber=1219 ks_clear /src/htslib/./htslib/kstring.h linenumber=1222 kputw /src/htslib/./htslib/kstring.h linenumber=1227 kputc_ /src/htslib/./htslib/kstring.h linenumber=1228 kputs /src/htslib/./htslib/kstring.h linenumber=1230 kputs /src/htslib/./htslib/kstring.h linenumber=1232 memcmp linenumber=1239 bam_endpos /src/htslib/sam.c linenumber=1241 memcmp linenumber=1247 memcmp linenumber=1254 memcmp linenumber=1258 memcmp linenumber=1262 memcmp linenumber=1266 memcmp linenumber=1270 memcmp linenumber=1274 memcmp linenumber=1278 memcmp linenumber=1282 memcmp linenumber=1286 memcmp linenumber=1290 memcmp linenumber=1294 memcmp linenumber=1298 hts_log /src/htslib/hts.c linenumber=1303 memcmp linenumber=1311 memcmp linenumber=1331 bam_get_library /src/htslib/sam.c linenumber=1334 bam_aux_get /src/htslib/sam.c linenumber=1178 sam_hdr_find_tag_id /src/htslib/header.c linenumber=1185 ks_clear /src/htslib/./htslib/kstring.h linenumber=1335 kputs /src/htslib/./htslib/kstring.h linenumber=1335 memcmp linenumber=1341 memcmp linenumber=1345 memcmp linenumber=1349 sam_hdr_tid2name /src/htslib/header.c linenumber=1352 ks_clear /src/htslib/./htslib/kstring.h linenumber=1353 kputs /src/htslib/./htslib/kstring.h linenumber=1353 memcmp linenumber=1355 memcmp linenumber=1363 memcmp linenumber=1371 memcmp linenumber=1375 memcmp linenumber=1383 bam_cigar2qlen /src/htslib/sam.c linenumber=1385 memcmp linenumber=1387 ks_clear /src/htslib/./htslib/kstring.h linenumber=1390 kputs /src/htslib/./htslib/kstring.h linenumber=1390 memcmp linenumber=1392 ks_clear /src/htslib/./htslib/kstring.h linenumber=1394 ks_resize /src/htslib/./htslib/kstring.h linenumber=1395 memcmp linenumber=1405 bam_cigar2rlen /src/htslib/sam.c linenumber=1407 memcmp linenumber=1409 sam_hdr_tid2name /src/htslib/header.c linenumber=1412 ks_clear /src/htslib/./htslib/kstring.h linenumber=1413 kputs /src/htslib/./htslib/kstring.h linenumber=1413 memcmp linenumber=1415 sam_hdr_tid2name /src/htslib/header.c linenumber=1418 ks_clear /src/htslib/./htslib/kstring.h linenumber=1419 kputs /src/htslib/./htslib/kstring.h linenumber=1419 memcmp linenumber=1421 memcmp linenumber=1429 ks_clear /src/htslib/./htslib/kstring.h linenumber=1431 ks_resize /src/htslib/./htslib/kstring.h linenumber=1432 nibble2base /src/htslib/./sam_internal.h linenumber=1434 memcmp linenumber=1439 memcmp linenumber=1470 bam_aux_get /src/htslib/sam.c linenumber=1482 ks_clear /src/htslib/./htslib/kstring.h linenumber=1490 kputs /src/htslib/./htslib/kstring.h linenumber=1490 ks_clear /src/htslib/./htslib/kstring.h linenumber=1495 kputsn /src/htslib/./htslib/kstring.h linenumber=1495 bam_aux2i /src/htslib/sam.c linenumber=1502 get_int_aux_val /src/htslib/sam.c linenumber=5123 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=5107 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=5109 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=5110 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=5111 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=5112 __errno_location linenumber=5114 bam_aux2f /src/htslib/sam.c linenumber=1508 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=5130 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=5131 get_int_aux_val /src/htslib/sam.c linenumber=5132 hts_log /src/htslib/hts.c linenumber=1512 hts_log /src/htslib/hts.c linenumber=1541 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1542 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1547 sam_write1 /src/htslib/sam.c linenumber=107 bam_write_idx1 /src/htslib/sam.c linenumber=4563 bam_write1 /src/htslib/sam.c linenumber=938 hts_log /src/htslib/hts.c linenumber=869 __errno_location linenumber=870 hts_log /src/htslib/hts.c linenumber=877 bgzf_flush_try /src/htslib/bgzf.c linenumber=889 lazy_flush /src/htslib/bgzf.c linenumber=2000 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=891 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=893 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=893 bgzf_write /src/htslib/bgzf.c linenumber=198 swap_data /src/htslib/sam.c linenumber=894 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=896 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=898 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=899 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=901 bam_cigar2rlen /src/htslib/sam.c linenumber=905 hts_log /src/htslib/hts.c linenumber=909 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=918 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=919 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=920 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=921 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=922 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=923 