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=1322 isalnum_c /src/htslib/./textutils_internal.h linenumber=1188 __ctype_b_loc linenumber=169 tolower_c /src/htslib/./textutils_internal.h linenumber=1189 tolower linenumber=179 pthread_mutex_lock linenumber=1197 load_hfile_plugins /src/htslib/hfile.c linenumber=1198 kh_init_scheme_string /src/htslib/hfile.c linenumber=1121 calloc linenumber=975 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1125 hts_log /src/htslib/hts.c linenumber=1062 __errno_location linenumber=5306 get_severity_tag /src/htslib/hts.c linenumber=5310 fprintf linenumber=5310 vfprintf linenumber=5313 fprintf linenumber=5316 __errno_location linenumber=5318 try_exe_add_scheme_handler /src/htslib/hfile.c linenumber=1066 hts_log /src/htslib/hts.c linenumber=1067 kh_put_scheme_string /src/htslib/hfile.c linenumber=1071 kh_resize_scheme_string /src/htslib/hfile.c linenumber=975 __errno_location linenumber=975 realloc linenumber=975 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=975 strcmp linenumber=975 __errno_location linenumber=1073 strerror linenumber=1073 hts_log /src/htslib/hts.c linenumber=1073 priority /src/htslib/hfile.c linenumber=1077 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1126 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1127 init_add_plugin /src/htslib/hfile.c linenumber=1128 hts_log /src/htslib/hts.c linenumber=1087 hts_log /src/htslib/hts.c linenumber=1099 hts_log /src/htslib/hts.c linenumber=1104 hfile_plugin_init_mem /src/htslib/hfile.c linenumber=1128 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=929 init_add_plugin /src/htslib/hfile.c linenumber=1129 hfile_plugin_init_crypt4gh_needed /src/htslib/hfile.c linenumber=1129 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=964 init_add_plugin /src/htslib/hfile.c linenumber=1148 hfile_plugin_init_libcurl /src/htslib/hfile_libcurl.c linenumber=1148 hts_version /src/htslib/hts.c linenumber=1699 curl_global_init linenumber=1707 __errno_location linenumber=1708 curl_share_init linenumber=1710 curl_global_cleanup linenumber=1711 __errno_location linenumber=1711 curl_share_setopt linenumber=1712 share_lock /src/htslib/hfile_libcurl.c linenumber=1712 pthread_mutex_lock linenumber=312 curl_share_setopt linenumber=1713 share_unlock /src/htslib/hfile_libcurl.c linenumber=1713 pthread_mutex_unlock linenumber=316 curl_share_setopt linenumber=1714 curl_share_cleanup linenumber=1716 curl_global_cleanup linenumber=1717 __errno_location linenumber=1718 getenv linenumber=1722 strdup linenumber=1723 kh_init_auth_map /src/htslib/hfile_libcurl.c linenumber=1724 calloc linenumber=70 __errno_location linenumber=1726 kh_destroy_auth_map /src/htslib/hfile_libcurl.c linenumber=1728 curl_share_cleanup linenumber=1729 curl_global_cleanup linenumber=1730 __errno_location linenumber=1731 getenv linenumber=1735 strcmp linenumber=1736 getenv linenumber=1742 atoi linenumber=1743 getenv linenumber=1744 atol linenumber=1745 getenv linenumber=1746 atol linenumber=1747 getenv linenumber=1748 atol linenumber=1749 getenv linenumber=1750 atol linenumber=1751 curl_version_info linenumber=1754 ksprintf /src/htslib/kstring.c linenumber=1755 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=1761 init_add_plugin /src/htslib/hfile.c linenumber=1151 hfile_plugin_init_gcs /src/htslib/hfile_gcs.c linenumber=1151 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=169 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=170 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=171 init_add_plugin /src/htslib/hfile.c linenumber=1154 hfile_plugin_init_s3 /src/htslib/hfile_s3.c linenumber=1154 hts_version /src/htslib/hts.c linenumber=2602 curl_global_init linenumber=2609 __errno_location linenumber=2613 curl_share_init linenumber=2617 curl_global_cleanup linenumber=2620 __errno_location linenumber=2621 curl_share_setopt linenumber=2625 share_lock /src/htslib/hfile_s3.c linenumber=2625 pthread_mutex_lock linenumber=1136 curl_share_setopt linenumber=2626 share_unlock /src/htslib/hfile_s3.c linenumber=2626 pthread_mutex_unlock linenumber=1140 curl_share_setopt linenumber=2627 curl_share_cleanup linenumber=2630 curl_global_cleanup linenumber=2631 __errno_location linenumber=2632 curl_version_info linenumber=2636 ksprintf /src/htslib/kstring.c linenumber=2637 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2642 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2643 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2644 atexit linenumber=1162 hfile_exit /src/htslib/hfile.c linenumber=1162 hfile_shutdown /src/htslib/hfile.c linenumber=1010 pthread_mutex_lock linenumber=988 kh_destroy_scheme_string /src/htslib/hfile.c linenumber=991 pthread_mutex_unlock linenumber=1005 pthread_mutex_destroy linenumber=1011 pthread_mutex_unlock linenumber=1199 pthread_mutex_unlock linenumber=1202 kh_get_scheme_string /src/htslib/hfile.c linenumber=1204 strchr linenumber=1324 strcmp linenumber=1338 hopen_fd_stdinout /src/htslib/hfile.c linenumber=1338 strchr linenumber=766 snprintf linenumber=768 hdopen /src/htslib/hfile.c linenumber=772 blksize /src/htslib/hfile.c linenumber=740 fstat linenumber=652 hfile_init /src/htslib/hfile.c linenumber=740 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=744 strchr linenumber=745 hopen_fd /src/htslib/hfile.c linenumber=1339 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=1563 strdup linenumber=1570 ed_is_big /src/htslib/./htslib/hts.h linenumber=1571 strchr linenumber=1574 strncpy linenumber=1575 strncpy linenumber=1579 strchr linenumber=1583 hts_detect_format2 /src/htslib/hts.c linenumber=1586 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=1596 hopen_htsget_redirect /src/htslib/multipart.c linenumber=1601 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=5169 realloc linenumber=5173 __errno_location linenumber=5187 strerror linenumber=5187 hts_log /src/htslib/hts.c linenumber=5187 exit linenumber=5188 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=1606 __errno_location linenumber=522 hfile_destroy /src/htslib/hfile.c linenumber=526 __errno_location linenumber=527 hts_crypt4gh_redirect /src/htslib/hts.c linenumber=1614 strlen linenumber=1533 snprintf linenumber=1544 strchr linenumber=1545 snprintf linenumber=1545 hopen /src/htslib/hfile.c linenumber=1546 hts_detect_format2 /src/htslib/hts.c linenumber=1631 strchr linenumber=1634 strchr linenumber=1638 strchr linenumber=1639 strchr linenumber=1640 strchr linenumber=1641 strchr linenumber=1644 strchr linenumber=1645 strchr linenumber=1646 abort linenumber=1655 format_category /src/htslib/hts.c linenumber=1660 __errno_location linenumber=1666 bgzf_hopen /src/htslib/bgzf.c linenumber=1672 strchr linenumber=559 bgzf_read_init /src/htslib/bgzf.c linenumber=560 hpeek /src/htslib/hfile.c linenumber=404 calloc linenumber=407 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=411 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=415 memcmp linenumber=416 hts_log /src/htslib/hts.c linenumber=417 razf_info /src/htslib/bgzf.c linenumber=418 strcmp linenumber=337 hseek /src/htslib/hfile.c linenumber=340 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=341 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=342 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=342 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=1621 hts_log /src/htslib/hts.c linenumber=345 hts_log /src/htslib/hts.c linenumber=356 __errno_location linenumber=421 kh_init_bgzf_cache /src/htslib/bgzf.c linenumber=430 calloc linenumber=87 strchr linenumber=562 bgzf_write_init /src/htslib/bgzf.c linenumber=563 calloc linenumber=455 mode2level /src/htslib/bgzf.c linenumber=467 strchr linenumber=449 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=475 strchr linenumber=481 calloc linenumber=485 deflateInit2_ linenumber=491 bgzf_zerr /src/htslib/bgzf.c linenumber=493 __errno_location linenumber=380 strerror linenumber=380 snprintf linenumber=395 hts_log /src/htslib/hts.c linenumber=493 __errno_location linenumber=500 strerror linenumber=500 hts_log /src/htslib/hts.c linenumber=500 __errno_location linenumber=566 ed_is_big /src/htslib/./htslib/hts.h linenumber=569 cram_dopen /src/htslib/cram/cram_io.c linenumber=1678 calloc linenumber=5012 cram_read_file_def /src/htslib/cram/cram_io.c linenumber=5032 hread /src/htslib/cram/../htslib/hfile.h linenumber=4399 memcmp linenumber=4404 hts_log /src/htslib/hts.c linenumber=4410 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5038 cram_init_varint /src/htslib/cram/cram_io.c linenumber=4970 cram_read_SAM_hdr /src/htslib/cram/cram_io.c linenumber=5040 int32_decode /src/htslib/cram/cram_io.c linenumber=4457 hread /src/htslib/cram/../htslib/hfile.h linenumber=769 hread /src/htslib/cram/../htslib/hfile.h linenumber=4469 cram_read_container /src/htslib/cram/cram_io.c linenumber=4477 int32_decode /src/htslib/cram/cram_io.c linenumber=3550 crc32 linenumber=3561 calloc linenumber=3606 __errno_location linenumber=3612 cram_free_container /src/htslib/cram/cram_io.c linenumber=3613 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=3462 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=4092 cram_free_block /src/htslib/cram/cram_io.c linenumber=4122 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4124 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4126 cram_free_block /src/htslib/cram/cram_io.c linenumber=3465 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3471 free_bam_list /src/htslib/cram/cram_io.c linenumber=4153 bam_destroy1 /src/htslib/sam.c linenumber=3443 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=474 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=476 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=484 cram_free_block /src/htslib/cram/cram_io.c linenumber=4158 cram_free_block /src/htslib/cram/cram_io.c linenumber=4167 cram_free_block /src/htslib/cram/cram_io.c linenumber=4178 cram_free_slice_header /src/htslib/cram/cram_io.c linenumber=4185 cram_free_block /src/htslib/cram/cram_io.c linenumber=4188 cram_free_block /src/htslib/cram/cram_io.c linenumber=4191 cram_free_block /src/htslib/cram/cram_io.c linenumber=4194 cram_free_block /src/htslib/cram/cram_io.c linenumber=4197 cram_free_block /src/htslib/cram/cram_io.c linenumber=4200 cram_free_block /src/htslib/cram/cram_io.c linenumber=4203 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4218 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4221 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4223 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3480 cram_stats_free /src/htslib/cram/cram_stats.c linenumber=3485 kh_destroy_m_i2i /src/htslib/cram/cram_structs.h linenumber=214 cram_free_block /src/htslib/cram/cram_io.c linenumber=3507 cram_free_block /src/htslib/cram/cram_io.c linenumber=3508 kh_destroy_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3513 free_bam_list /src/htslib/cram/cram_io.c linenumber=3520 cram_free_container /src/htslib/cram/cram_io.c linenumber=3623 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3626 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=3627 cram_free_container /src/htslib/cram/cram_io.c linenumber=3628 cram_free_container /src/htslib/cram/cram_io.c linenumber=3633 int32_decode /src/htslib/cram/cram_io.c linenumber=3641 cram_free_container /src/htslib/cram/cram_io.c linenumber=3642 hts_log /src/htslib/hts.c linenumber=3654 cram_free_container /src/htslib/cram/cram_io.c linenumber=3655 cram_free_container /src/htslib/cram/cram_io.c linenumber=4489 cram_read_block /src/htslib/cram/cram_io.c linenumber=4493 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1160 hts_log /src/htslib/hts.c linenumber=1162 crc32 linenumber=1165 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1166 crc32 linenumber=1167 hread /src/htslib/cram/../htslib/hfile.h linenumber=1182 hread /src/htslib/cram/../htslib/hfile.h linenumber=1194 int32_decode /src/htslib/cram/cram_io.c linenumber=1202 cram_free_container /src/htslib/cram/cram_io.c linenumber=4494 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=4497 crc32 linenumber=1323 hts_log /src/htslib/hts.c linenumber=1326 __assert_fail linenumber=1336 hts_log /src/htslib/hts.c linenumber=1347 zlib_mem_inflate /src/htslib/cram/cram_io.c linenumber=1351 __assert_fail linenumber=911 __assert_fail linenumber=914 __assert_fail linenumber=915 inflateInit2_ linenumber=933 hts_log /src/htslib/hts.c linenumber=935 inflate linenumber=941 hts_log /src/htslib/hts.c linenumber=944 inflateEnd linenumber=947 inflateEnd linenumber=951 BZ2_bzBuffToBuffDecompress linenumber=1370 lzma_mem_inflate /src/htslib/cram/cram_io.c linenumber=1391 lzma_easy_decoder_memusage linenumber=1057 lzma_stream_decoder linenumber=1057 realloc linenumber=1067 lzma_code linenumber=1075 hts_log /src/htslib/hts.c linenumber=1077 lzma_code linenumber=1088 hts_log /src/htslib/hts.c linenumber=1090 realloc linenumber=1094 lzma_end linenumber=1099 lzma_end linenumber=1104 rans_uncompress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1412 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=1430 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=1443 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=1462 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=1481 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=4498 cram_free_block /src/htslib/cram/cram_io.c linenumber=4499 int32_get_blk /src/htslib/cram/cram_io.c linenumber=4509 cram_free_container /src/htslib/cram/cram_io.c linenumber=4512 cram_free_block /src/htslib/cram/cram_io.c linenumber=4513 cram_free_container /src/htslib/cram/cram_io.c linenumber=4517 cram_free_block /src/htslib/cram/cram_io.c linenumber=4518 cram_free_block /src/htslib/cram/cram_io.c linenumber=4523 cram_read_block /src/htslib/cram/cram_io.c linenumber=4527 cram_free_container /src/htslib/cram/cram_io.c linenumber=4528 cram_free_block /src/htslib/cram/cram_io.c linenumber=4536 cram_free_container /src/htslib/cram/cram_io.c linenumber=4543 hread /src/htslib/cram/../htslib/hfile.h linenumber=4548 cram_free_container /src/htslib/cram/cram_io.c linenumber=4549 cram_free_container /src/htslib/cram/cram_io.c linenumber=4557 sam_hdr_init /src/htslib/sam.c linenumber=4561 calloc linenumber=112 sam_hdr_add_lines /src/htslib/header.c linenumber=4567 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1687 sam_hrecs_new /src/htslib/header.c linenumber=1307 calloc linenumber=2770 kh_init_sam_hrecs_t /src/htslib/./header.h linenumber=2775 calloc linenumber=168 kh_init_m_s2i /src/htslib/./header.h linenumber=2784 calloc linenumber=169 kh_init_m_s2i /src/htslib/./header.h linenumber=2791 kh_init_m_s2i /src/htslib/./header.h linenumber=2799 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2802 next_power_2 /src/htslib/cram/pooled_alloc.c linenumber=76 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2805 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2808 sam_hrecs_init_type_order /src/htslib/header.c linenumber=2811 calloc linenumber=76 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2818 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2821 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2824 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2827 sam_hrecs_refs_from_targets_array /src/htslib/header.c linenumber=1313 hts_log /src/htslib/hts.c linenumber=1209 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1214 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=1223 kh_resize_m_s2i /src/htslib/./header.h linenumber=169 __errno_location linenumber=169 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=169 string_dup /src/htslib/cram/string_alloc.c linenumber=1229 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=1235 __ac_FNV1a_hash_string /src/htslib/./cram/../htslib/khash.h linenumber=80 strcmp linenumber=80 kh_put_m_s2i /src/htslib/./header.h linenumber=1243 strcmp linenumber=169 hts_log /src/htslib/hts.c linenumber=1246 __errno_location linenumber=1258 strerror linenumber=1258 hts_log /src/htslib/hts.c linenumber=1258 kh_get_m_s2i /src/htslib/./header.h linenumber=1262 kh_del_m_s2i /src/htslib/./header.h linenumber=1263 sam_hrecs_free /src/htslib/header.c linenumber=1314 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2854 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2857 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2863 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2869 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2878 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2881 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2884 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1321 strlen linenumber=1011 sam_hrecs_error /src/htslib/header.c linenumber=1015 hts_log /src/htslib/hts.c linenumber=65 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1026 sam_hrecs_error /src/htslib/header.c linenumber=928 isalpha_c /src/htslib/./textutils_internal.h linenumber=933 __ctype_b_loc linenumber=170 sam_hrecs_error /src/htslib/header.c linenumber=934 TYPEKEY /src/htslib/./header.h linenumber=938 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=944 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=949 kh_resize_sam_hrecs_t /src/htslib/./header.h linenumber=168 realloc linenumber=168 TYPEKEY /src/htslib/./header.h linenumber=956 parse_comment_line /src/htslib/header.c linenumber=958 sam_hrecs_error /src/htslib/header.c linenumber=815 warn_if_known_stderr /src/htslib/header.c linenumber=816 kmemmem /src/htslib/kstring.c linenumber=799 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=800 hts_log /src/htslib/hts.c linenumber=790 hts_log /src/htslib/hts.c linenumber=791 kmemmem /src/htslib/kstring.c linenumber=801 known_stderr /src/htslib/header.c linenumber=802 kmemmem /src/htslib/kstring.c linenumber=803 known_stderr /src/htslib/header.c linenumber=804 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=823 string_ndup /src/htslib/cram/string_alloc.c linenumber=825 parse_noncomment_line /src/htslib/header.c linenumber=965 TYPEKEY /src/htslib/./header.h linenumber=840 sam_hrecs_error /src/htslib/header.c linenumber=850 warn_if_known_stderr /src/htslib/header.c linenumber=851 sam_hrecs_error /src/htslib/header.c linenumber=861 warn_if_known_stderr /src/htslib/header.c linenumber=862 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=874 string_ndup /src/htslib/cram/string_alloc.c linenumber=876 sam_hrecs_global_list_add /src/htslib/header.c linenumber=973 TYPEKEY /src/htslib/./header.h linenumber=510 __assert_fail linenumber=980 sam_hrecs_free_tags /src/htslib/header.c linenumber=997 pool_free /src/htslib/cram/pooled_alloc.c linenumber=707 pool_free /src/htslib/cram/pooled_alloc.c linenumber=998 TYPEKEY /src/htslib/./header.h linenumber=1038 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1053 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1057 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1071 TYPEKEY /src/htslib/./header.h linenumber=150 __assert_fail linenumber=161 __assert_fail linenumber=164 strtoll linenumber=166 __assert_fail linenumber=171 hts_log /src/htslib/hts.c linenumber=178 hts_log /src/htslib/hts.c linenumber=183 hts_log /src/htslib/hts.c linenumber=189 kh_get_m_s2i /src/htslib/./header.h linenumber=195 snprintf linenumber=207 sam_hrecs_update /src/htslib/header.c linenumber=209 sam_hrecs_vupdate /src/htslib/header.c linenumber=3031 sam_hrecs_find_key /src/htslib/header.c linenumber=2989 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=2991 strlen linenumber=3001 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=3002 string_alloc /src/htslib/cram/string_alloc.c linenumber=3002 snprintf linenumber=3006 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=213 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=227 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=231 strcmp linenumber=241 hts_log /src/htslib/hts.c linenumber=242 hts_log /src/htslib/hts.c linenumber=250 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=256 kh_put_m_s2i /src/htslib/./header.h linenumber=267 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=271 TYPEKEY /src/htslib/./header.h linenumber=280 sam_hrecs_find_key /src/htslib/header.c linenumber=281 hts_log /src/htslib/hts.c linenumber=286 __assert_fail linenumber=289 kh_get_m_s2i /src/htslib/./header.h linenumber=292 __assert_fail linenumber=295 hts_log /src/htslib/hts.c linenumber=297 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=308 kh_put_m_s2i /src/htslib/./header.h linenumber=320 TYPEKEY /src/htslib/./header.h linenumber=328 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=335 __assert_fail linenumber=353 hts_log /src/htslib/hts.c linenumber=357 kh_get_m_s2i /src/htslib/./header.h linenumber=362 kh_put_m_s2i /src/htslib/./header.h linenumber=392 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=404 sam_hrecs_free /src/htslib/header.c linenumber=1322 add_stub_ref_sq_lines /src/htslib/header.c linenumber=1327 snprintf linenumber=1289 sam_hrecs_add /src/htslib/header.c linenumber=1290 sam_hrecs_vadd /src/htslib/header.c linenumber=692 TYPEKEY /src/htslib/./header.h linenumber=564 strncmp linenumber=566 sam_hrecs_find_type_id /src/htslib/header.c linenumber=566 kh_get_m_s2i /src/htslib/./header.h linenumber=2916 kh_get_m_s2i /src/htslib/./header.h linenumber=2924 kh_get_m_s2i /src/htslib/./header.h linenumber=2932 TYPEKEY /src/htslib/./header.h linenumber=2939 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=2939 sam_hrecs_vupdate /src/htslib/header.c linenumber=567 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=569 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=571 __assert_fail linenumber=582 sam_hrecs_global_list_add /src/htslib/header.c linenumber=596 __assert_fail linenumber=599 __assert_fail linenumber=600 __assert_fail linenumber=601 __assert_fail linenumber=602 strncmp linenumber=611 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=616 strncmp linenumber=619 strlen linenumber=620 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=621 string_alloc /src/htslib/cram/string_alloc.c linenumber=621 snprintf linenumber=622 strlen linenumber=626 string_ndup /src/htslib/cram/string_alloc.c linenumber=627 strncmp linenumber=648 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=651 strncmp linenumber=654 strlen linenumber=655 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=656 string_alloc /src/htslib/cram/string_alloc.c linenumber=656 snprintf linenumber=657 strlen linenumber=661 string_ndup /src/htslib/cram/string_alloc.c linenumber=662 TYPEKEY /src/htslib/./header.h linenumber=676 sam_hrecs_update_hashes /src/htslib/header.c linenumber=676 strncmp linenumber=679 hts_log /src/htslib/hts.c linenumber=1297 sam_hrecs_free /src/htslib/header.c linenumber=1328 rebuild_target_arrays /src/htslib/header.c linenumber=1334 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1178 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1092 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1097 strcmp linenumber=1112 kh_get_s2i /src/htslib/hts.c linenumber=1117 kh_del_s2i /src/htslib/hts.c linenumber=1119 strdup linenumber=1123 kh_get_s2i /src/htslib/hts.c linenumber=1134 kh_del_s2i /src/htslib/hts.c linenumber=1136 kh_init_s2i /src/htslib/hts.c linenumber=1142 calloc linenumber=80 kh_put_s2i /src/htslib/hts.c linenumber=1148 kh_resize_s2i /src/htslib/hts.c linenumber=80 __errno_location linenumber=80 realloc linenumber=80 kh_get_s2i /src/htslib/hts.c linenumber=1159 kh_del_s2i /src/htslib/hts.c linenumber=1161 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1692 rebuild_target_arrays /src/htslib/header.c linenumber=1695 redact_header_text /src/htslib/header.c linenumber=1699 __assert_fail linenumber=1551 sam_hdr_destroy /src/htslib/sam.c linenumber=4569 sam_hrecs_free /src/htslib/header.c linenumber=138 kh_destroy_s2i /src/htslib/hts.c linenumber=140 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5041 calloc linenumber=5047 strncpy linenumber=5060 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5063 strrchr linenumber=5068 strdup linenumber=5068 refs_create /src/htslib/cram/cram_io.c linenumber=5076 calloc linenumber=2212 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2219 kh_init_refs /src/htslib/cram/cram_structs.h linenumber=2227 calloc linenumber=684 pthread_mutex_init linenumber=2230 refs_free /src/htslib/cram/cram_io.c linenumber=2235 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2181 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2193 mfclose /src/htslib/cram/mFILE.c linenumber=2163 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=2197 bgzf_close /src/htslib/bgzf.c linenumber=2204 bgzf_flush /src/htslib/bgzf.c linenumber=2106 mt_queue /src/htslib/bgzf.c linenumber=1975 pthread_mutex_lock linenumber=1879 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=1880 pthread_mutex_unlock linenumber=1882 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=1891 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=1891 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1379 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1383 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1384 hts_crc32 /src/htslib/bgzf.c linenumber=1387 crc32 linenumber=638 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1388 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1389 job_cleanup /src/htslib/bgzf.c linenumber=1891 pthread_mutex_lock linenumber=1349 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1350 pthread_mutex_unlock linenumber=1351 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=1900 bgzf_encode_func /src/htslib/bgzf.c linenumber=1900 bgzf_compress /src/htslib/bgzf.c linenumber=1358 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=652 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=653 deflateInit2_ linenumber=664 bgzf_zerr /src/htslib/bgzf.c linenumber=666 hts_log /src/htslib/hts.c linenumber=666 deflate linenumber=669 deflateEnd linenumber=671 bgzf_zerr /src/htslib/bgzf.c linenumber=674 hts_log /src/htslib/hts.c linenumber=674 deflateEnd linenumber=682 deflateEnd linenumber=685 bgzf_zerr /src/htslib/bgzf.c linenumber=686 hts_log /src/htslib/hts.c linenumber=686 packInt16 /src/htslib/bgzf.c linenumber=694 crc32 linenumber=696 packInt32 /src/htslib/bgzf.c linenumber=697 packInt32 /src/htslib/bgzf.c linenumber=698 job_cleanup /src/htslib/bgzf.c linenumber=1900 job_cleanup /src/htslib/bgzf.c linenumber=1910 pthread_mutex_lock linenumber=1911 pthread_mutex_unlock linenumber=1913 mt_flush_queue /src/htslib/bgzf.c linenumber=1976 pthread_mutex_lock linenumber=1926 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=1929 pthread_mutex_lock linenumber=335 pthread_mutex_unlock linenumber=337 pthread_mutex_unlock linenumber=1931 hts_usleep /src/htslib/./hts_internal.h linenumber=1932 nanosleep linenumber=162 pthread_mutex_lock linenumber=1933 pthread_mutex_unlock linenumber=1935 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=1941 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=1982 pthread_mutex_unlock linenumber=1984 hflush /src/htslib/hfile.c linenumber=1991 flush_buffer /src/htslib/hfile.c linenumber=392 __errno_location linenumber=394 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1998 bgzf_index_grow /src/htslib/bgzf.c linenumber=2395 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=303 deflate_block /src/htslib/bgzf.c linenumber=2002 bgzf_compress /src/htslib/bgzf.c linenumber=731 bgzf_gzip_compress /src/htslib/bgzf.c linenumber=733 deflate linenumber=712 bgzf_zerr /src/htslib/bgzf.c linenumber=714 hts_log /src/htslib/hts.c linenumber=714 hts_log /src/htslib/hts.c linenumber=718 hts_log /src/htslib/hts.c linenumber=737 bgzf_zerr /src/htslib/bgzf.c linenumber=2004 hts_log /src/htslib/hts.c linenumber=2004 hwrite /src/htslib/./htslib/hfile.h linenumber=2007 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=2008 bgzf_close_mt /src/htslib/bgzf.c linenumber=2107 mt_destroy /src/htslib/bgzf.c linenumber=2096 pthread_mutex_lock linenumber=1830 pthread_cond_signal linenumber=1832 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=1833 pthread_mutex_lock linenumber=925 pthread_cond_signal linenumber=927 pthread_mutex_unlock linenumber=928 pthread_mutex_unlock linenumber=1834 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=1839 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=1843 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=1848 pthread_mutex_destroy linenumber=1851 pthread_mutex_destroy linenumber=1852 pthread_mutex_destroy linenumber=1853 pthread_cond_destroy linenumber=1854 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1856 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=1859 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=1861 fflush linenumber=1867 deflate_block /src/htslib/bgzf.c linenumber=2111 bgzf_zerr /src/htslib/bgzf.c linenumber=2113 hts_log /src/htslib/hts.c linenumber=2113 bgzf_close_mt /src/htslib/bgzf.c linenumber=2114 hwrite /src/htslib/./htslib/hfile.h linenumber=2117 hflush /src/htslib/hfile.c linenumber=2118 hts_log /src/htslib/hts.c linenumber=2119 bgzf_close_mt /src/htslib/bgzf.c linenumber=2125 inflateEnd linenumber=2130 deflateEnd linenumber=2131 bgzf_zerr /src/htslib/bgzf.c linenumber=2133 hts_log /src/htslib/hts.c linenumber=2133 hclose /src/htslib/hfile.c linenumber=2137 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=2139 free_cache /src/htslib/bgzf.c linenumber=2141 kh_destroy_bgzf_cache /src/htslib/bgzf.c linenumber=929 bgzf_clear_private_data /src/htslib/./bgzf_internal.h linenumber=931 __assert_fail linenumber=59 pthread_mutex_destroy linenumber=2206 pthread_mutex_init linenumber=5112 pthread_mutex_init linenumber=5113 pthread_mutex_init linenumber=5114 pthread_mutex_init linenumber=5115 cram_new_metrics /src/htslib/cram/cram_io.c linenumber=5118 calloc linenumber=2072 kh_init_m_metrics /src/htslib/cram/cram_structs.h linenumber=5123 calloc linenumber=294 refs_from_header /src/htslib/cram/cram_io.c linenumber=5133 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2525 hts_realloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=2535 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2549 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=684 strcmp linenumber=684 calloc linenumber=2554 string_dup /src/htslib/cram/string_alloc.c linenumber=2560 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2565 sam_hrecs_find_key /src/htslib/header.c linenumber=2566 string_dup /src/htslib/cram/string_alloc.c linenumber=2567 sam_hrecs_find_key /src/htslib/header.c linenumber=2569 strtoll linenumber=2571 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2578 kh_resize_refs /src/htslib/cram/cram_structs.h linenumber=684 __errno_location linenumber=684 realloc linenumber=684 cram_set_option /src/htslib/cram/cram_io.c linenumber=1681 cram_set_voption /src/htslib/cram/cram_io.c linenumber=5390 __errno_location linenumber=5417 __errno_location linenumber=5423 strdup linenumber=5429 __errno_location linenumber=5437 __errno_location linenumber=5443 __errno_location linenumber=5447 __errno_location linenumber=5451 __errno_location linenumber=5455 __errno_location linenumber=5459 __errno_location linenumber=5463 __errno_location linenumber=5467 __errno_location linenumber=5477 __errno_location linenumber=5481 __errno_location linenumber=5485 __errno_location linenumber=5489 __errno_location linenumber=5493 __errno_location linenumber=5497 refs_free /src/htslib/cram/cram_io.c linenumber=5505 cram_seek_to_refpos /src/htslib/cram/cram_index.c linenumber=5512 cram_index_query /src/htslib/cram/cram_index.c linenumber=577 cram_seek /src/htslib/cram/cram_io.c linenumber=578 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5154 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3726 pthread_mutex_lock linenumber=262 pthread_mutex_unlock linenumber=264 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3727 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=3730 cram_free_container /src/htslib/cram/cram_io.c linenumber=3739 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3743 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3744 cram_free_container /src/htslib/cram/cram_io.c linenumber=3759 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3763 cram_free_container /src/htslib/cram/cram_io.c linenumber=3773 hseek /src/htslib/hfile.c linenumber=5156 pthread_mutex_lock linenumber=586 pthread_mutex_unlock linenumber=594 cram_free_container /src/htslib/cram/cram_io.c linenumber=597 cram_free_container /src/htslib/cram/cram_io.c linenumber=599 pthread_mutex_lock linenumber=611 pthread_mutex_unlock linenumber=613 pthread_mutex_lock linenumber=5513 pthread_mutex_unlock linenumber=5518 pthread_mutex_lock linenumber=5524 pthread_mutex_unlock linenumber=5537 cram_load_reference /src/htslib/cram/cram_io.c linenumber=5542 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3346 strlen linenumber=2290 refs_create /src/htslib/cram/cram_io.c linenumber=2296 bgzf_close /src/htslib/bgzf.c linenumber=2300 strstr linenumber=2305 string_ndup /src/htslib/cram/string_alloc.c linenumber=2307 snprintf linenumber=2310 strcmp linenumber=2313 string_ndup /src/htslib/cram/string_alloc.c linenumber=2315 snprintf linenumber=2318 string_dup /src/htslib/cram/string_alloc.c linenumber=2321 snprintf linenumber=2323 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=2327 strncmp linenumber=2250 hisremote /src/htslib/hfile.c linenumber=2253 find_scheme_handler /src/htslib/hfile.c linenumber=1350 snprintf linenumber=2256 access linenumber=2257 fai_build /src/htslib/faidx.c linenumber=2258 fai_build3 /src/htslib/faidx.c linenumber=597 fai_build3_core /src/htslib/faidx.c linenumber=592 bgzf_open /src/htslib/bgzf.c linenumber=504 strchr linenumber=515 hopen /src/htslib/hfile.c linenumber=517 bgzf_read_init /src/htslib/bgzf.c linenumber=518 hclose_abruptly /src/htslib/hfile.c linenumber=519 strchr linenumber=521 hopen /src/htslib/hfile.c linenumber=523 bgzf_write_init /src/htslib/bgzf.c linenumber=524 __errno_location linenumber=528 ed_is_big /src/htslib/./htslib/hts.h linenumber=530 __errno_location linenumber=507 strerror linenumber=507 hts_log /src/htslib/hts.c linenumber=507 bgzf_index_build_init /src/htslib/bgzf.c linenumber=512 bgzf_index_destroy /src/htslib/bgzf.c linenumber=2386 calloc linenumber=2387 hts_log /src/htslib/hts.c linenumber=513 fai_build_core /src/htslib/faidx.c linenumber=518 calloc linenumber=171 kh_init_s /src/htslib/faidx.c linenumber=172 bgzf_getc_ /src/htslib/faidx.c linenumber=178 bgzf_getc /src/htslib/bgzf.c linenumber=66 bgzf_read_block /src/htslib/bgzf.c linenumber=2325 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=1034 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=1035 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1039 mt_destroy /src/htslib/bgzf.c linenumber=1043 hts_log /src/htslib/hts.c linenumber=1056 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1059 hts_log /src/htslib/hts.c linenumber=1066 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1076 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1090 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1092 pthread_mutex_lock linenumber=1101 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1102 pthread_mutex_unlock linenumber=1103 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1112 bgzf_htell /src/htslib/bgzf.c linenumber=1123 pthread_mutex_lock linenumber=1012 pthread_mutex_unlock linenumber=1014 htell /src/htslib/./htslib/hfile.h linenumber=1017 hread /src/htslib/./htslib/hfile.h linenumber=1128 __errno_location linenumber=1131 strerror linenumber=1131 hts_log /src/htslib/hts.c linenumber=1131 inflate_gzip_block /src/htslib/bgzf.c linenumber=1151 hread /src/htslib/./htslib/hfile.h linenumber=861 inflate linenumber=875 bgzf_zerr /src/htslib/bgzf.c linenumber=879 hts_log /src/htslib/hts.c linenumber=879 hpeek /src/htslib/hfile.c linenumber=887 inflateReset linenumber=889 bgzf_zerr /src/htslib/bgzf.c linenumber=891 hts_log /src/htslib/hts.c linenumber=891 hts_log /src/htslib/hts.c linenumber=902 hts_log /src/htslib/hts.c linenumber=1154 load_block_from_cache /src/htslib/bgzf.c linenumber=1163 kh_get_bgzf_cache /src/htslib/bgzf.c linenumber=941 hseek /src/htslib/hfile.c linenumber=948 hts_log /src/htslib/hts.c linenumber=951 exit linenumber=952 hread /src/htslib/./htslib/hfile.h linenumber=1168 hts_log /src/htslib/hts.c linenumber=1172 check_header /src/htslib/bgzf.c linenumber=1178 unpackInt16 /src/htslib/bgzf.c linenumber=917 unpackInt16 /src/htslib/bgzf.c linenumber=919 hts_log /src/htslib/hts.c linenumber=1181 hread /src/htslib/./htslib/hfile.h linenumber=1191 calloc linenumber=1194 inflateInit2_ linenumber=1196 bgzf_zerr /src/htslib/bgzf.c linenumber=1199 hts_log /src/htslib/hts.c linenumber=1199 inflate_gzip_block /src/htslib/bgzf.c linenumber=1205 hts_log /src/htslib/hts.c linenumber=1208 unpackInt16 /src/htslib/bgzf.c linenumber=1219 hts_log /src/htslib/hts.c linenumber=1222 hread /src/htslib/./htslib/hfile.h linenumber=1230 hts_log /src/htslib/hts.c linenumber=1232 inflate_block /src/htslib/bgzf.c linenumber=1239 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=828 bgzf_uncompress /src/htslib/bgzf.c linenumber=829 inflateInit2_ linenumber=792 bgzf_zerr /src/htslib/bgzf.c linenumber=794 hts_log /src/htslib/hts.c linenumber=794 inflate linenumber=797 bgzf_zerr /src/htslib/bgzf.c linenumber=798 hts_log /src/htslib/hts.c linenumber=798 inflateEnd linenumber=799 bgzf_zerr /src/htslib/bgzf.c linenumber=800 hts_log /src/htslib/hts.c linenumber=800 inflateEnd linenumber=804 bgzf_zerr /src/htslib/bgzf.c linenumber=805 hts_log /src/htslib/hts.c linenumber=805 crc32 linenumber=810 hts_log /src/htslib/hts.c linenumber=816 bgzf_zerr /src/htslib/bgzf.c linenumber=1240 hts_log /src/htslib/hts.c linenumber=1240 bgzf_htell /src/htslib/bgzf.c linenumber=1248 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1255 cache_block /src/htslib/bgzf.c linenumber=1261 kh_del_bgzf_cache /src/htslib/bgzf.c linenumber=986 kh_put_bgzf_cache /src/htslib/bgzf.c linenumber=992 kh_resize_bgzf_cache /src/htslib/bgzf.c linenumber=87 __errno_location linenumber=87 realloc linenumber=87 bgzf_htell /src/htslib/bgzf.c linenumber=2330 hts_log /src/htslib/hts.c linenumber=184 hts_log /src/htslib/hts.c linenumber=194 bgzf_getc_ /src/htslib/faidx.c linenumber=204 hts_log /src/htslib/hts.c linenumber=207 __ctype_b_loc linenumber=219 hts_log /src/htslib/hts.c linenumber=219 fai_insert_index /src/htslib/faidx.c linenumber=227 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 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=122 hts_log /src/htslib/hts.c linenumber=123 strdup linenumber=130 __errno_location linenumber=132 strerror linenumber=132 hts_log /src/htslib/hts.c linenumber=132 kh_put_s /src/htslib/faidx.c linenumber=137 kh_resize_s /src/htslib/faidx.c linenumber=80 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=80 __errno_location linenumber=139 strerror linenumber=139 hts_log /src/htslib/hts.c linenumber=139 hts_log /src/htslib/hts.c linenumber=144 __ctype_b_loc linenumber=236 kputc_ /src/htslib/./htslib/kstring.h linenumber=237 ks_resize /src/htslib/./htslib/kstring.h linenumber=270 bgzf_getc_ /src/htslib/faidx.c linenumber=242 kputsn /src/htslib/./htslib/kstring.h linenumber=244 hts_log /src/htslib/hts.c linenumber=248 bgzf_getc_ /src/htslib/faidx.c linenumber=253 bgzf_utell /src/htslib/bgzf.c linenumber=256 bgzf_getc_ /src/htslib/faidx.c linenumber=273 bgzf_utell /src/htslib/bgzf.c linenumber=274 hts_log /src/htslib/hts.c linenumber=278 isgraph_ /src/htslib/faidx.c linenumber=289 bgzf_getc_ /src/htslib/faidx.c linenumber=290 hts_log /src/htslib/hts.c linenumber=305 bgzf_getc_ /src/htslib/faidx.c linenumber=315 bgzf_utell /src/htslib/bgzf.c linenumber=316 hts_log /src/htslib/hts.c linenumber=319 hts_log /src/htslib/hts.c linenumber=327 isgraph_ /src/htslib/faidx.c linenumber=343 bgzf_getc_ /src/htslib/faidx.c linenumber=344 hts_log /src/htslib/hts.c linenumber=349 hts_log /src/htslib/hts.c linenumber=354 fai_insert_index /src/htslib/faidx.c linenumber=367 hts_log /src/htslib/hts.c linenumber=370 fai_destroy /src/htslib/faidx.c linenumber=379 kh_destroy_s /src/htslib/faidx.c linenumber=488 bgzf_close /src/htslib/bgzf.c linenumber=489 hts_log /src/htslib/hts.c linenumber=522 ksprintf /src/htslib/kstring.c linenumber=534 ksprintf /src/htslib/kstring.c linenumber=539 bgzf_index_dump /src/htslib/bgzf.c linenumber=544 hts_log /src/htslib/hts.c linenumber=2460 __errno_location linenumber=2461 get_name_suffix /src/htslib/bgzf.c linenumber=2467 strlen linenumber=2412 snprintf linenumber=2415 hopen /src/htslib/hfile.c linenumber=2472 bgzf_index_dump_hfile /src/htslib/bgzf.c linenumber=2478 hts_log /src/htslib/hts.c linenumber=2428 __errno_location linenumber=2429 bgzf_flush /src/htslib/bgzf.c linenumber=2433 hwrite_uint64 /src/htslib/bgzf.c linenumber=2439 ed_is_big /src/htslib/./htslib/hts.h linenumber=2405 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2405 hwrite /src/htslib/./htslib/hfile.h linenumber=2406 hwrite_uint64 /src/htslib/bgzf.c linenumber=2443 hwrite_uint64 /src/htslib/bgzf.c linenumber=2444 __errno_location linenumber=2449 strerror linenumber=2449 hts_log /src/htslib/hts.c linenumber=2449 hclose /src/htslib/hfile.c linenumber=2480 __errno_location linenumber=2492 strerror linenumber=2492 hts_log /src/htslib/hts.c linenumber=2492 hclose_abruptly /src/htslib/hfile.c linenumber=2494 hts_log /src/htslib/hts.c linenumber=545 bgzf_close /src/htslib/bgzf.c linenumber=550 __errno_location linenumber=554 strerror linenumber=554 hts_log /src/htslib/hts.c linenumber=554 hopen /src/htslib/hfile.c linenumber=558 __errno_location linenumber=561 strerror linenumber=561 hts_log /src/htslib/hts.c linenumber=561 fai_save /src/htslib/faidx.c linenumber=565 kh_get_s /src/htslib/faidx.c linenumber=391 __assert_fail linenumber=392 snprintf linenumber=396 snprintf linenumber=400 hputs /src/htslib/./htslib/hfile.h linenumber=406 strlen linenumber=280 hputs2 /src/htslib/hfile.c linenumber=284 hwrite2 /src/htslib/hfile.c linenumber=443 hputs /src/htslib/./htslib/hfile.h linenumber=407 strerror linenumber=566 hts_log /src/htslib/hts.c linenumber=566 hclose /src/htslib/hfile.c linenumber=570 __errno_location linenumber=571 strerror linenumber=571 hts_log /src/htslib/hts.c linenumber=571 fai_destroy /src/htslib/faidx.c linenumber=577 __errno_location linenumber=581 bgzf_close /src/htslib/bgzf.c linenumber=584 fai_destroy /src/htslib/faidx.c linenumber=585 __errno_location linenumber=586 bgzf_open /src/htslib/bgzf.c linenumber=2262 perror linenumber=2263 bgzf_index_load /src/htslib/bgzf.c linenumber=2267 get_name_suffix /src/htslib/bgzf.c linenumber=2547 hopen /src/htslib/hfile.c linenumber=2552 bgzf_index_load_hfile /src/htslib/bgzf.c linenumber=2558 calloc linenumber=2508 hread_uint64 /src/htslib/bgzf.c linenumber=2511 hread /src/htslib/./htslib/hfile.h linenumber=2501 ed_is_big /src/htslib/./htslib/hts.h linenumber=2502 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2502 hread_uint64 /src/htslib/bgzf.c