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=924 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=925 swap_data /src/htslib/sam.c linenumber=927 bgzf_flush_try /src/htslib/bgzf.c linenumber=941 hts_idx_amend_last /src/htslib/hts.c linenumber=944 bam_write1 /src/htslib/sam.c linenumber=946 bam_endpos /src/htslib/sam.c linenumber=950 bgzf_idx_push /src/htslib/bgzf.c linenumber=950 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=951 sam_hdr_tid2len /src/htslib/header.c linenumber=951 kh_get_s2i /src/htslib/hts.c linenumber=2443 hts_log /src/htslib/hts.c linenumber=951 cram_put_bam_seq /src/htslib/cram/cram_encode.c linenumber=4566 cram_new_container /src/htslib/cram/cram_io.c linenumber=4053 pthread_mutex_lock linenumber=4059 pthread_mutex_unlock linenumber=4062 hts_log /src/htslib/hts.c linenumber=4087 pthread_mutex_lock linenumber=4090 hts_log /src/htslib/hts.c linenumber=4093 pthread_mutex_unlock linenumber=4095 cram_next_container /src/htslib/cram/cram_encode.c linenumber=4104 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=3308 hts_log /src/htslib/hts.c linenumber=3314 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=3319 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3325 cram_free_container /src/htslib/cram/cram_io.c linenumber=3333 cram_new_container /src/htslib/cram/cram_io.c linenumber=3336 pthread_mutex_lock linenumber=3341 cram_new_slice /src/htslib/cram/cram_io.c linenumber=3353 calloc linenumber=4507 calloc linenumber=4511 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4519 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4521 cram_new_block /src/htslib/cram/cram_io.c linenumber=4524 cram_new_block /src/htslib/cram/cram_io.c linenumber=4525 cram_new_block /src/htslib/cram/cram_io.c linenumber=4526 cram_new_block /src/htslib/cram/cram_io.c linenumber=4527 cram_new_block /src/htslib/cram/cram_io.c linenumber=4528 cram_new_block /src/htslib/cram/cram_io.c linenumber=4529 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4540 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4541 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4542 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4552 pthread_mutex_lock linenumber=4136 hts_log /src/htslib/hts.c linenumber=4138 pthread_mutex_unlock linenumber=4149 pthread_mutex_lock linenumber=4152 calloc linenumber=4153 pthread_mutex_unlock linenumber=4154 pthread_mutex_lock linenumber=4168 calloc linenumber=4169 pthread_mutex_unlock linenumber=4170 pthread_mutex_lock linenumber=4174 pthread_mutex_unlock linenumber=4177 pthread_mutex_lock linenumber=4187 calloc linenumber=4194 pthread_mutex_unlock linenumber=4196 pthread_mutex_unlock linenumber=4200 bam_copy1 /src/htslib/sam.c linenumber=4205 bam_dup1 /src/htslib/sam.c linenumber=4208 bam_init1 /src/htslib/sam.c linenumber=500 bam_copy1 /src/htslib/sam.c linenumber=502 bam_destroy1 /src/htslib/sam.c linenumber=503 bam_cigar2qlen /src/htslib/sam.c linenumber=4220 hts_log /src/htslib/hts.c linenumber=4222 pthread_create linenumber=4589 sam_dispatcher_write /src/htslib/sam.c linenumber=4589 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3505 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3506 sam_state_err /src/htslib/sam.c linenumber=3508 bgzf_flush_try /src/htslib/bgzf.c linenumber=3523 bgzf_write /src/htslib/bgzf.c linenumber=3525 hwrite /src/htslib/./htslib/hfile.h linenumber=3528 bam_endpos /src/htslib/sam.c linenumber=3535 bgzf_idx_push /src/htslib/bgzf.c linenumber=3534 __errno_location linenumber=3538 sam_state_err /src/htslib/sam.c linenumber=3538 sam_hdr_tid2name /src/htslib/header.c linenumber=3539 sam_hdr_tid2len /src/htslib/header.c linenumber=3539 hts_log /src/htslib/hts.c linenumber=3539 bam_endpos /src/htslib/sam.c linenumber=3544 hts_idx_push /src/htslib/hts.c linenumber=3544 __errno_location linenumber=3546 sam_state_err /src/htslib/sam.c linenumber=3546 sam_hdr_tid2name /src/htslib/header.c linenumber=3547 sam_hdr_tid2len /src/htslib/header.c linenumber=3547 hts_log /src/htslib/hts.c linenumber=3547 __assert_fail linenumber=3554 pthread_mutex_lock linenumber=3557 pthread_mutex_unlock linenumber=3561 bgzf_write /src/htslib/bgzf.c linenumber=3608 bgzf_flush_try /src/htslib/bgzf.c linenumber=3616 bgzf_write /src/htslib/bgzf.c linenumber=3621 hwrite /src/htslib/./htslib/hfile.h linenumber=3628 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3633 pthread_mutex_lock linenumber=3636 pthread_mutex_unlock linenumber=3639 sam_state_err /src/htslib/sam.c linenumber=3642 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3643 __errno_location linenumber=3647 sam_state_err /src/htslib/sam.c linenumber=3647 hts_log /src/htslib/hts.c linenumber=4596 pthread_mutex_lock linenumber=4603 pthread_mutex_unlock linenumber=4610 