linenumber=2524 hread_uint64 /src/htslib/bgzf.c linenumber=2525 __errno_location linenumber=2531 strerror linenumber=2531 hts_log /src/htslib/hts.c linenumber=2531 hclose /src/htslib/hfile.c linenumber=2560 __errno_location linenumber=2571 strerror linenumber=2571 hts_log /src/htslib/hts.c linenumber=2571 hclose_abruptly /src/htslib/hfile.c linenumber=2573 hts_log /src/htslib/hts.c linenumber=2268 bgzf_close /src/htslib/bgzf.c linenumber=2269 hts_log /src/htslib/hts.c linenumber=2328 hopen /src/htslib/hfile.c linenumber=2332 hts_log /src/htslib/hts.c linenumber=2333 perror linenumber=2335 hgets /src/htslib/hfile.c linenumber=2338 __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=2348 string_dup /src/htslib/cram/string_alloc.c linenumber=2351 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2354 strtoll linenumber=2356 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2359 strtoll linenumber=2361 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2364 strtol linenumber=2366 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2369 strtol linenumber=2371 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2382 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2408 hclose /src/htslib/hfile.c linenumber=2420 hclose_abruptly /src/htslib/hfile.c linenumber=2426 refs_free /src/htslib/cram/cram_io.c linenumber=2429 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3351 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2448 strcmp linenumber=2460 __assert_fail linenumber=2460 hts_log /src/htslib/hts.c linenumber=2464 refs_free /src/htslib/cram/cram_io.c linenumber=3357 refs_create /src/htslib/cram/cram_io.c linenumber=3358 refs_from_header /src/htslib/cram/cram_io.c linenumber=3360 refs2id /src/htslib/cram/cram_io.c linenumber=3365 calloc linenumber=2490 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2496 hts_log /src/htslib/hts.c linenumber=2500 __isoc99_sscanf linenumber=5547 hts_log /src/htslib/hts.c linenumber=5548 hts_log /src/htslib/hts.c linenumber=5554 __errno_location linenumber=5556 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5566 __errno_location linenumber=5572 __errno_location linenumber=5578 hts_tpool_init /src/htslib/thread_pool.c linenumber=5582 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 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=5585 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=5599 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5598 __errno_location linenumber=5612 __errno_location linenumber=5618 __errno_location linenumber=5622 __errno_location linenumber=5626 __errno_location linenumber=5630 hts_log /src/htslib/hts.c linenumber=5669 __errno_location linenumber=5670 bgzf_hopen /src/htslib/bgzf.c linenumber=1693 __errno_location linenumber=1702 hts_process_opts /src/htslib/hts.c linenumber=1707 hts_parse_opt_list /src/htslib/hts.c linenumber=1513 strncpy linenumber=1409 hts_opt_add /src/htslib/hts.c linenumber=1412 strdup linenumber=1089 strchr linenumber=1094 strcmp linenumber=1099 strcmp linenumber=1100 get_int /src/htslib/hts.c linenumber=1102 get_int_kmg /src/htslib/hts.c linenumber=1064 strtol linenumber=1029 hts_log /src/htslib/hts.c linenumber=1033 hts_log /src/htslib/hts.c linenumber=1047 hts_log /src/htslib/hts.c linenumber=1052 strcmp linenumber=1105 strcmp linenumber=1106 get_int /src/htslib/hts.c linenumber=1108 strcmp linenumber=1111 get_int /src/htslib/hts.c linenumber=1114 strcmp linenumber=1117 strcmp linenumber=1118 get_int /src/htslib/hts.c linenumber=1120 strcmp linenumber=1123 strcmp linenumber=1124 get_int /src/htslib/hts.c linenumber=1126 strcmp linenumber=1129 strcmp linenumber=1130 get_int /src/htslib/hts.c linenumber=1132 strcmp linenumber=1135 strcmp linenumber=1136 get_int /src/htslib/hts.c linenumber=1138 strcmp linenumber=1141 strcmp linenumber=1142 get_int /src/htslib/hts.c linenumber=1144 strcmp linenumber=1147 strcmp linenumber=1148 get_int /src/htslib/hts.c linenumber=1150 strcmp linenumber=1153 strcmp linenumber=1154 get_int /src/htslib/hts.c linenumber=1156 strcmp linenumber=1159 strcmp linenumber=1160 get_int /src/htslib/hts.c linenumber=1162 strcmp linenumber=1165 strcmp linenumber=1166 get_int /src/htslib/hts.c linenumber=1168 strcmp linenumber=1171 strcmp linenumber=1172 get_int /src/htslib/hts.c linenumber=1174 strcmp linenumber=1177 strcmp linenumber=1178 get_int /src/htslib/hts.c linenumber=1180 strcmp linenumber=1183 strcmp linenumber=1184 get_int /src/htslib/hts.c linenumber=1186 strcmp linenumber=1189 strcmp linenumber=1190 strcmp linenumber=1193 strcmp linenumber=1194 strcmp linenumber=1197 strcmp linenumber=1198 strcmp linenumber=1201 strcmp linenumber=1202 strcmp linenumber=1205 strcmp linenumber=1206 strcmp linenumber=1209 strcmp linenumber=1210 strcmp linenumber=1213 strcmp linenumber=1214 atoi linenumber=1215 get_int /src/htslib/hts.c linenumber=1216 strcmp linenumber=1219 strcmp linenumber=1220 get_int /src/htslib/hts.c linenumber=1222 strcmp linenumber=1225 strcmp linenumber=1226 get_int_kmg /src/htslib/hts.c linenumber=1228 strcmp linenumber=1231 strcmp linenumber=1232 get_int /src/htslib/hts.c linenumber=1234 strcmp linenumber=1237 strcmp linenumber=1238 get_int /src/htslib/hts.c linenumber=1241 strcmp linenumber=1244 strcmp linenumber=1245 strcmp linenumber=1248 strcmp linenumber=1249 get_int /src/htslib/hts.c linenumber=1251 strcmp linenumber=1254 strcmp linenumber=1255 get_int /src/htslib/hts.c linenumber=1257 strcmp linenumber=1260 strcmp linenumber=1261 get_int_kmg /src/htslib/hts.c linenumber=1263 strcmp linenumber=1266 strcmp linenumber=1267 get_int /src/htslib/hts.c linenumber=1269 strcmp linenumber=1272 strcmp linenumber=1273 strcmp linenumber=1276 strcmp linenumber=1277 strcmp linenumber=1280 strcmp linenumber=1281 strcmp linenumber=1284 strcmp linenumber=1285 strcmp linenumber=1288 strcmp linenumber=1289 strcmp linenumber=1292 strcmp linenumber=1293 strcmp linenumber=1296 strcmp linenumber=1297 strcmp linenumber=1300 strcmp linenumber=1301 strcmp linenumber=1304 strcmp linenumber=1305 get_int /src/htslib/hts.c linenumber=1307 hts_log /src/htslib/hts.c linenumber=1311 hts_opt_apply /src/htslib/hts.c linenumber=1516 strdup linenumber=1349 hts_set_opt /src/htslib/hts.c linenumber=1359 hts_set_threads /src/htslib/hts.c linenumber=1897 sam_set_threads /src/htslib/sam.c linenumber=2022 hts_tpool_init /src/htslib/thread_pool.c linenumber=3778 sam_set_thread_pool /src/htslib/sam.c linenumber=3781 sam_state_create /src/htslib/sam.c linenumber=3750 calloc linenumber=3082 pthread_mutex_init linenumber=3754 pthread_mutex_init linenumber=3755 pthread_cond_init linenumber=3756 hts_tpool_size /src/htslib/thread_pool.c linenumber=3760 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=3761 sam_state_destroy /src/htslib/sam.c linenumber=3763 pthread_mutex_lock linenumber=3128 pthread_cond_signal linenumber=3131 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3134 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3141 pthread_mutex_unlock linenumber=3142 hts_usleep /src/htslib/./hts_internal.h linenumber=3143 pthread_mutex_lock linenumber=3144 pthread_mutex_unlock linenumber=3147 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3153 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=832 sam_format_worker /src/htslib/sam.c linenumber=3153 pthread_mutex_lock linenumber=3687 pthread_mutex_unlock linenumber=3692 calloc linenumber=3695 sam_state_err /src/htslib/sam.c linenumber=3697 pthread_mutex_lock linenumber=3096 pthread_mutex_unlock linenumber=3099 sam_format1_append /src/htslib/sam.c linenumber=3709 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4356 __errno_location linenumber=279 ks_resize /src/htslib/./htslib/kstring.h linenumber=280 kputc_ /src/htslib/./htslib/kstring.h linenumber=4357 kputw /src/htslib/./htslib/kstring.h linenumber=4358 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=4358 kputs /src/htslib/./htslib/kstring.h linenumber=4360 kputc_ /src/htslib/./htslib/kstring.h linenumber=4361 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4362 kputll /src/htslib/./htslib/kstring.h linenumber=4363 ks_resize /src/htslib/./htslib/kstring.h linenumber=388 kputuw /src/htslib/./htslib/kstring.h linenumber=398 kputc_ /src/htslib/./htslib/kstring.h linenumber=4363 kputw /src/htslib/./htslib/kstring.h linenumber=4364 kputc_ /src/htslib/./htslib/kstring.h linenumber=4364 kputw /src/htslib/./htslib/kstring.h linenumber=4368 kputc_ /src/htslib/./htslib/kstring.h linenumber=4369 kputc_ /src/htslib/./htslib/kstring.h linenumber=4371 kputc_ /src/htslib/./htslib/kstring.h linenumber=4372 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4373 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4374 kputs /src/htslib/./htslib/kstring.h linenumber=4376 kputc_ /src/htslib/./htslib/kstring.h linenumber=4377 kputll /src/htslib/./htslib/kstring.h linenumber=4379 kputc_ /src/htslib/./htslib/kstring.h linenumber=4379 kputll /src/htslib/./htslib/kstring.h linenumber=4380 kputc_ /src/htslib/./htslib/kstring.h linenumber=4380 ks_resize /src/htslib/./htslib/kstring.h linenumber=4383 nibble2base /src/htslib/./sam_internal.h linenumber=4387 add33 /src/htslib/sam.c linenumber=4397 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4403 kputc_ /src/htslib/./htslib/kstring.h linenumber=4409 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4410 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1498 kputc_ /src/htslib/./htslib/kstring.h linenumber=1499 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1501 kputw /src/htslib/./htslib/kstring.h linenumber=1502 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1505 kputw /src/htslib/./htslib/kstring.h linenumber=1506 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1510 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1511 kputuw /src/htslib/./htslib/kstring.h linenumber=1511 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1516 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1517 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=241 kputw /src/htslib/./htslib/kstring.h linenumber=1517 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1522 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1523 kputuw /src/htslib/./htslib/kstring.h linenumber=1523 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1528 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1529 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=252 kputw /src/htslib/./htslib/kstring.h linenumber=1529 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1533 kputc /src/htslib/./htslib/kstring.h linenumber=1534 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1539 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=314 ksprintf /src/htslib/kstring.c linenumber=1539 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=1549 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=330 ksprintf /src/htslib/kstring.c linenumber=1549 kputc_ /src/htslib/./htslib/kstring.h linenumber=1553 kputc_ /src/htslib/./htslib/kstring.h linenumber=1554 kputc_ /src/htslib/./htslib/kstring.h linenumber=1555 kputsn /src/htslib/./htslib/kstring.h linenumber=1556 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1583 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1587 kputc /src/htslib/./htslib/kstring.h linenumber=1588 ks_expand /src/htslib/./htslib/kstring.h linenumber=1591 __errno_location linenumber=183 ks_resize /src/htslib/./htslib/kstring.h linenumber=184 kputw /src/htslib/./htslib/kstring.h linenumber=1594 ks_expand /src/htslib/./htslib/kstring.h linenumber=1599 kputuw /src/htslib/./htslib/kstring.h linenumber=1602 ks_expand /src/htslib/./htslib/kstring.h linenumber=1607 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1610 kputw /src/htslib/./htslib/kstring.h linenumber=1610 ks_expand /src/htslib/./htslib/kstring.h linenumber=1615 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1618 kputuw /src/htslib/./htslib/kstring.h linenumber=1618 ks_expand /src/htslib/./htslib/kstring.h linenumber=1623 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1626 kputw /src/htslib/./htslib/kstring.h linenumber=1626 ks_expand /src/htslib/./htslib/kstring.h linenumber=1631 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1634 kputuw /src/htslib/./htslib/kstring.h linenumber=1634 ks_expand /src/htslib/./htslib/kstring.h linenumber=1639 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1643 kputd /src/htslib/kstring.c linenumber=1643 __errno_location linenumber=1656 hts_log /src/htslib/hts.c linenumber=1660 __errno_location linenumber=1661 kputsn /src/htslib/./htslib/kstring.h linenumber=4413 hts_log /src/htslib/hts.c linenumber=4419 __errno_location linenumber=4421 hts_log /src/htslib/hts.c linenumber=4425 __errno_location linenumber=4426 __errno_location linenumber=3710 sam_state_err /src/htslib/sam.c linenumber=3710 kputc /src/htslib/./htslib/kstring.h linenumber=3713 pthread_mutex_lock linenumber=3716 pthread_mutex_unlock linenumber=3730 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3157 pthread_mutex_lock linenumber=3158 pthread_mutex_unlock linenumber=3160 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3162 hts_usleep /src/htslib/./hts_internal.h linenumber=3163 pthread_mutex_lock linenumber=3164 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=3167 pthread_mutex_unlock linenumber=3169 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3172 pthread_join linenumber=3177 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=3183 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3186 pthread_mutex_destroy linenumber=3189 pthread_mutex_destroy linenumber=3190 pthread_cond_destroy linenumber=3191 sam_free_sp_bams /src/htslib/sam.c linenumber=3206 sam_free_sp_bams /src/htslib/sam.c linenumber=3211 bam_hdr_destroy /src/htslib/./htslib/sam.h linenumber=3217 sam_hdr_destroy /src/htslib/sam.c linenumber=404 bgzf_thread_pool /src/htslib/bgzf.c linenumber=3768 calloc linenumber=1768 hts_tpool_size /src/htslib/thread_pool.c linenumber=1773 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=1776 hts_tpool_process_ref_incr /src/htslib/thread_pool.c linenumber=1778 pthread_mutex_lock linenumber=270 pthread_mutex_unlock linenumber=272 pool_create /src/htslib/cram/pooled_alloc.c linenumber=1780 pthread_mutex_init linenumber=1784 pthread_mutex_init linenumber=1785 pthread_mutex_init linenumber=1786 pthread_cond_init linenumber=1787 pthread_create linenumber=1792 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3784 hts_get_bgzfp /src/htslib/hts.c linenumber=2024 bgzf_mt /src/htslib/bgzf.c linenumber=2024 hts_tpool_init /src/htslib/thread_pool.c linenumber=1810 bgzf_thread_pool /src/htslib/bgzf.c linenumber=1815 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=1816 hts_set_opt /src/htslib/hts.c linenumber=2026 hts_hfile /src/htslib/hts.c linenumber=1901 bgzf_hfile /src/htslib/bgzf.c linenumber=1875 cram_hfile /src/htslib/./cram/cram_io.h linenumber=1876 bgzf_hfile /src/htslib/bgzf.c linenumber=1882 hfile_set_blksize /src/htslib/hfile.c linenumber=1905 hts_log /src/htslib/hts.c linenumber=1906 hts_log /src/htslib/hts.c linenumber=1911 hts_set_thread_pool /src/htslib/hts.c linenumber=1921 sam_set_thread_pool /src/htslib/sam.c linenumber=2033 hts_get_bgzfp /src/htslib/hts.c linenumber=2035 bgzf_thread_pool /src/htslib/bgzf.c linenumber=2035 hts_set_opt /src/htslib/hts.c linenumber=2037 hts_set_cache_size /src/htslib/hts.c linenumber=1928 hts_get_bgzfp /src/htslib/hts.c linenumber=2045 bgzf_set_cache_size /src/htslib/bgzf.c linenumber=2045 fastq_state_set /src/htslib/sam.c linenumber=1937 fastq_state_init /src/htslib/sam.c linenumber=3848 calloc linenumber=3814 strcpy linenumber=3817 regcomp linenumber=3821 strcmp linenumber=3868 kh_init_tag /src/htslib/sam.c linenumber=3870 calloc linenumber=64 strlen linenumber=3873 hts_log /src/htslib/hts.c linenumber=3877 kh_put_tag /src/htslib/sam.c linenumber=3881 kh_resize_tag /src/htslib/sam.c linenumber=64 __errno_location linenumber=64 realloc linenumber=64 strncpy linenumber=3893 strcmp linenumber=3903 isalpha_c /src/htslib/./textutils_internal.h linenumber=3907 isalnum_c /src/htslib/./textutils_internal.h linenumber=3907 strncpy linenumber=3912 hts_log /src/htslib/hts.c linenumber=3926 regfree linenumber=3936 regcomp linenumber=3937 hts_log /src/htslib/hts.c linenumber=3938 fastq_state_set /src/htslib/sam.c linenumber=1946 fastq_state_set /src/htslib/sam.c linenumber=1958 cram_set_option /src/htslib/cram/cram_io.c linenumber=1970 hts_set_filter_expression /src/htslib/hts.c linenumber=1978 hts_filter_free /src/htslib/hts_expr.c linenumber=2067 regfree linenumber=951 hts_filter_init /src/htslib/hts_expr.c linenumber=2074 calloc linenumber=932 strlen linenumber=936 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=937 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=2011 hts_set_opt /src/htslib/hts.c linenumber=1363 hts_opt_free /src/htslib/hts.c linenumber=1517 hts_opt_free /src/htslib/hts.c linenumber=1521 hclose_abruptly /src/htslib/hfile.c linenumber=1715 hts_log /src/htslib/hts.c linenumber=1720 hclose_abruptly /src/htslib/hfile.c linenumber=1723 hclose /src/htslib/hfile.c linenumber=188 abort linenumber=189 hts_close /src/htslib/hts.c linenumber=194 __errno_location linenumber=1740 bgzf_close /src/htslib/bgzf.c linenumber=1748 cram_eof /src/htslib/cram/cram_io.c linenumber=1753 hts_log /src/htslib/hts.c linenumber=1755 cram_close /src/htslib/cram/cram_io.c linenumber=1762 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=5278 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=5280 pthread_mutex_lock linenumber=4015 reset_metrics /src/htslib/cram/cram_io.c linenumber=4018 pthread_mutex_unlock linenumber=3983 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3984 pthread_mutex_lock linenumber=3985 pthread_mutex_unlock linenumber=4021 cram_flush_container /src/htslib/cram/cram_io.c linenumber=4024 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=3872 pthread_mutex_lock linenumber=1823 hts_log /src/htslib/hts.c linenumber=1826 hts_log /src/htslib/hts.c linenumber=1831 pthread_mutex_lock linenumber=1838 pthread_mutex_unlock linenumber=1840 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1852 pthread_mutex_lock linenumber=3168 hts_log /src/htslib/hts.c linenumber=3183 pthread_mutex_unlock linenumber=3184 pthread_mutex_lock linenumber=3201 hts_log /src/htslib/hts.c linenumber=3204 cram_populate_ref /src/htslib/cram/cram_io.c linenumber=3206 getenv linenumber=2723 getenv linenumber=2728 hts_log /src/htslib/hts.c linenumber=2732 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2737 sam_hrecs_find_key /src/htslib/header.c linenumber=2740 hts_log /src/htslib/hts.c linenumber=2743 expand_cache_path /src/htslib/cram/cram_io.c linenumber=2748 strchr linenumber=2634 strncpy linenumber=2636 strlen linenumber=2641 strcpy linenumber=2643 strtol linenumber=2652 strlen linenumber=2653 strncpy linenumber=2656 strlen linenumber=2675 strcpy linenumber=2677 strlen linenumber=2681 strcpy linenumber=2685 stat linenumber=2749 stat linenumber=2770 bgzf_open /src/htslib/bgzf.c linenumber=2772 string_dup /src/htslib/cram/string_alloc.c linenumber=2776 bgzf_close /src/htslib/bgzf.c linenumber=2779 open_path_mfile /src/htslib/cram/open_trace_file.c linenumber=2795 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=2797 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=2815 strstr linenumber=2818 strncmp linenumber=2819 hts_log /src/htslib/hts.c linenumber=2821 strncmp linenumber=2825 bgzf_close /src/htslib/bgzf.c linenumber=2830 refs_load_fai /src/htslib/cram/cram_io.c linenumber=2834 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=2836 bgzf_close /src/htslib/bgzf.c linenumber=2840 refs2id /src/htslib/cram/cram_io.c linenumber=2848 expand_cache_path /src/htslib/cram/cram_io.c linenumber=2861 hts_log /src/htslib/hts.c linenumber=2864 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2865 strrchr linenumber=2693 is_directory /src/htslib/cram/cram_io.c linenumber=2698 stat linenumber=2620 mkdir linenumber=2703 chmod linenumber=2704 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2709 mkdir linenumber=2710 chmod linenumber=2711 hts_open_tmpfile /src/htslib/hts.c linenumber=2867 getpid linenumber=2080 time linenumber=2087 clock linenumber=2087 ks_clear /src/htslib/./htslib/kstring.h linenumber=2090 ksprintf /src/htslib/kstring.c linenumber=2091 hopen /src/htslib/hfile.c linenumber=2093 __errno_location linenumber=2094 perror linenumber=2869 hts_md5_init /src/htslib/md5.c linenumber=2881 hts_md5_reset /src/htslib/md5.c linenumber=329 hclose_abruptly /src/htslib/hfile.c linenumber=2882 unlink linenumber=2883 hts_md5_update /src/htslib/md5.c linenumber=2887 body /src/htslib/md5.c linenumber=260 body /src/htslib/md5.c linenumber=264 hts_md5_final /src/htslib/md5.c linenumber=2888 body /src/htslib/md5.c linenumber=283 body /src/htslib/md5.c linenumber=300 hts_md5_destroy /src/htslib/md5.c linenumber=2889 hts_md5_hex /src/htslib/md5.c linenumber=2890 strncmp linenumber=2892 hts_log /src/htslib/hts.c linenumber=2893 hclose_abruptly /src/htslib/hfile.c linenumber=2894 unlink linenumber=2895 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=2900 hclose /src/htslib/hfile.c linenumber=2901 chmod linenumber=2902 rename linenumber=2903 __errno_location linenumber=2904 strerror linenumber=2904 hts_log /src/htslib/hts.c linenumber=2904 unlink linenumber=2906 hts_log /src/htslib/hts.c linenumber=3207 hts_log /src/htslib/hts.c linenumber=3209 pthread_mutex_unlock linenumber=3210 pthread_mutex_unlock linenumber=3211 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3216 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3248 cram_ref_load /src/htslib/cram/cram_io.c linenumber=3251 __assert_fail linenumber=3077 __assert_fail linenumber=3087 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3091 strcmp linenumber=3099 bgzf_close /src/htslib/bgzf.c linenumber=3101 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3104 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3110 bgzf_useek /src/htslib/bgzf.c linenumber=2999 hseek /src/htslib/hfile.c linenumber=2593 bgzf_read_block /src/htslib/bgzf.c linenumber=2601 bgzf_seek_common /src/htslib/bgzf.c linenumber=2626 pthread_mutex_lock linenumber=2213 pthread_cond_signal linenumber=2220 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=2221 pthread_cond_wait linenumber=2223 pthread_cond_signal linenumber=2228 abort linenumber=2231 __errno_location linenumber=2239 pthread_mutex_unlock linenumber=2240 pthread_mutex_unlock linenumber=2248 hseek /src/htslib/hfile.c linenumber=2250 bgzf_read_block /src/htslib/bgzf.c linenumber=2629 __assert_fail linenumber=2641 perror linenumber=3000 bgzf_read /src/htslib/bgzf.c linenumber=3008 __assert_fail linenumber=1270 bgzf_read_block /src/htslib/bgzf.c linenumber=1275 hts_log /src/htslib/hts.c linenumber=1277 bgzf_htell /src/htslib/bgzf.c linenumber=1287 hts_log /src/htslib/hts.c linenumber=1292 bgzf_htell /src/htslib/bgzf.c linenumber=1307 perror linenumber=3009 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3026 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3031 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3040 hts_log /src/htslib/hts.c linenumber=3047 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=3054 toupper linenumber=180 pthread_mutex_unlock linenumber=3252 pthread_mutex_unlock linenumber=3253 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3261 pthread_mutex_unlock linenumber=3277 pthread_mutex_unlock linenumber=3278 pthread_mutex_unlock linenumber=3298 pthread_mutex_unlock linenumber=3299 strcmp linenumber=3304 bgzf_close /src/htslib/bgzf.c linenumber=3306 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3309 pthread_mutex_unlock linenumber=3310 pthread_mutex_unlock linenumber=3311 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3316 pthread_mutex_unlock linenumber=3317 pthread_mutex_unlock linenumber=3318 pthread_mutex_unlock linenumber=3331 pthread_mutex_unlock linenumber=3332 hts_log /src/htslib/hts.c linenumber=1856 hts_log /src/htslib/hts.c linenumber=1858 pthread_mutex_lock linenumber=1860 pthread_mutex_unlock linenumber=1863 hts_log /src/htslib/hts.c linenumber=1868 hts_log /src/htslib/hts.c linenumber=1871 hts_log /src/htslib/hts.c linenumber=1872 hts_log /src/htslib/hts.c linenumber=1875 pthread_mutex_lock linenumber=1877 pthread_mutex_unlock linenumber=1879 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1882 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1764 sam_hrecs_find_key /src/htslib/header.c linenumber=1769 hts_md5_init /src/htslib/md5.c linenumber=1780 hts_md5_update /src/htslib/md5.c linenumber=1782 hts_md5_final /src/htslib/md5.c linenumber=1783 hts_md5_destroy /src/htslib/md5.c linenumber=1784 hts_md5_hex /src/htslib/md5.c linenumber=1785 strcmp linenumber=1788 hts_log /src/htslib/hts.c linenumber=1789 hts_log /src/htslib/hts.c linenumber=1791 cram_ref_incr /src/htslib/cram/cram_io.c linenumber=1915 pthread_mutex_lock linenumber=2929 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=2930 pthread_mutex_unlock linenumber=2931 cram_get_ref /src/htslib/cram/cram_io.c linenumber=1922 validate_md5 /src/htslib/cram/cram_encode.c linenumber=1923 hts_log /src/htslib/hts.c linenumber=1926 __assert_fail linenumber=1941 lossy_read_names /src/htslib/cram/cram_encode.c linenumber=1945 kh_init_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1287 calloc linenumber=55 expected_template_count /src/htslib/cram/cram_encode.c linenumber=1305 bam_aux_get /src/htslib/sam.c linenumber=1240 bam_aux_first /src/htslib/sam.c linenumber=4891 __errno_location linenumber=4847 skip_aux /src/htslib/sam.c linenumber=4850 aux_type2size /src/htslib/sam.c linenumber=4822 memchr linenumber=4826 aux_type2size /src/htslib/sam.c linenumber=4830 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=4831 hts_log /src/htslib/hts.c linenumber=4859 __errno_location linenumber=4861 skip_aux /src/htslib/sam.c linenumber=4894 bam_aux_next /src/htslib/sam.c linenumber=4891 skip_aux /src/htslib/sam.c linenumber=4868 __errno_location linenumber=4870 skip_aux /src/htslib/sam.c linenumber=4873 hts_log /src/htslib/hts.c linenumber=4882 __errno_location linenumber=4884 hts_log /src/htslib/hts.c linenumber=4905 __errno_location linenumber=4907 bam_data_end /src/htslib/cram/cram_encode.c linenumber=1242 bam_aux2i_end /src/htslib/cram/cram_encode.c linenumber=1242 __errno_location linenumber=1194 __errno_location linenumber=1200 __errno_location linenumber=1206 le_to_i16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1209 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=241 __errno_location linenumber=1212 le_to_u16 /src/htslib/cram/../htslib/hts_endian.h linenumber=1215 __errno_location linenumber=1218 le_to_i32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1221 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=252 __errno_location linenumber=1224 le_to_u32 /src/htslib/cram/../htslib/hts_endian.h linenumber=1227 __errno_location linenumber=1229 bam_aux_get /src/htslib/sam.c linenumber=1247 kh_put_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1308 kh_resize_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=55 __errno_location linenumber=55 realloc linenumber=55 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=55 strcmp linenumber=55 kh_get_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1340 kh_destroy_m_s2u64 /src/htslib/cram/cram_encode.c linenumber=1353 cram_generate_reference /src/htslib/cram/cram_encode.c linenumber=1956 extend_ref /src/htslib/cram/cram_encode.c linenumber=1695 realloc linenumber=1463 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1469 hts_log /src/htslib/hts.c linenumber=1708 cram_add_to_ref /src/htslib/cram/cram_encode.c linenumber=1713 bam_aux_get /src/htslib/sam.c linenumber=1599 cram_add_to_ref_MD /src/htslib/cram/cram_encode.c linenumber=1603 bam_cigar2rlen /src/htslib/sam.c linenumber=1499 extend_ref /src/htslib/cram/cram_encode.c linenumber=1503 __ctype_b_loc linenumber=1513 hts_str2uint /src/htslib/cram/../textutils_internal.h linenumber=1516 extend_ref /src/htslib/cram/cram_encode.c linenumber=1518 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1523 hts_log /src/htslib/hts.c linenumber=1530 __ctype_b_loc linenumber=1549 extend_ref /src/htslib/cram/cram_encode.c linenumber=1550 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1553 hts_log /src/htslib/hts.c linenumber=1559 extend_ref /src/htslib/cram/cram_encode.c linenumber=1567 next_cigar_op /src/htslib/cram/cram_encode.c linenumber=1570 hts_log /src/htslib/hts.c linenumber=1576 extend_ref /src/htslib/cram/cram_encode.c linenumber=1631 extend_ref /src/htslib/cram/cram_encode.c linenumber=1660 hts_log /src/htslib/hts.c linenumber=1966 hts_log /src/htslib/hts.c linenumber=1970 pthread_mutex_lock linenumber=1973 pthread_mutex_unlock linenumber=1977 pthread_mutex_lock linenumber=1981 pthread_mutex_unlock linenumber=1983 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2002 pthread_mutex_lock linenumber=2959 cram_ref_decr_locked /src/htslib/cram/cram_io.c linenumber=2960 __assert_fail linenumber=2944 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2950 pthread_mutex_unlock linenumber=2961 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2004 hts_log /src/htslib/hts.c linenumber=2005 validate_md5 /src/htslib/cram/cram_encode.c linenumber=2009 process_one_read /src/htslib/cram/cram_encode.c linenumber=2021 bam_aux_get /src/htslib/sam.c linenumber=3318 bam_aux_get /src/htslib/sam.c linenumber=3327 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3334 kh_init_m_i2i /src/htslib/cram/cram_structs.h linenumber=65 kh_put_m_i2i /src/htslib/cram/cram_structs.h linenumber=70 kh_resize_m_i2i /src/htslib/cram/cram_structs.h linenumber=64 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3336 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3356 block_grow /src/htslib/cram/cram_io.h linenumber=3372 block_resize /src/htslib/cram/cram_io.h linenumber=236 block_resize_exact /src/htslib/cram/cram_io.h linenumber=225 realloc linenumber=209 block_grow /src/htslib/cram/cram_io.h linenumber=3373 nibble2base /src/htslib/cram/../sam_internal.h linenumber=3378 hts_log /src/htslib/hts.c linenumber=3391 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3400 hts_log /src/htslib/hts.c linenumber=3436 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3449 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=3450 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=261 cram_add_substitution /src/htslib/cram/cram_encode.c linenumber=3513 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2553 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2560 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2561 block_append_char /src/htslib/cram/cram_io.h linenumber=2562 block_grow /src/htslib/cram/cram_io.h linenumber=254 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2564 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2519 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2527 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2530 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2535 cram_add_bases 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cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2302 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2302 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2311 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2311 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2318 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2318 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2324 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2324 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2330 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2330 cram_stats_encoding /src/htslib/cram/cram_stats.c linenumber=2336 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2336 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2345 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2370 cram_encoder_init /src/htslib/cram/cram_codecs.c linenumber=2376 cram_encoder_init 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linenumber=566 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=567 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=568 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=570 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=571 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=572 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=573 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=593 rans_compress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=838 rans_compress_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1603 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1583 rans_compress_bound_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1222 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1294 rans_compress_to_4x16 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fprintf linenumber=953 fprintf linenumber=955 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1496 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1500 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1501 rans_enc_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1531 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1623 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=742 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=755 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=799 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=870 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=885 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=895 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=912 hts_pack /src/htslib/htscodecs/htscodecs/pack.c linenumber=929 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=942 BZ2_bzBuffToBuffCompress linenumber=964 arith_compress_O0_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=985 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=443 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=461 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=464 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=471 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=474 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=475 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=476 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=481 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=490 SIMPLE_MODEL258_normalize 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/src/htslib/htscodecs/htscodecs/utils.c linenumber=655 arith_compress_O1 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=993 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=174 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=185 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=200 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=203 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=204 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=205 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=209 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=213 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=215 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=220 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=222 arith_compress_O0 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=995 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=100 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=118 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=121 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=122 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=123 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=126 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=128 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=134 tok3_encode_names /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1635 create_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1463 build_trie /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1477 calloc linenumber=482 pool_create /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=505 pool_alloc /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=506 new_pool /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=133 realloc linenumber=86 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1478 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1496 encode_name /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1502 search_trie /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=700 __ctype_b_loc linenumber=613 __ctype_b_loc linenumber=614 __ctype_b_loc linenumber=615 __ctype_b_loc linenumber=616 __ctype_b_loc linenumber=617 calloc linenumber=645 __ctype_b_loc linenumber=667 strlen linenumber=711 encode_token_dup /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=712 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=465 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=342 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=316 realloc linenumber=302 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=343 encode_token_diff /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=727 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=470 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=743 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=443 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=444 memcmp linenumber=758 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=759 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=324 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=761 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=415 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=416 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=764 __ctype_b_loc linenumber=785 __ctype_b_loc linenumber=791 __ctype_b_loc linenumber=792 memcmp linenumber=809 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=815 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=822 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=828 __ctype_b_loc linenumber=842 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=856 encode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=863 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=375 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=376 encode_token_int1_ /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=869 descriptor_grow 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block_append /src/htslib/cram/cram_io.h linenumber=625 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=108 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=109 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=110 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=111 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=113 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=118 kh_init_map /src/htslib/cram/cram_structs.h linenumber=128 calloc linenumber=83 kh_put_map /src/htslib/cram/cram_structs.h linenumber=131 kh_resize_map /src/htslib/cram/cram_structs.h linenumber=83 __errno_location 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 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/src/htslib/cram/../htslib/hfile.h linenumber=3824 cram_write_container /src/htslib/cram/cram_io.c linenumber=3827 itf8_put /src/htslib/cram/cram_io.c linenumber=3767 crc32 linenumber=3795 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=3803 htell /src/htslib/cram/../htslib/hfile.h linenumber=3830 cram_write_block /src/htslib/cram/cram_io.c linenumber=3833 __assert_fail linenumber=1252 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1254 hputc2 /src/htslib/hfile.c linenumber=268 flush_buffer /src/htslib/hfile.c linenumber=403 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1255 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1259 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1264 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1267 __assert_fail linenumber=1272 crc32 linenumber=1284 crc32 linenumber=1287 crc32 linenumber=1289 int32_encode /src/htslib/cram/cram_io.c linenumber=1292 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=784 htell /src/htslib/cram/../htslib/hfile.h linenumber=3837 cram_write_block /src/htslib/cram/cram_io.c linenumber=3842 cram_write_block /src/htslib/cram/cram_io.c linenumber=3846 htell /src/htslib/cram/../htslib/hfile.h linenumber=3850 cram_index_slice /src/htslib/cram/cram_index.c linenumber=3854 hts_log /src/htslib/hts.c linenumber=702 cram_index_build_multiref /src/htslib/cram/cram_index.c linenumber=708 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=640 cram_dependent_data_series /src/htslib/cram/cram_decode.c linenumber=2390 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=615 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=621 hts_calloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=628 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=689 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=2335 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=2336 hts_log /src/htslib/hts.c linenumber=2348 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=705 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=735 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=751 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=780 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=826 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2411 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2412 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2413 strcmp linenumber=2425 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2433 hts_log /src/htslib/hts.c linenumber=2443 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2448 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=2451 hts_log /src/htslib/hts.c linenumber=2457 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2468 hts_log /src/htslib/hts.c linenumber=2477 pthread_mutex_lock linenumber=2482 pthread_mutex_lock linenumber=2483 pthread_mutex_unlock linenumber=2489 pthread_mutex_unlock linenumber=2490 hts_log /src/htslib/hts.c linenumber=2496 memcmp linenumber=2509 hts_log /src/htslib/hts.c linenumber=2519 hts_log /src/htslib/hts.c linenumber=2527 hts_md5_init /src/htslib/md5.c linenumber=2532 hts_md5_update /src/htslib/md5.c linenumber=2537 hts_md5_final /src/htslib/md5.c linenumber=2538 hts_md5_destroy /src/htslib/md5.c linenumber=2539 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2541 hts_md5_init /src/htslib/md5.c linenumber=2543 hts_md5_update /src/htslib/md5.c linenumber=2545 hts_md5_final /src/htslib/md5.c linenumber=2546 hts_md5_destroy /src/htslib/md5.c linenumber=2547 memcmp linenumber=2553 sam_hdr_tid2name /src/htslib/header.c linenumber=2555 hts_log /src/htslib/hts.c linenumber=2557 md5_print /src/htslib/cram/cram_decode.c linenumber=2559 hts_log /src/htslib/hts.c linenumber=2559 md5_print /src/htslib/cram/cram_decode.c linenumber=2560 hts_log /src/htslib/hts.c linenumber=2560 