pthread_mutex_unlock linenumber=4612 calloc linenumber=4613 calloc linenumber=4614 bam_copy1 /src/htslib/sam.c linenumber=4627 pthread_mutex_lock linenumber=4634 pthread_mutex_unlock linenumber=4636 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=4639 sam_format_worker /src/htslib/sam.c linenumber=4639 cleanup_sp_bams /src/htslib/sam.c linenumber=4639 cleanup_sp_lines /src/htslib/sam.c linenumber=4639 pthread_mutex_unlock linenumber=4642 pthread_mutex_unlock linenumber=4645 sam_format1 /src/htslib/sam.c linenumber=4654 sam_format1_append /src/htslib/sam.c linenumber=4411 kputc /src/htslib/./htslib/kstring.h linenumber=4655 bgzf_flush_try /src/htslib/bgzf.c linenumber=4657 bgzf_write /src/htslib/bgzf.c linenumber=4659 hwrite /src/htslib/./htslib/hfile.h linenumber=4661 bam_endpos /src/htslib/sam.c linenumber=4666 bgzf_idx_push /src/htslib/bgzf.c linenumber=4666 sam_hdr_tid2name /src/htslib/header.c linenumber=4668 sam_hdr_tid2len /src/htslib/header.c linenumber=4668 hts_log /src/htslib/hts.c linenumber=4668 bam_endpos /src/htslib/sam.c linenumber=4673 hts_idx_push /src/htslib/hts.c linenumber=4673 sam_hdr_tid2name /src/htslib/header.c linenumber=4675 sam_hdr_tid2len /src/htslib/header.c linenumber=4675 hts_log /src/htslib/hts.c linenumber=4675 fastq_state_init /src/htslib/sam.c linenumber=4690 fastq_format1 /src/htslib/sam.c linenumber=4695 kputc /src/htslib/./htslib/kstring.h linenumber=4424 kputs /src/htslib/./htslib/kstring.h linenumber=4424 bam_aux_get /src/htslib/sam.c linenumber=4446 kputc /src/htslib/./htslib/kstring.h linenumber=4448 isalpha_c /src/htslib/./textutils_internal.h linenumber=4451 toupper_c /src/htslib/./textutils_internal.h linenumber=4451 kputc /src/htslib/./htslib/kstring.h linenumber=4451 kputs /src/htslib/./htslib/kstring.h linenumber=4456 kputs /src/htslib/./htslib/kstring.h linenumber=4464 kputs /src/htslib/./htslib/kstring.h linenumber=4467 bam_aux_get /src/htslib/sam.c linenumber=4477 ksprintf /src/htslib/kstring.c linenumber=4478 isupper_c /src/htslib/./textutils_internal.h linenumber=4482 __ctype_b_loc linenumber=177 islower_c /src/htslib/./textutils_internal.h linenumber=4482 __ctype_b_loc linenumber=173 hts_log /src/htslib/hts.c linenumber=4483 strlen linenumber=4484 strlen linenumber=4492 isalpha_c /src/htslib/./textutils_internal.h linenumber=4495 islower_c /src/htslib/./textutils_internal.h linenumber=4497 toupper_c /src/htslib/./textutils_internal.h linenumber=4498 kh_get_tag /src/htslib/sam.c linenumber=4509 kputc_ /src/htslib/./htslib/kstring.h linenumber=4510 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4511 skip_aux /src/htslib/sam.c linenumber=4514 kputsn /src/htslib/./htslib/kstring.h linenumber=4517 ks_resize /src/htslib/./htslib/kstring.h linenumber=4520 kputc_ /src/htslib/./htslib/kstring.h linenumber=4521 kputc_ /src/htslib/./htslib/kstring.h linenumber=4527 kputc_ /src/htslib/./htslib/kstring.h linenumber=4530 kputsn /src/htslib/./htslib/kstring.h linenumber=4535 kputc_ /src/htslib/./htslib/kstring.h linenumber=4539 kputc_ /src/htslib/./htslib/kstring.h linenumber=4542 kputc_ /src/htslib/./htslib/kstring.h linenumber=4545 kputc /src/htslib/./htslib/kstring.h linenumber=4548 bgzf_flush_try /src/htslib/bgzf.c linenumber=4698 bgzf_write /src/htslib/bgzf.c linenumber=4700 hwrite /src/htslib/./htslib/hfile.h linenumber=4703 __errno_location linenumber=4710 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 hts_log /src/htslib/hts.c linenumber=2619 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 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=602 calloc linenumber=559 hts_idx_load3 /src/htslib/hts.c linenumber=562 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=568 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=571 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=572 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=573 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=574 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=575 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=576 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=577 get_tid /src/htslib/tbx.c linenumber=585 kh_init_s2i /src/htslib/hts.c linenumber=70 kh_put_s2i /src/htslib/hts.c linenumber=75 strdup linenumber=79 kh_del_s2i /src/htslib/hts.c linenumber=84 kh_get_s2i /src/htslib/hts.c linenumber=88 __errno_location linenumber=586 strerror linenumber=586 hts_log /src/htslib/hts.c linenumber=586 strlen linenumber=584 hts_log /src/htslib/hts.c linenumber=593 tbx_destroy /src/htslib/tbx.c linenumber=596 hts_idx_destroy /src/htslib/hts.c linenumber=522 kh_destroy_s2i /src/htslib/hts.c linenumber=523 tbx_seqnames /src/htslib/tbx.c linenumber=2655 calloc linenumber=621 calloc linenumber=624 __assert_fail