sam_hdr_find_tag_id /src/htslib/header.c linenumber=2562 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2325 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2330 sam_hrecs_find_key /src/htslib/header.c linenumber=2334 kputsn /src/htslib/./htslib/kstring.h linenumber=2339 hts_log /src/htslib/hts.c linenumber=2563 hts_log /src/htslib/hts.c linenumber=2564 ks_free /src/htslib/cram/../htslib/kstring.h linenumber=2565 ks_initialize /src/htslib/cram/../htslib/kstring.h linenumber=238 pthread_mutex_lock linenumber=2571 pthread_mutex_lock linenumber=2572 calloc linenumber=2573 pthread_mutex_unlock linenumber=2574 pthread_mutex_unlock linenumber=2575 hts_log /src/htslib/hts.c linenumber=2633 pthread_mutex_lock linenumber=2644 pthread_mutex_unlock linenumber=2646 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2649 pthread_mutex_lock linenumber=2658 pthread_mutex_unlock linenumber=2663 pthread_mutex_lock linenumber=2665 pthread_mutex_unlock linenumber=2667 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2670 pthread_mutex_lock linenumber=2675 pthread_mutex_lock linenumber=2676 pthread_mutex_unlock linenumber=2678 pthread_mutex_unlock linenumber=2679 hts_log /src/htslib/hts.c linenumber=2690 hts_log /src/htslib/hts.c linenumber=2701 pthread_mutex_lock linenumber=2718 pthread_mutex_unlock linenumber=2720 hts_log /src/htslib/hts.c linenumber=2758 hts_log /src/htslib/hts.c linenumber=2806 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2847 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2875 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2884 cram_decode_aux_1_0 /src/htslib/cram/cram_decode.c linenumber=2911 map_find /src/htslib/cram/cram_decode.c linenumber=1962 block_append /src/htslib/cram/cram_io.h linenumber=1965 cram_decode_aux /src/htslib/cram/cram_decode.c linenumber=2913 strlen linenumber=2022 map_find /src/htslib/cram/cram_decode.c linenumber=2050 block_append /src/htslib/cram/cram_io.h linenumber=2054 aux_ele_size /src/htslib/cram/cram_decode.c linenumber=2063 hts_log /src/htslib/hts.c linenumber=2088 block_resize /src/htslib/cram/cram_io.h linenumber=2919 block_resize /src/htslib/cram/cram_io.h linenumber=2927 hts_log /src/htslib/hts.c linenumber=2937 cram_decode_seq /src/htslib/cram/cram_decode.c linenumber=2944 block_append /src/htslib/cram/cram_io.h linenumber=1125 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1156 hts_log /src/htslib/hts.c linenumber=1195 hts_log /src/htslib/hts.c linenumber=1206 memchr linenumber=1236 add_md_char /src/htslib/cram/cram_decode.c linenumber=1242 block_append_uint /src/htslib/cram/cram_io.h linenumber=1077 block_grow /src/htslib/cram/cram_io.h linenumber=274 append_uint32 /src/htslib/cram/cram_io.h linenumber=278 block_append_char /src/htslib/cram/cram_io.h linenumber=1078 block_append_uint /src/htslib/cram/cram_io.h linenumber=1371 add_md_char /src/htslib/cram/cram_decode.c linenumber=1383 block_append_uint /src/htslib/cram/cram_io.h linenumber=1412 block_append_char /src/htslib/cram/cram_io.h linenumber=1415 block_append /src/htslib/cram/cram_io.h linenumber=1416 block_append_char /src/htslib/cram/cram_io.h linenumber=1426 block_append /src/htslib/cram/cram_io.h linenumber=1427 block_append_uint /src/htslib/cram/cram_io.h linenumber=1430 block_append_uint /src/htslib/cram/cram_io.h linenumber=1509 block_append_uint /src/htslib/cram/cram_io.h linenumber=1513 block_append_char /src/htslib/cram/cram_io.h linenumber=1522 block_append_uint /src/htslib/cram/cram_io.h linenumber=1587 block_append_char /src/htslib/cram/cram_io.h linenumber=1594 hts_log /src/htslib/hts.c linenumber=1693 memchr linenumber=1737 add_md_char /src/htslib/cram/cram_decode.c linenumber=1748 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1769 block_append_uint /src/htslib/cram/cram_io.h linenumber=1793 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1799 block_append_char /src/htslib/cram/cram_io.h linenumber=1836 block_append /src/htslib/cram/cram_io.h linenumber=1888 hts_log /src/htslib/hts.c linenumber=1907 pthread_mutex_lock linenumber=2996 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3001 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3006 pthread_mutex_unlock linenumber=3008 cram_decode_slice_xref /src/htslib/cram/cram_decode.c linenumber=3011 hts_log /src/htslib/hts.c linenumber=2235 cram_free_block /src/htslib/cram/cram_io.c linenumber=3018 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3032 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3033 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3034 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3035 bulk_cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3046 pthread_mutex_lock linenumber=2310 pthread_mutex_unlock linenumber=2315 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2321 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=2330 bam_get_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=2338 calloc linenumber=2347 calloc linenumber=2352 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=2359 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=2364 hts_log /src/htslib/hts.c linenumber=3159 strlen linenumber=3167 append_uint64 /src/htslib/cram/cram_io.h linenumber=3176 append_uint32 /src/htslib/cram/cram_io.h linenumber=347 append_uint32 /src/htslib/cram/cram_io.h linenumber=350 append_sub32 /src/htslib/cram/cram_io.h linenumber=352 append_uint32 /src/htslib/cram/cram_io.h linenumber=354 append_sub32 /src/htslib/cram/cram_io.h linenumber=356 append_uint64 /src/htslib/cram/cram_io.h linenumber=3180 bam_get_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3218 bam_set1 /src/htslib/sam.c linenumber=3226 bam_cigar2rqlens /src/htslib/sam.c linenumber=555 hts_log /src/htslib/hts.c linenumber=565 __errno_location linenumber=572 hts_log /src/htslib/hts.c linenumber=576 __errno_location linenumber=577 hts_log /src/htslib/hts.c linenumber=581 __errno_location linenumber=582 hts_log /src/htslib/hts.c linenumber=586 __errno_location linenumber=587 subtract_check_underflow /src/htslib/sam.c linenumber=592 subtract_check_underflow /src/htslib/sam.c linenumber=593 subtract_check_underflow /src/htslib/sam.c linenumber=594 subtract_check_underflow /src/htslib/sam.c linenumber=595 subtract_check_underflow /src/htslib/sam.c linenumber=596 hts_log /src/htslib/hts.c linenumber=598 __errno_location linenumber=599 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=605 realloc_bam_data /src/htslib/./sam_internal.h linenumber=605 sam_realloc_bam_data /src/htslib/sam.c linenumber=50 __errno_location linenumber=446 __errno_location linenumber=451 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=455 realloc linenumber=456 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=462 bam_set_mempolicy /src/htslib/./htslib/sam.h linenumber=462 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=612 strncpy linenumber=624 bam_tag2cigar /src/htslib/sam.c linenumber=3257 bam_aux_get /src/htslib/sam.c linenumber=708 __errno_location linenumber=709 __errno_location linenumber=711 __errno_location linenumber=712 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=723 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=733 __errno_location linenumber=57 sam_realloc_bam_data /src/htslib/sam.c linenumber=61 bam_endpos /src/htslib/sam.c linenumber=744 bam_cigar2rlen /src/htslib/sam.c linenumber=685 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=744 hts_log /src/htslib/hts.c linenumber=746 bam_cigar2qlen /src/htslib/sam.c linenumber=750 hts_log /src/htslib/hts.c linenumber=753 pthread_mutex_lock linenumber=3053 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3056 pthread_mutex_unlock linenumber=3059 hts_log /src/htslib/hts.c linenumber=650 snprintf linenumber=663 strlen linenumber=667 bgzf_write /src/htslib/bgzf.c linenumber=667 hwrite /src/htslib/./htslib/hfile.h linenumber=2029 __assert_fail linenumber=2034 lazy_flush /src/htslib/bgzf.c linenumber=2044 mt_queue /src/htslib/bgzf.c linenumber=1950 bgzf_flush /src/htslib/bgzf.c linenumber=1952 snprintf linenumber=677 strlen linenumber=681 bgzf_write /src/htslib/bgzf.c linenumber=681 snprintf linenumber=710 strlen linenumber=714 bgzf_write /src/htslib/bgzf.c linenumber=714 __errno_location linenumber=4035 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=4036 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=844 cram_flush_thread /src/htslib/cram/cram_io.c linenumber=4036 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=3887 hts_log /src/htslib/hts.c linenumber=3888 __errno_location linenumber=4037 cram_flush_result /src/htslib/cram/cram_io.c linenumber=4038 hts_tpool_next_result /src/htslib/thread_pool.c linenumber=3903 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=3904 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3908 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=3916 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3923 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3932 cram_free_container /src/htslib/cram/cram_io.c linenumber=3945 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3950 cram_free_container /src/htslib/cram/cram_io.c linenumber=3957 hts_usleep /src/htslib/cram/../hts_internal.h linenumber=4043 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5285 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=5288 cram_flush_result /src/htslib/cram/cram_io.c linenumber=5290 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=5298 pthread_mutex_destroy linenumber=5301 pthread_mutex_destroy linenumber=5302 pthread_mutex_destroy linenumber=5303 pthread_mutex_destroy linenumber=5304 cram_write_eof_block /src/htslib/cram/cram_io.c linenumber=5308 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=5229 cram_write_container /src/htslib/cram/cram_io.c linenumber=5234 cram_write_block /src/htslib/cram/cram_io.c linenumber=5235 cram_close /src/htslib/cram/cram_io.c linenumber=5236 free_bam_list /src/htslib/cram/cram_io.c linenumber=5314 hclose /src/htslib/hfile.c linenumber=5318 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5322 sam_hdr_destroy /src/htslib/sam.c linenumber=5325 cram_free_container /src/htslib/cram/cram_io.c linenumber=5330 cram_free_container /src/htslib/cram/cram_io.c linenumber=5333 refs_free /src/htslib/cram/cram_io.c linenumber=5336 kh_destroy_m_metrics /src/htslib/cram/cram_structs.h linenumber=5352 cram_index_free /src/htslib/cram/cram_index.c linenumber=5356 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=376 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=363 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=5359 bgzf_close /src/htslib/bgzf.c linenumber=5362 cram_free_block /src/htslib/cram/cram_io.c linenumber=5237 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=5241 cram_free_block /src/htslib/cram/cram_io.c linenumber=5242 sam_state_destroy /src/htslib/sam.c linenumber=1773 fastq_state_destroy /src/htslib/sam.c linenumber=1776 kh_destroy_tag /src/htslib/sam.c linenumber=3833 ks_free /src/htslib/./htslib/kstring.h linenumber=3834 ks_initialize /src/htslib/./htslib/kstring.h linenumber=238 ks_free /src/htslib/./htslib/kstring.h linenumber=3835 ks_free /src/htslib/./htslib/kstring.h linenumber=3836 regfree linenumber=3837 bgzf_close /src/htslib/bgzf.c linenumber=1779 hclose /src/htslib/hfile.c linenumber=1781 hts_idx_close_otf_fp /src/htslib/hts.c linenumber=1794 need_idx_ugly_delay_hack /src/htslib/hts.c linenumber=3015 idx_write_uint64 /src/htslib/hts.c linenumber=3017 ed_is_big /src/htslib/./htslib/hts.h linenumber=2836 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2836 bgzf_write /src/htslib/bgzf.c linenumber=2837 bgzf_close /src/htslib/bgzf.c linenumber=3019 __errno_location linenumber=1797 sam_hdr_destroy /src/htslib/sam.c linenumber=1798 hts_idx_destroy /src/htslib/hts.c linenumber=1799 cram_index_free /src/htslib/cram/cram_index.c linenumber=2797 kh_destroy_bin /src/htslib/hts.c linenumber=2809 hts_filter_free /src/htslib/hts_expr.c linenumber=1800 __errno_location linenumber=1805 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=994 strncpy linenumber=901 strchr linenumber=903 strchr linenumber=931 strchr linenumber=937 strstr linenumber=943 strdup linenumber=945 hopen /src/htslib/hfile.c linenumber=951 hts_hopen /src/htslib/hts.c linenumber=954 hts_opt_apply /src/htslib/hts.c linenumber=968 __errno_location linenumber=970 __errno_location linenumber=971 __errno_location linenumber=974 __errno_location linenumber=983 strerror linenumber=983 hts_log /src/htslib/hts.c linenumber=983 hclose_abruptly /src/htslib/hfile.c linenumber=988 abort linenumber=69 sam_hdr_read /src/htslib/sam.c linenumber=86 __errno_location linenumber=1936 bam_hdr_read /src/htslib/sam.c linenumber=1942 bgzf_check_EOF /src/htslib/bgzf.c linenumber=240 pthread_mutex_lock linenumber=2157 pthread_cond_signal linenumber=2163 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=2164 pthread_mutex_unlock linenumber=2168 pthread_cond_wait linenumber=2171 pthread_cond_signal linenumber=2176 abort linenumber=2181 pthread_mutex_unlock linenumber=2186 bgzf_check_EOF_common /src/htslib/bgzf.c linenumber=2188 htell /src/htslib/./htslib/hfile.h linenumber=1565 hseek /src/htslib/hfile.c linenumber=1566 __errno_location linenumber=1567 hclearerr /src/htslib/./htslib/hfile.h linenumber=1567 __errno_location linenumber=1574 hclearerr /src/htslib/./htslib/hfile.h linenumber=1574 hread /src/htslib/./htslib/hfile.h linenumber=1578 hseek /src/htslib/hfile.c linenumber=1579 memcmp linenumber=1580 perror linenumber=242 hts_log /src/htslib/hts.c linenumber=244 bgzf_read /src/htslib/bgzf.c linenumber=247 memcmp linenumber=248 hts_log /src/htslib/hts.c linenumber=249 sam_hdr_init /src/htslib/sam.c linenumber=252 bgzf_read /src/htslib/bgzf.c linenumber=256 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=258 bgzf_read /src/htslib/bgzf.c linenumber=268 bgzf_read /src/htslib/bgzf.c linenumber=271 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=273 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=1610 calloc linenumber=283 calloc linenumber=285 bgzf_read /src/htslib/bgzf.c linenumber=294 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=296 bgzf_read /src/htslib/bgzf.c linenumber=303 realloc linenumber=311 bgzf_read /src/htslib/bgzf.c linenumber=317 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=319 hts_log /src/htslib/hts.c linenumber=329 hts_log /src/htslib/hts.c linenumber=331 hts_log /src/htslib/hts.c linenumber=336 sam_hdr_destroy /src/htslib/sam.c linenumber=341 sam_hdr_sanitise /src/htslib/sam.c linenumber=1942 hts_log /src/htslib/hts.c linenumber=1869 sam_hdr_destroy /src/htslib/sam.c linenumber=1870 hts_log /src/htslib/hts.c linenumber=1882 hts_log /src/htslib/hts.c linenumber=1887 hts_log /src/htslib/hts.c linenumber=1891 sam_hdr_destroy /src/htslib/sam.c linenumber=1892 realloc linenumber=1896 sam_hdr_destroy /src/htslib/sam.c linenumber=1898 sam_hdr_dup /src/htslib/sam.c linenumber=1946 sam_hdr_init /src/htslib/sam.c linenumber=175 calloc linenumber=184 calloc linenumber=186 strdup linenumber=192 sam_hdr_dup_sdict /src/htslib/sam.c linenumber=199 kh_init_s2i /src/htslib/hts.c linenumber=149 kh_get_s2i /src/htslib/hts.c linenumber=157 kh_put_s2i /src/htslib/hts.c linenumber=159 kh_destroy_s2i /src/htslib/hts.c linenumber=161 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=205 kputsn /src/htslib/./htslib/kstring.h linenumber=2416 sam_hrecs_rebuild_lines /src/htslib/header.c linenumber=2418 kputsn /src/htslib/./htslib/kstring.h linenumber=771 build_header_line /src/htslib/header.c linenumber=775 kputc_ /src/htslib/./htslib/kstring.h linenumber=757 kputsn /src/htslib/./htslib/kstring.h linenumber=758 kputc_ /src/htslib/./htslib/kstring.h linenumber=760 kputsn /src/htslib/./htslib/kstring.h linenumber=761 kputc /src/htslib/./htslib/kstring.h linenumber=777 ks_release /src/htslib/./htslib/kstring.h linenumber=206 ks_release /src/htslib/./htslib/kstring.h linenumber=211 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=213 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=217 sam_hdr_destroy /src/htslib/sam.c linenumber=227 sam_hdr_sanitise /src/htslib/sam.c linenumber=1946 sam_hdr_create /src/htslib/sam.c linenumber=1950 sam_hdr_init /src/htslib/sam.c linenumber=1915 sam_hdr_build_from_sam_file /src/htslib/header.c linenumber=1919 sam_hrecs_new /src/htslib/header.c linenumber=1376 hts_getline /src/htslib/hts.c linenumber=1385 hts_log /src/htslib/hts.c linenumber=2138 abort linenumber=2139 kgetline2 /src/htslib/kstring.c linenumber=2145 ks_resize /src/htslib/./htslib/kstring.h linenumber=322 hgetln_wrapper /src/htslib/hts.c linenumber=2145 hgetln /src/htslib/./htslib/hfile.h linenumber=2131 herrno /src/htslib/./htslib/hfile.h linenumber=2147 __errno_location linenumber=2147 bgzf_getline /src/htslib/bgzf.c linenumber=2153 bgzf_read_block /src/htslib/bgzf.c linenumber=2344 memchr linenumber=2351 ks_expand /src/htslib/./htslib/kstring.h linenumber=2357 bgzf_htell /src/htslib/bgzf.c linenumber=2362 hts_log /src/htslib/hts.c linenumber=2157 isalpha_c /src/htslib/./textutils_internal.h linenumber=1393 sam_hrecs_error /src/htslib/header.c linenumber=1394 strncmp linenumber=1399 kputc /src/htslib/./htslib/kstring.h linenumber=1402 valid_sam_header_type /src/htslib/header.c linenumber=1406 hts_log /src/htslib/hts.c linenumber=1407 warn_if_known_stderr /src/htslib/header.c linenumber=1408 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1412 TYPEKEY /src/htslib/./header.h linenumber=1417 kputsn /src/htslib/./htslib/kstring.h linenumber=1423 kputc /src/htslib/./htslib/kstring.h linenumber=1426 bgzf_peek /src/htslib/bgzf.c linenumber=1430 bgzf_read_block /src/htslib/bgzf.c linenumber=1321 hts_log /src/htslib/hts.c linenumber=1322 hpeek /src/htslib/hfile.c linenumber=1433 strstr linenumber=1451 hopen /src/htslib/hfile.c linenumber=1455 khgetline /src/htslib/hfile.c linenumber=1460 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=1461 strtoll linenumber=1469 kputs /src/htslib/./htslib/kstring.h linenumber=1471 kputsn /src/htslib/./htslib/kstring.h linenumber=1472 kputs /src/htslib/./htslib/kstring.h linenumber=1473 kputll /src/htslib/./htslib/kstring.h linenumber=1474 kputc /src/htslib/./htslib/kstring.h linenumber=1475 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1479 ks_free /src/htslib/./htslib/kstring.h linenumber=1491 hclose /src/htslib/hfile.c linenumber=1492 hts_log /src/htslib/hts.c linenumber=1493 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1503 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1507 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1521 kputsn /src/htslib/./htslib/kstring.h linenumber=1527 ks_release /src/htslib/./htslib/kstring.h linenumber=1531 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1533 ks_free /src/htslib/./htslib/kstring.h linenumber=1539 sam_hdr_destroy /src/htslib/sam.c linenumber=1920 sam_hdr_destroy /src/htslib/sam.c linenumber=1925 sam_hdr_sanitise /src/htslib/sam.c linenumber=1926 sam_hdr_init /src/htslib/sam.c linenumber=1955 __errno_location linenumber=1958 __errno_location linenumber=1962 sam_hdr_incr_ref /src/htslib/header.c linenumber=1969 strlen linenumber=1974 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=2182 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2204 sam_hdr_write /src/htslib/sam.c linenumber=99 __errno_location linenumber=1982 bam_hdr_write /src/htslib/sam.c linenumber=1992 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=356 hts_log /src/htslib/hts.c linenumber=358 hts_log /src/htslib/hts.c linenumber=362 hts_log /src/htslib/hts.c linenumber=363 hts_log /src/htslib/hts.c linenumber=369 hts_log /src/htslib/hts.c linenumber=372 hts_log /src/htslib/hts.c linenumber=373 bgzf_write /src/htslib/bgzf.c linenumber=379 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=382 bgzf_write /src/htslib/bgzf.c linenumber=383 bgzf_write /src/htslib/bgzf.c linenumber=385 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=387 bgzf_write /src/htslib/bgzf.c linenumber=388 bgzf_write /src/htslib/bgzf.c linenumber=390 bgzf_write /src/htslib/bgzf.c linenumber=392 bgzf_write /src/htslib/bgzf.c linenumber=394 strlen linenumber=400 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=402 bgzf_write /src/htslib/bgzf.c linenumber=403 bgzf_write /src/htslib/bgzf.c linenumber=405 bgzf_write /src/htslib/bgzf.c linenumber=407 ed_swap_4 /src/htslib/./htslib/hts.h linenumber=409 bgzf_write /src/htslib/bgzf.c linenumber=410 bgzf_write /src/htslib/bgzf.c linenumber=412 bgzf_flush /src/htslib/bgzf.c linenumber=415 cram_set_header2 /src/htslib/cram/cram_io.c linenumber=1997 sam_hdr_destroy /src/htslib/sam.c linenumber=2603 sam_hdr_dup /src/htslib/sam.c linenumber=2604 refs_from_header /src/htslib/cram/cram_io.c linenumber=2608 cram_load_reference /src/htslib/cram/cram_io.c linenumber=1999 cram_write_SAM_hdr /src/htslib/cram/cram_io.c linenumber=2000 cram_write_file_def /src/htslib/cram/cram_io.c linenumber=4631 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4429 sam_hrecs_find_rg /src/htslib/header.c linenumber=4637 sam_hdr_add_line /src/htslib/header.c linenumber=4638 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1720 sam_hrecs_vadd /src/htslib/header.c linenumber=1726 rebuild_target_arrays /src/htslib/header.c linenumber=1730 redact_header_text /src/htslib/header.c linenumber=1734 refs_from_header /src/htslib/cram/cram_io.c linenumber=4643 refs2id /src/htslib/cram/cram_io.c linenumber=4645 sam_hrecs_find_type_id /src/htslib/header.c linenumber=4655 sam_hrecs_find_key /src/htslib/header.c linenumber=4658 cram_get_ref /src/htslib/cram/cram_io.c linenumber=4670 hts_log /src/htslib/hts.c linenumber=4674 hts_log /src/htslib/hts.c linenumber=4676 hts_log /src/htslib/hts.c linenumber=4677 pthread_mutex_lock linenumber=4679 pthread_mutex_unlock linenumber=4683 hts_md5_init /src/htslib/md5.c linenumber=4689 hts_md5_update /src/htslib/md5.c linenumber=4693 hts_md5_final /src/htslib/md5.c linenumber=4704 hts_md5_destroy /src/htslib/md5.c linenumber=4705 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=4706 hts_md5_hex /src/htslib/md5.c linenumber=4708 sam_hdr_update_line /src/htslib/header.c linenumber=4710 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1936 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1942 check_for_name_update /src/htslib/header.c linenumber=1951 TYPEKEY /src/htslib/./header.h linenumber=1898 TYPEKEY /src/htslib/./header.h linenumber=1900 TYPEKEY /src/htslib/./header.h linenumber=1902 sam_hrecs_find_key /src/htslib/header.c linenumber=1911 __assert_fail linenumber=1914 strcmp linenumber=1920 strcmp linenumber=1921 kh_get_m_s2i /src/htslib/./header.h linenumber=1922 hts_log /src/htslib/hts.c linenumber=1955 TYPEKEY /src/htslib/./header.h linenumber=1959 hts_log /src/htslib/hts.c linenumber=1961 sam_hrecs_vupdate /src/htslib/header.c linenumber=1965 kh_get_m_s2i /src/htslib/./header.h linenumber=1976 sam_hrecs_find_key /src/htslib/header.c linenumber=1977 __assert_fail linenumber=1979 __assert_fail linenumber=1980 __assert_fail linenumber=1981 kh_del_m_s2i /src/htslib/./header.h linenumber=1983 kh_put_m_s2i /src/htslib/./header.h linenumber=1984 hts_log /src/htslib/hts.c linenumber=1986 TYPEKEY /src/htslib/./header.h linenumber=1992 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1992 rebuild_target_arrays /src/htslib/header.c linenumber=1995 redact_header_text /src/htslib/header.c linenumber=1998 full_path /src/htslib/cram/cram_io.c linenumber=4716 strlen linenumber=4585 hisremote /src/htslib/hfile.c linenumber=4586 hts_log /src/htslib/hts.c linenumber=4588 strncpy linenumber=4591 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=4597 strncpy linenumber=4599 getcwd linenumber=4605 strlen linenumber=4606 strncpy linenumber=4607 snprintf linenumber=4612 sam_hdr_update_line /src/htslib/header.c linenumber=4717 sam_hdr_remove_tag_all /src/htslib/header.c linenumber=4724 strcmp linenumber=3236 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=3240 TYPEKEY /src/htslib/./header.h linenumber=3245 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3245 sam_hrecs_remove_key /src/htslib/header.c linenumber=3253 sam_hrecs_find_key /src/htslib/header.c linenumber=3073 TYPEKEY /src/htslib/./header.h linenumber=3077 __assert_fail linenumber=3078 sam_hrecs_find_key /src/htslib/header.c linenumber=3079 __assert_fail linenumber=3081 kh_get_m_s2i /src/htslib/./header.h linenumber=3082 sam_hrecs_remove_ref_altnames /src/htslib/header.c linenumber=3084 kstrtok /src/htslib/kstring.c linenumber=125 ks_clear /src/htslib/./htslib/kstring.h linenumber=126 kputsn /src/htslib/./htslib/kstring.h linenumber=126 kh_get_m_s2i /src/htslib/./header.h linenumber=130 strcmp linenumber=133 kh_del_m_s2i /src/htslib/./header.h linenumber=134 pool_free /src/htslib/cram/pooled_alloc.c linenumber=3095 hts_log /src/htslib/hts.c linenumber=4725 sam_hdr_length /src/htslib/header.c linenumber=4731 sam_hdr_rebuild /src/htslib/header.c linenumber=1599 rebuild_target_arrays /src/htslib/header.c linenumber=1633 hts_log /src/htslib/hts.c linenumber=1634 sam_hdr_link_pg /src/htslib/header.c linenumber=1643 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2512 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2521 calloc linenumber=2525 __assert_fail linenumber=2536 kh_get_m_s2i /src/htslib/./header.h linenumber=2546 hts_log /src/htslib/hts.c linenumber=2549 hts_log /src/htslib/hts.c linenumber=2556 redact_header_text /src/htslib/header.c linenumber=2585 hts_log /src/htslib/hts.c linenumber=1644 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1649 ks_free /src/htslib/./htslib/kstring.h linenumber=1650 hts_log /src/htslib/hts.c linenumber=1651 ks_len /src/htslib/./htslib/kstring.h linenumber=1659 ks_release /src/htslib/./htslib/kstring.h linenumber=1660 hts_log /src/htslib/hts.c linenumber=4733 int32_encode /src/htslib/cram/cram_io.c linenumber=4737 sam_hdr_str /src/htslib/header.c linenumber=4741 sam_hdr_rebuild /src/htslib/header.c linenumber=1606 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4741 cram_new_block /src/htslib/cram/cram_io.c linenumber=4745 cram_new_container /src/htslib/cram/cram_io.c linenumber=4746 calloc linenumber=3383 calloc linenumber=3411 cram_new_compression_header /src/htslib/cram/cram_io.c linenumber=3415 calloc linenumber=4060 cram_new_block /src/htslib/cram/cram_io.c linenumber=4064 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4069 cram_free_block /src/htslib/cram/cram_io.c linenumber=4070 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4075 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4076 cram_free_block /src/htslib/cram/cram_io.c linenumber=4077 cram_stats_create /src/htslib/cram/cram_stats.c linenumber=3420 calloc linenumber=50 kh_init_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3424 calloc linenumber=380 cram_free_block /src/htslib/cram/cram_io.c linenumber=4752 cram_free_container /src/htslib/cram/cram_io.c linenumber=4753 int32_put_blk /src/htslib/cram/cram_io.c linenumber=4757 block_append /src/htslib/cram/cram_io.h linenumber=815 sam_hdr_str /src/htslib/header.c linenumber=4760 block_append /src/htslib/cram/cram_io.h linenumber=4760 cram_compress_block /src/htslib/cram/cram_io.c linenumber=4765 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=2068 cram_free_block /src/htslib/cram/cram_io.c linenumber=4777 cram_free_container /src/htslib/cram/cram_io.c linenumber=4778 calloc linenumber=4805 cram_free_block /src/htslib/cram/cram_io.c linenumber=4806 cram_free_container /src/htslib/cram/cram_io.c linenumber=4807 block_append /src/htslib/cram/cram_io.h linenumber=4810 cram_write_container /src/htslib/cram/cram_io.c linenumber=4815 cram_free_block /src/htslib/cram/cram_io.c linenumber=4816 cram_free_container /src/htslib/cram/cram_io.c linenumber=4817 cram_write_block /src/htslib/cram/cram_io.c linenumber=4821 cram_free_block /src/htslib/cram/cram_io.c linenumber=4822 cram_free_container /src/htslib/cram/cram_io.c linenumber=4823 block_resize /src/htslib/cram/cram_io.h linenumber=4828 cram_write_block /src/htslib/cram/cram_io.c linenumber=4833 cram_free_block /src/htslib/cram/cram_io.c linenumber=4834 cram_free_container /src/htslib/cram/cram_io.c linenumber=4835 cram_free_block /src/htslib/cram/cram_io.c linenumber=4840 cram_free_container /src/htslib/cram/cram_io.c linenumber=4841 hflush /src/htslib/hfile.c linenumber=4844 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=2018 strstr linenumber=2026 bgzf_write /src/htslib/bgzf.c linenumber=2034 hwrite /src/htslib/./htslib/hfile.h linenumber=2036 kputsn /src/htslib/./htslib/kstring.h linenumber=2046 kputs /src/htslib/./htslib/kstring.h linenumber=2047 kputsn /src/htslib/./htslib/kstring.h linenumber=2048 kputw /src/htslib/./htslib/kstring.h linenumber=2049 kputc /src/htslib/./htslib/kstring.h linenumber=2050 bgzf_write /src/htslib/bgzf.c linenumber=2055 hwrite /src/htslib/./htslib/hfile.h linenumber=2057 bgzf_flush /src/htslib/bgzf.c linenumber=2064 hflush /src/htslib/hfile.c linenumber=2066 __errno_location linenumber=2078 sam_hdr_dup /src/htslib/sam.c linenumber=2084 sam_hdr_destroy /src/htslib/sam.c linenumber=2085 bam_init1 /src/htslib/sam.c linenumber=102 calloc linenumber=435 sam_read1 /src/htslib/sam.c linenumber=106 sam_read1_bam /src/htslib/sam.c linenumber=4298 bam_read1 /src/htslib/sam.c linenumber=4160 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=817 bgzf_read /src/htslib/bgzf.c linenumber=168 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=822 bgzf_read /src/htslib/bgzf.c linenumber=830 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=833 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=834 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=835 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=840 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=843 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=844 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=845 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=846 realloc_bam_data /src/htslib/./sam_internal.h linenumber=853 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=856 fixup_missing_qname_nul /src/htslib/sam.c linenumber=858 realloc_bam_data /src/htslib/./sam_internal.h linenumber=796 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=863 swap_data /src/htslib/sam.c linenumber=865 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=783 bam_tag2cigar /src/htslib/sam.c linenumber=867 bam_cigar2rqlens /src/htslib/sam.c linenumber=874 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=876 hts_log /src/htslib/hts.c linenumber=880 __errno_location linenumber=4164 sam_read1_cram /src/htslib/sam.c linenumber=4302 cram_get_bam_seq /src/htslib/cram/cram_decode.c linenumber=4173 cram_get_seq /src/htslib/cram/cram_decode.c linenumber=3690 pthread_mutex_lock linenumber=3622 pthread_mutex_unlock linenumber=3625 cram_next_slice /src/htslib/cram/cram_decode.c linenumber=3628 cram_first_slice /src/htslib/cram/cram_decode.c linenumber=3336 cram_free_container /src/htslib/cram/cram_io.c linenumber=3279 cram_read_container /src/htslib/cram/cram_io.c linenumber=3281 cram_seek /src/htslib/cram/cram_io.c linenumber=3297 cram_free_container /src/htslib/cram/cram_io.c linenumber=3299 cram_read_container /src/htslib/cram/cram_io.c linenumber=3301 cram_read_block /src/htslib/cram/cram_io.c linenumber=3312 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3317 calloc linenumber=149 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=157 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=178 kh_init_map /src/htslib/cram/cram_structs.h linenumber=186 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=194 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=213 kh_put_map /src/htslib/cram/cram_structs.h linenumber=226 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=228 kh_put_map /src/htslib/cram/cram_structs.h linenumber=238 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=240 kh_put_map /src/htslib/cram/cram_structs.h linenumber=250 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=252 kh_put_map /src/htslib/cram/cram_structs.h linenumber=262 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=264 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=274 kh_put_map /src/htslib/cram/cram_structs.h linenumber=305 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=307 cram_decode_TD /src/htslib/cram/cram_decode.c linenumber=314 cram_new_block /src/htslib/cram/cram_io.c linenumber=80 hts_log /src/htslib/hts.c linenumber=84 cram_free_block /src/htslib/cram/cram_io.c linenumber=85 cram_free_block /src/htslib/cram/cram_io.c linenumber=95 cram_free_block /src/htslib/cram/cram_io.c linenumber=100 block_append /src/htslib/cram/cram_io.h linenumber=104 block_append_char /src/htslib/cram/cram_io.h linenumber=109 calloc linenumber=122 cram_free_block /src/htslib/cram/cram_io.c linenumber=123 cram_free_block /src/htslib/cram/cram_io.c linenumber=137 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=316 kh_put_map /src/htslib/cram/cram_structs.h linenumber=323 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=325 hts_log /src/htslib/hts.c linenumber=333 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=340 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=357 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=371 hts_log /src/htslib/hts.c linenumber=454 hts_log /src/htslib/hts.c linenumber=459 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=463 cram_encoding2str /src/htslib/cram/cram_codecs.c linenumber=2261 hts_log /src/htslib/hts.c linenumber=2261 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=466 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=476 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=489 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=504 cram_decoder_init /src/htslib/cram/cram_codecs.c linenumber=519 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=521 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=532 sam_hrecs_sort_order /src/htslib/header.c linenumber=3321 TYPEKEY /src/htslib/./header.h linenumber=3172 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3172 strcmp linenumber=3178 strcmp linenumber=3180 strcmp linenumber=3182 strcmp linenumber=3184 hts_log /src/htslib/hts.c linenumber=3185 pthread_mutex_lock linenumber=3322 pthread_mutex_unlock linenumber=3324 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3343 cram_free_container /src/htslib/cram/cram_io.c linenumber=3354 cram_read_container /src/htslib/cram/cram_io.c linenumber=3387 cram_free_container /src/htslib/cram/cram_io.c linenumber=3400 cram_free_container /src/htslib/cram/cram_io.c linenumber=3413 cram_free_container /src/htslib/cram/cram_io.c linenumber=3422 cram_free_container /src/htslib/cram/cram_io.c linenumber=3435 hseek /src/htslib/hfile.c linenumber=3438 cram_read_block /src/htslib/cram/cram_io.c linenumber=3448 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3454 sam_hrecs_sort_order /src/htslib/header.c linenumber=3459 pthread_mutex_lock linenumber=3460 pthread_mutex_unlock linenumber=3462 cram_free_container /src/htslib/cram/cram_io.c linenumber=3473 cram_read_slice /src/htslib/cram/cram_io.c linenumber=3478 cram_read_block /src/htslib/cram/cram_io.c linenumber=4301 calloc linenumber=4302 cram_decode_slice_header /src/htslib/cram/cram_decode.c linenumber=4312 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=959 calloc linenumber=969 hts_log /src/htslib/hts.c linenumber=982 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1005 cram_content_type2str /src/htslib/cram/cram_io.c linenumber=4317 hts_log /src/htslib/hts.c linenumber=4317 hts_log /src/htslib/hts.c linenumber=4323 calloc linenumber=4327 cram_read_block /src/htslib/cram/cram_io.c linenumber=4332 calloc linenumber=4343 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4357 cram_new_block /src/htslib/cram/cram_io.c linenumber=4360 cram_new_block /src/htslib/cram/cram_io.c linenumber=4361 cram_new_block /src/htslib/cram/cram_io.c linenumber=4362 cram_new_block /src/htslib/cram/cram_io.c linenumber=4363 cram_new_block /src/htslib/cram/cram_io.c linenumber=4364 cram_new_block /src/htslib/cram/cram_io.c linenumber=4365 cram_free_block /src/htslib/cram/cram_io.c linenumber=4376 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4379 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3493 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3502 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3511 cram_decode_slice_mt /src/htslib/cram/cram_decode.c linenumber=3523 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3090 hts_tpool_process_sz /src/htslib/thread_pool.c linenumber=3100 pthread_mutex_lock linenumber=307 pthread_mutex_unlock linenumber=309 __errno_location linenumber=3102 __errno_location linenumber=3103 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=3104 cram_decode_slice_thread /src/htslib/cram/cram_decode.c linenumber=3104 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3076 __errno_location linenumber=3107 __errno_location linenumber=3113 hts_log /src/htslib/hts.c linenumber=3524 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3525 hts_tpool_process_len /src/htslib/thread_pool.c linenumber=3546 pthread_mutex_lock linenumber=293 pthread_mutex_unlock linenumber=295 hts_tpool_process_qsize /src/htslib/thread_pool.c linenumber=3547 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3558 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3563 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3565 hts_log /src/htslib/hts.c linenumber=3566 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3570 hts_log /src/htslib/hts.c linenumber=3575 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3577 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3581 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3653 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3660 bam_get_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3696 bam_copy1 /src/htslib/sam.c linenumber=3700 realloc_bam_data /src/htslib/./sam_internal.h linenumber=490 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3707 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3713 cram_eof /src/htslib/cram/cram_io.c linenumber=4175 sam_read1_sam /src/htslib/sam.c linenumber=4306 sam_parse1 /src/htslib/sam.c linenumber=4186 strchr linenumber=2728 hts_log /src/htslib/hts.c linenumber=2730 hts_log /src/htslib/hts.c linenumber=2731 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2733 parse_sam_flag /src/htslib/sam.c linenumber=2743 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2512 strtoul linenumber=2518 strchr linenumber=2747 strcmp linenumber=2748 hts_log /src/htslib/hts.c linenumber=2749 bam_name2id /src/htslib/./htslib/sam.h linenumber=2750 sam_hdr_name2tid /src/htslib/header.c linenumber=788 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2436 kh_get_m_s2i /src/htslib/./header.h linenumber=2444 hts_log /src/htslib/hts.c linenumber=2751 hts_strprint /src/htslib/textutils.c linenumber=2752 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=2752 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2756 hts_log /src/htslib/hts.c linenumber=2759 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2765 bam_parse_cigar /src/htslib/sam.c linenumber=2771 hts_log /src/htslib/hts.c linenumber=2959 read_ncigar /src/htslib/sam.c linenumber=2964 isdigit_c /src/htslib/./textutils_internal.h linenumber=2873 hts_log /src/htslib/hts.c linenumber=2875 hts_log /src/htslib/hts.c linenumber=2879 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2972 hts_log /src/htslib/hts.c linenumber=2973 parse_cigar /src/htslib/sam.c linenumber=2985 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2899 hts_log /src/htslib/hts.c linenumber=2901 hts_log /src/htslib/hts.c linenumber=2905 hts_log /src/htslib/hts.c linenumber=2911 bam_cigar2rlen /src/htslib/sam.c linenumber=2776 hts_log /src/htslib/hts.c linenumber=2779 strchr linenumber=2781 hts_log /src/htslib/hts.c linenumber=2784 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2786 strchr linenumber=2789 strcmp linenumber=2790 strcmp linenumber=2792 bam_name2id /src/htslib/./htslib/sam.h linenumber=2795 hts_log /src/htslib/hts.c linenumber=2796 hts_strprint /src/htslib/textutils.c linenumber=2797 hts_log /src/htslib/hts.c linenumber=2797 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2801 hts_log /src/htslib/hts.c linenumber=2804 hts_str2int /src/htslib/./textutils_internal.h linenumber=2809 hts_log /src/htslib/hts.c linenumber=2811 strchr linenumber=2814 strcmp linenumber=2815 hts_log /src/htslib/hts.c linenumber=2816 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2819 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2829 hts_log /src/htslib/hts.c linenumber=2835 hts_log /src/htslib/hts.c linenumber=2839 aux_parse /src/htslib/sam.c linenumber=2844 hts_log /src/htslib/hts.c linenumber=2567 isspace_c /src/htslib/./textutils_internal.h linenumber=2571 isspace_c /src/htslib/./textutils_internal.h linenumber=2574 isspace_c /src/htslib/./textutils_internal.h linenumber=2576 kh_get_tag /src/htslib/sam.c linenumber=2583 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2591 isspace_c /src/htslib/./textutils_internal.h linenumber=2595 hts_log /src/htslib/hts.c linenumber=2595 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2598 hts_str2int /src/htslib/./textutils_internal.h linenumber=2605 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2611 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=275 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2615 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=283 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2619 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2625 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2629 strtod linenumber=2635 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2635 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=345 strtod linenumber=2639 double_to_le /src/htslib/./htslib/hts_endian.h linenumber=2639 u64_to_le /src/htslib/./htslib/hts_endian.h linenumber=359 strchr linenumber=2642 strlen linenumber=2643 isspace_c /src/htslib/./textutils_internal.h linenumber=2644 hts_log /src/htslib/hts.c linenumber=2644 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2647 isspace_c /src/htslib/./textutils_internal.h linenumber=2654 hts_log /src/htslib/hts.c linenumber=2654 sam_parse_B_vals /src/htslib/sam.c linenumber=2657 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2507 hts_log /src/htslib/hts.c linenumber=2387 aux_type2size /src/htslib/sam.c linenumber=2397 hts_log /src/htslib/hts.c linenumber=2399 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2416 hts_log /src/htslib/hts.c linenumber=2417 sam_parse_Bc_vals /src/htslib/sam.c linenumber=2430 grow_B_array /src/htslib/sam.c linenumber=2261 __errno_location linenumber=2236 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2241 hts_log /src/htslib/hts.c linenumber=2242 hts_str2int /src/htslib/./textutils_internal.h linenumber=2264 