linenumber=634 __assert_fail linenumber=639 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=1544 ks_resize /src/htslib/./htslib/kstring.h linenumber=1552 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1564 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1568 kputsn /src/htslib/./htslib/kstring.h linenumber=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=1584 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1604 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1608 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=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 hts_log /src/htslib/hts.c 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=6435 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6446 strlen linenumber=186 memcmp linenumber=191 memcmp linenumber=192 memcmp linenumber=193 memcmp linenumber=194 strcmp linenumber=6450 strcmp linenumber=6451 strlen linenumber=6456 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6459 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=1676 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=1667 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=1634 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1637 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1640 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=1643 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=263 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6464 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6468 strncmp linenumber=6472 strncmp linenumber=6473 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6484 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6489 bcf_get_info /src/htslib/vcf.c linenumber=6494 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6042 bcf_get_info_id /src/htslib/vcf.c linenumber=6044 bcf_unpack /src/htslib/vcf.c linenumber=6061 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=6495 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6498 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6500 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6506 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6513 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6522 bcf_get_fmt /src/htslib/vcf.c linenumber=6529 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6035 bcf_get_fmt_id /src/htslib/vcf.c linenumber=6037 bcf_unpack /src/htslib/vcf.c linenumber=6050 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6532 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=6534 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6539 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6569 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6573 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6577 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6581 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6613 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6617 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6621 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6625 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 hts_log /src/htslib/hts.c 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 kputll /src/htslib/./htslib/kstring.h linenumber=4336 kputc_ /src/htslib/./htslib/kstring.h linenumber=4337 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=4344 kputs /src/htslib/./htslib/kstring.h linenumber=4345 kputc_ /src/htslib/./htslib/kstring.h linenumber=4348 bcf_float_is_missing /src/htslib/./htslib/vcf.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=6373 kputc /src/htslib/./htslib/kstring.h linenumber=6373 kputw /src/htslib/./htslib/kstring.h linenumber=6373 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6375 kputc /src/htslib/./htslib/kstring.h linenumber=6375 kputw /src/htslib/./htslib/kstring.h linenumber=6375 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6377 kputc /src/htslib/./htslib/kstring.h linenumber=6377 kputw /src/htslib/./htslib/kstring.h linenumber=6377 kputc /src/htslib/./htslib/kstring.h linenumber=6379 hts_log /src/htslib/hts.c linenumber=6380 get_hdr_aux /src/htslib/vcf.c linenumber=6384 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6394 ks_resize /src/htslib/./htslib/kstring.h linenumber=474 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6396 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6403 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=6321 strlen linenumber=6295 snprintf linenumber=6296 snprintf linenumber=6299 add_desc_to_buffer /src/htslib/vcf.c linenumber=6330 bcf_seqname_safe /src/htslib/./htslib/vcf.h 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 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 ====================================