sam_parse_BC_vals /src/htslib/sam.c linenumber=2433 grow_B_array /src/htslib/sam.c linenumber=2275 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2279 sam_parse_Bs_vals /src/htslib/sam.c linenumber=2436 grow_B_array /src/htslib/sam.c linenumber=2295 hts_str2int /src/htslib/./textutils_internal.h linenumber=2298 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2298 sam_parse_BS_vals /src/htslib/sam.c linenumber=2439 grow_B_array /src/htslib/sam.c linenumber=2310 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2314 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2314 sam_parse_Bi_vals /src/htslib/sam.c linenumber=2442 grow_B_array /src/htslib/sam.c linenumber=2331 hts_str2int /src/htslib/./textutils_internal.h linenumber=2334 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2334 sam_parse_BI_vals /src/htslib/sam.c linenumber=2445 grow_B_array /src/htslib/sam.c linenumber=2346 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2350 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2350 sam_parse_Bf_vals /src/htslib/sam.c linenumber=2448 grow_B_array /src/htslib/sam.c linenumber=2367 strtod linenumber=2370 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2370 hts_log /src/htslib/hts.c linenumber=2453 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2456 hts_str2int /src/htslib/./textutils_internal.h linenumber=2470 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2479 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2481 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2483 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2487 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2489 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2491 isspace_c /src/htslib/./textutils_internal.h linenumber=2659 hts_strprint /src/htslib/textutils.c linenumber=2659 hts_log /src/htslib/hts.c linenumber=2659 isspace_c /src/htslib/./textutils_internal.h linenumber=2665 hts_log /src/htslib/hts.c linenumber=2665 bam_tag2cigar /src/htslib/sam.c linenumber=2847 bam_cigar2qlen /src/htslib/sam.c linenumber=2851 hts_log /src/htslib/hts.c linenumber=2853 sam_state_destroy /src/htslib/sam.c linenumber=4197 __errno_location linenumber=4198 bgzf_seek /src/htslib/bgzf.c linenumber=4201 bgzf_seek_common /src/htslib/bgzf.c linenumber=2278 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=4212 pthread_create linenumber=4216 sam_dispatcher_read /src/htslib/sam.c linenumber=4216 ks_resize /src/htslib/./htslib/kstring.h linenumber=3360 pthread_mutex_lock linenumber=3365 pthread_cond_signal linenumber=3369 pthread_mutex_unlock linenumber=3370 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3371 pthread_mutex_unlock linenumber=3377 pthread_mutex_lock linenumber=3379 pthread_mutex_unlock linenumber=3385 calloc linenumber=3389 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3393 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3404 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=3417 hread /src/htslib/./htslib/hfile.h linenumber=3419 __errno_location linenumber=3421 sam_state_err /src/htslib/sam.c linenumber=3421 hts_realloc_pse /src/htslib/./htslib/hts_alloc.h linenumber=3438 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=3443 __assert_fail linenumber=3444 __assert_fail linenumber=3445 ks_resize /src/htslib/./htslib/kstring.h linenumber=3451 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=3463 sam_parse_worker /src/htslib/sam.c linenumber=3463 pthread_mutex_lock linenumber=3250 pthread_mutex_unlock linenumber=3255 calloc linenumber=3258 calloc linenumber=3263 sam_state_err /src/htslib/sam.c linenumber=3265 sam_state_err /src/htslib/sam.c linenumber=3276 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3286 sam_state_err /src/htslib/sam.c linenumber=3289 strchr linenumber=3305 sam_parse1 /src/htslib/sam.c linenumber=3317 __errno_location linenumber=3318 sam_state_err /src/htslib/sam.c linenumber=3318 cleanup_sp_lines /src/htslib/sam.c linenumber=3319 __assert_fail linenumber=3231 sam_free_sp_bams /src/htslib/sam.c linenumber=3234 pthread_mutex_lock linenumber=3328 sam_free_sp_bams /src/htslib/sam.c linenumber=3335 cleanup_sp_lines /src/htslib/sam.c linenumber=3463 cleanup_sp_bams /src/htslib/sam.c linenumber=3463 sam_free_sp_bams /src/htslib/sam.c linenumber=3345 pthread_mutex_lock linenumber=3466 pthread_mutex_unlock linenumber=3468 pthread_mutex_unlock linenumber=3473 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3477 sam_parse_eof /src/htslib/sam.c linenumber=3477 pthread_mutex_lock linenumber=3483 pthread_cond_wait linenumber=3485 pthread_cond_signal linenumber=3488 pthread_mutex_unlock linenumber=3489 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3490 pthread_mutex_unlock linenumber=3494 pthread_mutex_lock linenumber=3500 pthread_cond_signal linenumber=3502 pthread_mutex_unlock linenumber=3503 pthread_mutex_lock linenumber=3506 pthread_mutex_unlock linenumber=3509 __errno_location linenumber=3516 sam_state_err /src/htslib/sam.c linenumber=3516 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3517 hts_log /src/htslib/hts.c linenumber=4223 __errno_location linenumber=4231 pthread_mutex_lock linenumber=4235 pthread_mutex_unlock linenumber=4237 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=4241 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4244 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4245 pthread_mutex_lock linenumber=4248 pthread_mutex_unlock linenumber=4250 bam_copy1 /src/htslib/sam.c linenumber=4255 pthread_mutex_lock linenumber=4258 pthread_mutex_unlock linenumber=4261 hts_getline /src/htslib/hts.c linenumber=4274 sam_parse1 /src/htslib/sam.c linenumber=4277 hts_log /src/htslib/hts.c linenumber=4280 fastq_state_init /src/htslib/sam.c linenumber=4313 fastq_parse1 /src/htslib/sam.c linenumber=4318 hts_getline /src/htslib/hts.c linenumber=3971 strpbrk linenumber=3987 isspace_c /src/htslib/./textutils_internal.h linenumber=3999 isspace_c /src/htslib/./textutils_internal.h linenumber=4007 hts_getline /src/htslib/hts.c linenumber=4015 kputsn /src/htslib/./htslib/kstring.h linenumber=4021 hts_getline /src/htslib/hts.c linenumber=4030 kputsn /src/htslib/./htslib/kstring.h linenumber=4034 isdigit_c /src/htslib/./textutils_internal.h linenumber=4047 regexec linenumber=4061 hts_log /src/htslib/hts.c linenumber=4066 isalpha_c /src/htslib/./textutils_internal.h linenumber=4074 bam_set1 /src/htslib/sam.c linenumber=4094 bam_aux_append /src/htslib/sam.c linenumber=4106 __assert_fail linenumber=4789 realloc_bam_data /src/htslib/./sam_internal.h linenumber=4793 __errno_location linenumber=4813 isdigit_c /src/htslib/./textutils_internal.h linenumber=4118 strtol linenumber=4119 isdigit_c /src/htslib/./textutils_internal.h linenumber=4133 isspace_c /src/htslib/./textutils_internal.h linenumber=4136 bam_aux_append /src/htslib/sam.c linenumber=4145 aux_parse /src/htslib/sam.c linenumber=4152 __errno_location linenumber=4322 __errno_location linenumber=4326 sam_passes_filter /src/htslib/sam.c linenumber=4331 hts_filter_eval2 /src/htslib/hts_expr.c linenumber=1569 ks_free /src/htslib/./htslib/kstring.h linenumber=1006 hts_filter_eval_ /src/htslib/hts_expr.c linenumber=1009 expression /src/htslib/hts_expr.c linenumber=964 hts_log /src/htslib/hts.c linenumber=922 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=923 ks_clear /src/htslib/./htslib/kstring.h linenumber=80 and_expr /src/htslib/hts_expr.c linenumber=926 eq_expr /src/htslib/hts_expr.c linenumber=866 cmp_expr /src/htslib/hts_expr.c linenumber=747 bitor_expr /src/htslib/hts_expr.c linenumber=674 bitxor_expr /src/htslib/hts_expr.c linenumber=629 bitand_expr /src/htslib/hts_expr.c linenumber=587 add_expr /src/htslib/hts_expr.c linenumber=545 mul_expr /src/htslib/hts_expr.c linenumber=497 unary_expr /src/htslib/hts_expr.c linenumber=447 ws /src/htslib/hts_expr.c linenumber=384 simple_expr /src/htslib/hts_expr.c linenumber=386 ws /src/htslib/hts_expr.c linenumber=304 expression /src/htslib/hts_expr.c linenumber=306 ws /src/htslib/hts_expr.c linenumber=307 fprintf linenumber=309 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=319 __ctype_b_loc linenumber=365 strtod linenumber=386 strtod linenumber=409 ks_clear /src/htslib/./htslib/kstring.h linenumber=337 kputsn /src/htslib/./htslib/kstring.h linenumber=337 func_expr /src/htslib/hts_expr.c linenumber=364 strncmp linenumber=169 expression /src/htslib/hts_expr.c linenumber=170 expr_func_avg /src/htslib/hts_expr.c linenumber=171 strncmp linenumber=176 expression /src/htslib/hts_expr.c linenumber=177 ws /src/htslib/hts_expr.c linenumber=182 expression /src/htslib/hts_expr.c linenumber=182 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=183 ks_free /src/htslib/./htslib/kstring.h linenumber=88 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=187 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=75 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=192 strncmp linenumber=197 expression /src/htslib/hts_expr.c linenumber=198 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=200 strncmp linenumber=202 expression /src/htslib/hts_expr.c linenumber=203 exp linenumber=205 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=208 strncmp linenumber=214 expression /src/htslib/hts_expr.c linenumber=215 expr_func_length /src/htslib/hts_expr.c linenumber=216 strncmp linenumber=217 expression /src/htslib/hts_expr.c linenumber=218 log linenumber=220 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=223 strncmp linenumber=228 expression /src/htslib/hts_expr.c linenumber=229 expr_func_min /src/htslib/hts_expr.c linenumber=230 strncmp linenumber=231 expression /src/htslib/hts_expr.c linenumber=232 expr_func_max /src/htslib/hts_expr.c linenumber=233 strncmp linenumber=238 expression /src/htslib/hts_expr.c linenumber=239 ws /src/htslib/hts_expr.c linenumber=246 expression /src/htslib/hts_expr.c linenumber=246 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=247 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=250 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=251 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=252 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=254 pow linenumber=258 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=259 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=264 strncmp linenumber=269 expression /src/htslib/hts_expr.c linenumber=270 sqrt linenumber=272 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=275 ws /src/htslib/hts_expr.c linenumber=283 fprintf linenumber=285 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=387 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=388 unary_expr /src/htslib/hts_expr.c linenumber=396 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=400 IS_VALID /src/htslib/hts_expr.c linenumber=407 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=411 unary_expr /src/htslib/hts_expr.c linenumber=416 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=417 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=418 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=421 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=422 IS_VALID /src/htslib/hts_expr.c linenumber=423 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=427 simple_expr /src/htslib/hts_expr.c linenumber=431 ws /src/htslib/hts_expr.c linenumber=453 unary_expr /src/htslib/hts_expr.c linenumber=455 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=456 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=459 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=460 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=462 IS_VALID /src/htslib/hts_expr.c linenumber=472 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=475 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=479 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=483 ws /src/htslib/hts_expr.c linenumber=503 mul_expr /src/htslib/hts_expr.c linenumber=506 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=507 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=510 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=513 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=526 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=533 ws /src/htslib/hts_expr.c linenumber=550 add_expr /src/htslib/hts_expr.c linenumber=552 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=553 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=556 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=559 IS_VALID /src/htslib/hts_expr.c linenumber=561 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=565 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=566 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=573 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=575 ws /src/htslib/hts_expr.c linenumber=592 bitand_expr /src/htslib/hts_expr.c linenumber=594 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=595 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=598 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=601 IS_VALID /src/htslib/hts_expr.c linenumber=603 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=607 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=608 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=615 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=617 ws /src/htslib/hts_expr.c linenumber=634 bitxor_expr /src/htslib/hts_expr.c linenumber=636 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=637 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=640 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=643 IS_VALID /src/htslib/hts_expr.c linenumber=645 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=649 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=650 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=657 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=659 ws /src/htslib/hts_expr.c linenumber=676 cmp_expr /src/htslib/hts_expr.c linenumber=682 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=683 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=684 strcmp linenumber=688 cmp_expr /src/htslib/hts_expr.c linenumber=694 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=695 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=696 strcmp linenumber=700 cmp_expr /src/htslib/hts_expr.c linenumber=706 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=707 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=708 strcmp linenumber=712 cmp_expr /src/htslib/hts_expr.c linenumber=718 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=719 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=720 strcmp linenumber=724 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=730 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=731 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=732 ws /src/htslib/hts_expr.c linenumber=749 eq_expr /src/htslib/hts_expr.c linenumber=759 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=762 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=763 strcmp linenumber=766 eq_expr /src/htslib/hts_expr.c linenumber=774 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=777 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=778 strcmp linenumber=781 eq_expr /src/htslib/hts_expr.c linenumber=790 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=792 regcomp linenumber=823 regerror linenumber=826 fprintf linenumber=827 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=830 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=831 regexec linenumber=837 regfree linenumber=841 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=851 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=852 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=853 ws /src/htslib/hts_expr.c linenumber=870 eq_expr /src/htslib/hts_expr.c linenumber=872 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=873 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=876 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=877 eq_expr /src/htslib/hts_expr.c linenumber=886 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=887 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=890 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=892 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=894 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=897 hts_expr_val_existsT /src/htslib/./htslib/hts_expr.h linenumber=899 hts_expr_val_undef /src/htslib/./htslib/hts_expr.h linenumber=902 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=913 ws /src/htslib/hts_expr.c linenumber=967 fprintf linenumber=968 hts_expr_val_exists /src/htslib/./htslib/hts_expr.h linenumber=979 bam_sym_lookup /src/htslib/sam.c linenumber=1569 memcmp linenumber=1247 ks_clear /src/htslib/./htslib/kstring.h linenumber=1250 kputw /src/htslib/./htslib/kstring.h linenumber=1255 kputc_ /src/htslib/./htslib/kstring.h linenumber=1256 kputs /src/htslib/./htslib/kstring.h linenumber=1258 kputs /src/htslib/./htslib/kstring.h linenumber=1260 memcmp linenumber=1267 bam_endpos /src/htslib/sam.c linenumber=1269 memcmp linenumber=1275 memcmp linenumber=1282 memcmp linenumber=1286 memcmp linenumber=1290 memcmp linenumber=1294 memcmp linenumber=1298 memcmp linenumber=1302 memcmp linenumber=1306 memcmp linenumber=1310 memcmp linenumber=1314 memcmp linenumber=1318 memcmp linenumber=1322 memcmp linenumber=1326 hts_log /src/htslib/hts.c linenumber=1331 memcmp linenumber=1339 memcmp linenumber=1359 bam_get_library /src/htslib/sam.c linenumber=1362 bam_aux_getZ /src/htslib/sam.c linenumber=1206 bam_aux_get /src/htslib/sam.c linenumber=4914 sam_hdr_find_tag_id /src/htslib/header.c linenumber=1213 ks_clear /src/htslib/./htslib/kstring.h linenumber=1363 kputs /src/htslib/./htslib/kstring.h linenumber=1363 memcmp linenumber=1369 memcmp linenumber=1373 memcmp linenumber=1377 sam_hdr_tid2name /src/htslib/header.c linenumber=1380 ks_clear /src/htslib/./htslib/kstring.h linenumber=1381 kputs /src/htslib/./htslib/kstring.h linenumber=1381 memcmp linenumber=1383 memcmp linenumber=1391 memcmp linenumber=1399 memcmp linenumber=1403 memcmp linenumber=1411 bam_cigar2qlen /src/htslib/sam.c linenumber=1413 memcmp linenumber=1415 ks_clear /src/htslib/./htslib/kstring.h linenumber=1418 kputs /src/htslib/./htslib/kstring.h linenumber=1418 memcmp linenumber=1420 ks_clear /src/htslib/./htslib/kstring.h linenumber=1422 ks_resize /src/htslib/./htslib/kstring.h linenumber=1423 memcmp linenumber=1434 bam_cigar2rlen /src/htslib/sam.c linenumber=1436 memcmp linenumber=1438 sam_hdr_tid2name /src/htslib/header.c linenumber=1441 ks_clear /src/htslib/./htslib/kstring.h linenumber=1442 kputs /src/htslib/./htslib/kstring.h linenumber=1442 memcmp linenumber=1444 sam_hdr_tid2name /src/htslib/header.c linenumber=1447 ks_clear /src/htslib/./htslib/kstring.h linenumber=1448 kputs /src/htslib/./htslib/kstring.h linenumber=1448 memcmp linenumber=1450 memcmp linenumber=1458 ks_clear /src/htslib/./htslib/kstring.h linenumber=1460 ks_resize /src/htslib/./htslib/kstring.h linenumber=1461 nibble2base /src/htslib/./sam_internal.h linenumber=1463 memcmp linenumber=1468 memcmp linenumber=1499 bam_aux_get /src/htslib/sam.c linenumber=1511 ks_clear /src/htslib/./htslib/kstring.h linenumber=1519 kputs /src/htslib/./htslib/kstring.h linenumber=1519 ks_clear /src/htslib/./htslib/kstring.h linenumber=1524 kputsn /src/htslib/./htslib/kstring.h linenumber=1524 bam_aux2i /src/htslib/sam.c linenumber=1531 get_int_aux_val /src/htslib/sam.c linenumber=5174 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=5158 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=5160 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=5161 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=5162 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=5163 __errno_location linenumber=5165 bam_aux2f /src/htslib/sam.c linenumber=1537 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=5181 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=5182 get_int_aux_val /src/htslib/sam.c linenumber=5183 hts_log /src/htslib/hts.c linenumber=1541 hts_log /src/htslib/hts.c linenumber=1570 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1571 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1576 sam_write1 /src/htslib/sam.c linenumber=107 bam_write_idx1 /src/htslib/sam.c linenumber=4585 bam_write1 /src/htslib/sam.c linenumber=964 hts_log /src/htslib/hts.c linenumber=895 __errno_location linenumber=896 hts_log /src/htslib/hts.c linenumber=903 bgzf_flush_try /src/htslib/bgzf.c linenumber=915 lazy_flush /src/htslib/bgzf.c linenumber=2019 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=917 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=919 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=919 bgzf_write /src/htslib/bgzf.c linenumber=198 swap_data /src/htslib/sam.c linenumber=920 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=922 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=924 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=925 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=927 bam_cigar2rlen /src/htslib/sam.c linenumber=931 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=944 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=945 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=946 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=947 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=948 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=949 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=950 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=951 swap_data /src/htslib/sam.c linenumber=953 bgzf_flush_try /src/htslib/bgzf.c linenumber=967 hts_idx_amend_last /src/htslib/hts.c linenumber=970 bam_write1 /src/htslib/sam.c linenumber=972 bam_endpos /src/htslib/sam.c linenumber=976 bgzf_idx_push /src/htslib/bgzf.c linenumber=976 hts_idx_push /src/htslib/hts.c linenumber=195 hts_idx_check_range /src/htslib/hts.c linenumber=2663 hts_idx_maxpos /src/htslib/hts.c linenumber=2641 hts_bin_maxpos /src/htslib/./htslib/hts.h linenumber=2636 hts_log /src/htslib/hts.c linenumber=2646 idx_format_name /src/htslib/hts.c linenumber=2651 hts_log /src/htslib/hts.c linenumber=2651 __errno_location linenumber=2655 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2670 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2674 hts_log /src/htslib/hts.c linenumber=2687 hts_log /src/htslib/hts.c linenumber=2692 hts_log /src/htslib/hts.c linenumber=2698 hts_log /src/htslib/hts.c linenumber=2703 kh_init_bin /src/htslib/hts.c linenumber=2708 calloc linenumber=2342 insert_to_l /src/htslib/hts.c linenumber=2713 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2458 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2717 insert_to_b /src/htslib/hts.c linenumber=2720 kh_put_bin /src/htslib/hts.c linenumber=2425 kh_resize_bin /src/htslib/hts.c linenumber=2342 __errno_location linenumber=2342 realloc linenumber=2342 calloc linenumber=2430 kh_del_bin /src/htslib/hts.c linenumber=2432 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2437 insert_to_b /src/htslib/hts.c linenumber=2725 insert_to_b /src/htslib/hts.c linenumber=2727 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=977 sam_hdr_tid2len /src/htslib/header.c linenumber=977 kh_get_s2i /src/htslib/hts.c linenumber=2478 hts_log /src/htslib/hts.c linenumber=977 cram_put_bam_seq /src/htslib/cram/cram_encode.c linenumber=4588 hts_log /src/htslib/hts.c linenumber=3971 __errno_location linenumber=3972 cram_new_container /src/htslib/cram/cram_io.c linenumber=3977 pthread_mutex_lock linenumber=3983 pthread_mutex_unlock linenumber=3986 hts_log /src/htslib/hts.c linenumber=4011 pthread_mutex_lock linenumber=4014 hts_log /src/htslib/hts.c linenumber=4017 pthread_mutex_unlock linenumber=4019 cram_next_container /src/htslib/cram/cram_encode.c linenumber=4028 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=3215 hts_log /src/htslib/hts.c linenumber=3221 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=3226 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3232 cram_free_container /src/htslib/cram/cram_io.c linenumber=3240 cram_new_container /src/htslib/cram/cram_io.c linenumber=3243 pthread_mutex_lock linenumber=3248 cram_new_slice /src/htslib/cram/cram_io.c linenumber=3260 calloc linenumber=4239 calloc linenumber=4243 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4251 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4253 cram_new_block /src/htslib/cram/cram_io.c linenumber=4256 cram_new_block /src/htslib/cram/cram_io.c linenumber=4257 cram_new_block /src/htslib/cram/cram_io.c linenumber=4258 cram_new_block /src/htslib/cram/cram_io.c linenumber=4259 cram_new_block /src/htslib/cram/cram_io.c linenumber=4260 cram_new_block /src/htslib/cram/cram_io.c linenumber=4261 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4272 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4273 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4274 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4284 pthread_mutex_lock linenumber=4060 hts_log /src/htslib/hts.c linenumber=4062 pthread_mutex_unlock linenumber=4073 pthread_mutex_lock linenumber=4076 calloc linenumber=4077 pthread_mutex_unlock linenumber=4078 pthread_mutex_lock linenumber=4092 calloc linenumber=4093 pthread_mutex_unlock linenumber=4094 pthread_mutex_lock linenumber=4098 pthread_mutex_unlock linenumber=4101 pthread_mutex_lock linenumber=4111 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4116 pthread_mutex_unlock linenumber=4119 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4125 calloc linenumber=4133 pthread_mutex_unlock linenumber=4136 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4141 pthread_mutex_unlock linenumber=4143 bam_copy1 /src/htslib/sam.c linenumber=4150 bam_cigar2qlen /src/htslib/sam.c linenumber=4160 hts_log /src/htslib/hts.c linenumber=4162 pthread_create linenumber=4611 sam_dispatcher_write /src/htslib/sam.c linenumber=4611 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3530 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3531 sam_state_err /src/htslib/sam.c linenumber=3533 bgzf_flush_try /src/htslib/bgzf.c linenumber=3548 bgzf_write /src/htslib/bgzf.c linenumber=3550 hwrite /src/htslib/./htslib/hfile.h linenumber=3553 bam_endpos /src/htslib/sam.c linenumber=3560 bgzf_idx_push /src/htslib/bgzf.c linenumber=3559 __errno_location linenumber=3563 sam_state_err /src/htslib/sam.c linenumber=3563 sam_hdr_tid2name /src/htslib/header.c linenumber=3564 sam_hdr_tid2len /src/htslib/header.c linenumber=3564 hts_log /src/htslib/hts.c linenumber=3564 bam_endpos /src/htslib/sam.c linenumber=3569 hts_idx_push /src/htslib/hts.c linenumber=3569 __errno_location linenumber=3571 sam_state_err /src/htslib/sam.c linenumber=3571 sam_hdr_tid2name /src/htslib/header.c linenumber=3572 sam_hdr_tid2len /src/htslib/header.c linenumber=3572 hts_log /src/htslib/hts.c linenumber=3572 __assert_fail linenumber=3579 pthread_mutex_lock linenumber=3582 pthread_mutex_unlock linenumber=3586 bgzf_write /src/htslib/bgzf.c linenumber=3633 bgzf_flush_try /src/htslib/bgzf.c linenumber=3641 bgzf_write /src/htslib/bgzf.c linenumber=3646 hwrite /src/htslib/./htslib/hfile.h linenumber=3653 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3658 pthread_mutex_lock linenumber=3661 pthread_mutex_unlock linenumber=3664 sam_state_err /src/htslib/sam.c linenumber=3667 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3668 __errno_location linenumber=3672 sam_state_err /src/htslib/sam.c linenumber=3672 hts_log /src/htslib/hts.c linenumber=4618 pthread_mutex_lock linenumber=4625 pthread_mutex_unlock linenumber=4632 pthread_mutex_unlock linenumber=4634 calloc linenumber=4635 calloc linenumber=4636 bam_copy1 /src/htslib/sam.c linenumber=4649 pthread_mutex_lock linenumber=4656 pthread_mutex_unlock linenumber=4658 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=4661 sam_format_worker /src/htslib/sam.c linenumber=4661 cleanup_sp_bams /src/htslib/sam.c linenumber=4661 cleanup_sp_lines /src/htslib/sam.c linenumber=4661 pthread_mutex_unlock linenumber=4664 pthread_mutex_unlock linenumber=4667 sam_format1 /src/htslib/sam.c linenumber=4676 sam_format1_append /src/htslib/sam.c linenumber=4433 kputc /src/htslib/./htslib/kstring.h linenumber=4677 bgzf_flush_try /src/htslib/bgzf.c linenumber=4679 bgzf_write /src/htslib/bgzf.c linenumber=4681 hwrite /src/htslib/./htslib/hfile.h linenumber=4683 bam_endpos /src/htslib/sam.c linenumber=4688 bgzf_idx_push /src/htslib/bgzf.c linenumber=4688 sam_hdr_tid2name /src/htslib/header.c linenumber=4690 sam_hdr_tid2len /src/htslib/header.c linenumber=4690 hts_log /src/htslib/hts.c linenumber=4690 bam_endpos /src/htslib/sam.c linenumber=4695 hts_idx_push /src/htslib/hts.c linenumber=4695 sam_hdr_tid2name /src/htslib/header.c linenumber=4697 sam_hdr_tid2len /src/htslib/header.c linenumber=4697 hts_log /src/htslib/hts.c linenumber=4697 fastq_state_init /src/htslib/sam.c linenumber=4712 fastq_format1 /src/htslib/sam.c linenumber=4717 kputc /src/htslib/./htslib/kstring.h linenumber=4446 kputs /src/htslib/./htslib/kstring.h linenumber=4446 bam_aux_getZ /src/htslib/sam.c linenumber=4468 kputc /src/htslib/./htslib/kstring.h linenumber=4470 isalpha_c /src/htslib/./textutils_internal.h linenumber=4473 toupper_c /src/htslib/./textutils_internal.h linenumber=4473 kputc /src/htslib/./htslib/kstring.h linenumber=4473 kputs /src/htslib/./htslib/kstring.h linenumber=4478 kputs /src/htslib/./htslib/kstring.h linenumber=4486 kputs /src/htslib/./htslib/kstring.h linenumber=4489 bam_aux_getZ /src/htslib/sam.c linenumber=4499 ksprintf /src/htslib/kstring.c linenumber=4500 isupper_c /src/htslib/./textutils_internal.h linenumber=4504 __ctype_b_loc linenumber=177 islower_c /src/htslib/./textutils_internal.h linenumber=4504 __ctype_b_loc linenumber=173 hts_log /src/htslib/hts.c linenumber=4505 strlen linenumber=4506 strlen linenumber=4514 isalpha_c /src/htslib/./textutils_internal.h linenumber=4517 islower_c /src/htslib/./textutils_internal.h linenumber=4519 toupper_c /src/htslib/./textutils_internal.h linenumber=4520 kh_get_tag /src/htslib/sam.c linenumber=4531 kputc_ /src/htslib/./htslib/kstring.h linenumber=4532 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4533 skip_aux /src/htslib/sam.c linenumber=4536 kputsn /src/htslib/./htslib/kstring.h linenumber=4539 ks_resize /src/htslib/./htslib/kstring.h linenumber=4542 kputc_ /src/htslib/./htslib/kstring.h linenumber=4543 kputc_ /src/htslib/./htslib/kstring.h linenumber=4549 kputc_ /src/htslib/./htslib/kstring.h linenumber=4552 kputsn /src/htslib/./htslib/kstring.h linenumber=4557 kputc_ /src/htslib/./htslib/kstring.h linenumber=4561 kputc_ /src/htslib/./htslib/kstring.h linenumber=4564 kputc_ /src/htslib/./htslib/kstring.h linenumber=4567 kputc /src/htslib/./htslib/kstring.h linenumber=4570 bgzf_flush_try /src/htslib/bgzf.c linenumber=4720 bgzf_write /src/htslib/bgzf.c linenumber=4722 hwrite /src/htslib/./htslib/hfile.h linenumber=4725 __errno_location linenumber=4732 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=1776 bcf_hdr_init /src/htslib/vcf.c linenumber=2677 calloc linenumber=1702 kh_init_vdict /src/htslib/vcf.c linenumber=1705 calloc linenumber=75 kh_resize_vdict /src/htslib/vcf.c linenumber=1708 __errno_location linenumber=75 realloc linenumber=75 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=75 calloc linenumber=1711 kh_init_hdict /src/htslib/vcf.c linenumber=1713 strchr linenumber=1721 bcf_hdr_append /src/htslib/vcf.c linenumber=1723 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1555 calloc linenumber=670 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=672 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=682 isalpha_c /src/htslib/./textutils_internal.h linenumber=699 isalnum_c /src/htslib/./textutils_internal.h linenumber=702 bcf_hrec_add_key /src/htslib/vcf.c linenumber=712 __assert_fail linenumber=443 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=444 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=447 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=451 is_escaped /src/htslib/vcf.c linenumber=732 bcf_hrec_set_val /src/htslib/vcf.c linenumber=754 __errno_location linenumber=470 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=473 __errno_location linenumber=483 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=486 isspace_c /src/htslib/./textutils_internal.h linenumber=771 hts_strprint /src/htslib/textutils.c linenumber=774 hts_log /src/htslib/hts.c linenumber=774 bcf_hrec_destroy /src/htslib/vcf.c linenumber=784 hts_strprint /src/htslib/textutils.c linenumber=791 bcf_hrec_destroy /src/htslib/vcf.c linenumber=795 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1557 get_hdr_aux /src/htslib/vcf.c linenumber=1188 bcf_hrec_check /src/htslib/vcf.c linenumber=1193 bcf_hrec_set_type /src/htslib/vcf.c linenumber=598 strcmp linenumber=528 strcmp linenumber=529 strcmp linenumber=530 strcmp linenumber=531 bcf_hrec_find_key /src/htslib/vcf.c linenumber=602 strcasecmp linenumber=522 bcf_hrec_find_key /src/htslib/vcf.c linenumber=612 strcmp linenumber=615 bcf_hrec_find_key /src/htslib/vcf.c linenumber=623 hts_log /src/htslib/hts.c linenumber=634 hts_log /src/htslib/hts.c linenumber=638 hts_log /src/htslib/hts.c linenumber=642 bcf_hdr_register_hrec /src/htslib/vcf.c linenumber=1195 bcf_hrec_set_type /src/htslib/vcf.c linenumber=1058 bcf_hdr_register_hrec_ctg /src/htslib/vcf.c linenumber=1062 bcf_hrec_find_key /src/htslib/vcf.c linenumber=842 bcf_hrec_find_key /src/htslib/vcf.c linenumber=845 strtoll linenumber=850 hts_log /src/htslib/hts.c linenumber=852 strdup linenumber=861 kh_get_vdict /src/htslib/vcf.c linenumber=866 strcmp linenumber=75 kh_put_vdict /src/htslib/vcf.c linenumber=873 kh_resize_vdict /src/htslib/vcf.c linenumber=75 bcf_hrec_find_key /src/htslib/vcf.c linenumber=877 strtol linenumber=881 kh_del_vdict /src/htslib/vcf.c linenumber=885 hts_log /src/htslib/hts.c linenumber=888 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=897 hts_log /src/htslib/hts.c linenumber=809 __errno_location linenumber=811 hts_resize_array_ /src/htslib/hts.c linenumber=821 hts_log /src/htslib/hts.c linenumber=5229 __errno_location linenumber=5230 realloc linenumber=5234 __errno_location linenumber=5236 __errno_location linenumber=5237 strerror linenumber=5237 hts_log /src/htslib/hts.c linenumber=5237 __errno_location linenumber=5238 abort linenumber=5247 abort linenumber=5258 kh_del_vdict /src/htslib/vcf.c linenumber=899 hrec_add_idx /src/htslib/vcf.c linenumber=905 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=497 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=501 strdup linenumber=505 kputw /src/htslib/./htslib/kstring.h linenumber=509 bcf_hdr_register_hrec_info /src/htslib/vcf.c linenumber=1067 strcmp linenumber=926 strcmp linenumber=927 strtol linenumber=930 hts_log /src/htslib/hts.c linenumber=933 strcmp linenumber=937 strcmp linenumber=939 strcmp linenumber=940 strcmp linenumber=941 strcmp linenumber=942 strcmp linenumber=943 hts_log /src/htslib/hts.c linenumber=946 strcmp linenumber=950 strcmp linenumber=953 strcmp linenumber=954 strcmp linenumber=955 strcmp linenumber=956 strcmp linenumber=957 strcmp linenumber=958 strcmp linenumber=959 strcmp linenumber=960 strcmp linenumber=961 __isoc99_sscanf linenumber=964 hts_log /src/htslib/hts.c linenumber=972 strdup linenumber=994 kh_get_vdict /src/htslib/vcf.c linenumber=998 strcmp linenumber=1002 hrec_add_idx /src/htslib/vcf.c linenumber=1013 hrec_add_idx /src/htslib/vcf.c linenumber=1026 kh_put_vdict /src/htslib/vcf.c linenumber=1032 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=1041 kh_del_vdict /src/htslib/vcf.c linenumber=1042 hrec_add_idx /src/htslib/vcf.c linenumber=1047 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1202 ksprintf /src/htslib/kstring.c linenumber=1206 kh_get_hdict /src/htslib/vcf.c linenumber=1211 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1215 bcf_get_version /src/htslib/vcf.c linenumber=1220 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=1659 ksprintf /src/htslib/kstring.c linenumber=1281 get_hdr_aux /src/htslib/vcf.c linenumber=1282 kh_get_hdict /src/htslib/vcf.c linenumber=1283 strcmp linenumber=1291 ksprintf /src/htslib/kstring.c linenumber=1304 get_hdr_aux /src/htslib/vcf.c linenumber=1305 kh_get_hdict /src/htslib/vcf.c linenumber=1306 strcmp linenumber=1314 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1315 strcmp linenumber=1316 kh_get_vdict /src/htslib/vcf.c linenumber=1321 hts_log /src/htslib/hts.c linenumber=1662 strstr linenumber=168 strchr linenumber=172 strtol linenumber=175 __errno_location linenumber=176 strtol linenumber=180 __errno_location linenumber=181 hts_log /src/htslib/hts.c linenumber=188 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1225 ksprintf /src/htslib/kstring.c linenumber=1227 kh_get_hdict /src/htslib/vcf.c linenumber=1232 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1236 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1244 bcf_hdr_unregister_hrec /src/htslib/vcf.c linenumber=1247 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1083 kh_get_vdict /src/htslib/vcf.c linenumber=1089 kh_put_hdict /src/htslib/vcf.c linenumber=1254 kh_resize_hdict /src/htslib/vcf.c linenumber=80 bcf_hdr_append /src/htslib/vcf.c linenumber=1725 kh_destroy_vdict /src/htslib/vcf.c linenumber=1732 hts_log /src/htslib/hts.c linenumber=2679 hts_getline /src/htslib/hts.c linenumber=2683 hopen /src/htslib/hfile.c linenumber=2692 hts_log /src/htslib/hts.c linenumber=2694 khgetline /src/htslib/hfile.c linenumber=2697 strchr linenumber=2698 kputs /src/htslib/./htslib/kstring.h linenumber=2700 kputsn /src/htslib/./htslib/kstring.h linenumber=2701 kputs /src/htslib/./htslib/kstring.h linenumber=2702 atol linenumber=2703 kputl /src/htslib/./htslib/kstring.h linenumber=2703 kputll /src/htslib/./htslib/kstring.h linenumber=446 kputsn /src/htslib/./htslib/kstring.h linenumber=2704 hclose /src/htslib/hfile.c linenumber=2707 hts_log /src/htslib/hts.c linenumber=2708 kputsn /src/htslib/./htslib/kstring.h linenumber=2713 kputc /src/htslib/./htslib/kstring.h linenumber=2714 hts_log /src/htslib/hts.c linenumber=2720 bcf_hdr_parse /src/htslib/vcf.c linenumber=2723 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1477 strcasecmp linenumber=1478 hts_log /src/htslib/hts.c linenumber=1479 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1480 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1481 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1486 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1487 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1488 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1494 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1495 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1496 __assert_fail linenumber=1501 __errno_location linenumber=1504 strerror linenumber=1504 hts_log /src/htslib/hts.c linenumber=1504 strncmp linenumber=1519 strchr linenumber=1520 hts_strprint /src/htslib/textutils.c linenumber=1523 hts_log /src/htslib/hts.c linenumber=1523 hts_log /src/htslib/hts.c linenumber=1540 bcf_hdr_parse_sample_line /src/htslib/vcf.c linenumber=1544 strlen linenumber=288 strncmp linenumber=288 hts_log /src/htslib/hts.c linenumber=290 strlen linenumber=294 strncmp linenumber=296 hts_log /src/htslib/hts.c linenumber=298 bcf_hdr_add_sample_len /src/htslib/vcf.c linenumber=308 isspace_c /src/htslib/./textutils_internal.h linenumber=234 hts_log /src/htslib/hts.c linenumber=237 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=250 kh_put_vdict /src/htslib/vcf.c linenumber=257 hts_log /src/htslib/hts.c linenumber=266 bcf_hdr_sync /src/htslib/vcf.c linenumber=1546 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=326 get_hdr_aux /src/htslib/vcf.c linenumber=340 bcf_hdr_check_sanity /src/htslib/vcf.c linenumber=1548 bcf_get_version /src/htslib/vcf.c linenumber=1332 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1411 kh_get_vdict /src/htslib/vcf.c linenumber=4748 atoi linenumber=1417 hts_log /src/htslib/hts.c linenumber=1422 hts_log /src/htslib/hts.c linenumber=1427 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1438 atoi linenumber=1453 hts_log /src/htslib/hts.c linenumber=1458 hts_log /src/htslib/hts.c linenumber=1463 tbx_index_load3 /src/htslib/tbx.c linenumber=2726 index_load /src/htslib/tbx.c linenumber=661 calloc linenumber=618 hts_idx_load3 /src/htslib/hts.c linenumber=621 idx_find_and_load /src/htslib/hts.c linenumber=5107 strstr linenumber=5040 strdup linenumber=5045 __errno_location linenumber=5047 strerror linenumber=5047 hts_log /src/htslib/hts.c linenumber=5047 hts_idx_load3 /src/htslib/hts.c linenumber=5052 hisremote /src/htslib/hfile.c linenumber=5111 stat linenumber=5113 hts_log /src/htslib/hts.c linenumber=5116 idx_test_and_fetch /src/htslib/hts.c linenumber=5121 hisremote /src/htslib/hfile.c linenumber=4745 strncmp linenumber=4750 strcspn linenumber=4750 kputsn /src/htslib/./htslib/kstring.h linenumber=4757 access linenumber=4758 hopen /src/htslib/hfile.c linenumber=4767 hts_log /src/htslib/hts.c linenumber=4768 hts_detect_format2 /src/htslib/hts.c linenumber=4772 hts_log /src/htslib/hts.c linenumber=4773 hts_log /src/htslib/hts.c linenumber=4778 hts_open_tmpfile /src/htslib/hts.c linenumber=4783 hts_log /src/htslib/hts.c linenumber=4784 hts_log /src/htslib/hts.c linenumber=4787 calloc linenumber=4788 __errno_location linenumber=4790 strerror linenumber=4790 hts_log /src/htslib/hts.c linenumber=4790 hread /src/htslib/./htslib/hfile.h linenumber=4793 hwrite /src/htslib/./htslib/hfile.h linenumber=4794 __errno_location linenumber=4795 strerror linenumber=4795 hts_log /src/htslib/hts.c linenumber=4795 hts_log /src/htslib/hts.c linenumber=4803 hclose /src/htslib/hfile.c linenumber=4806 __errno_location linenumber=4807 strerror linenumber=4807 hts_log /src/htslib/hts.c linenumber=4807 rename linenumber=4812 strerror linenumber=4813 hts_log /src/htslib/hts.c linenumber=4813 ks_clear /src/htslib/./htslib/kstring.h linenumber=4816 hclose /src/htslib/hfile.c linenumber=4825 hts_log /src/htslib/hts.c linenumber=4826 hopen /src/htslib/hfile.c linenumber=4834 hclose_abruptly /src/htslib/hfile.c linenumber=4835 strlen linenumber=4837 __errno_location linenumber=4842 hclose_abruptly /src/htslib/hfile.c linenumber=4843 hclose_abruptly /src/htslib/hfile.c linenumber=4844 unlink linenumber=4845 __errno_location linenumber=4848 strdup linenumber=5123 idx_read /src/htslib/hts.c linenumber=5131 bgzf_open /src/htslib/bgzf.c linenumber=3098 ed_is_big /src/htslib/./htslib/hts.h linenumber=3100 bgzf_read /src/htslib/bgzf.c linenumber=3101 memcmp linenumber=3103 bgzf_read /src/htslib/bgzf.c linenumber=3105 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3106 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3109 bgzf_read /src/htslib/bgzf.c linenumber=3110 bgzf_read /src/htslib/bgzf.c linenumber=3114 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3115 hts_idx_init /src/htslib/hts.c linenumber=3117 calloc linenumber=2509 calloc linenumber=2521 calloc linenumber=2523 idx_read_core /src/htslib/hts.c linenumber=3121 ed_is_big /src/htslib/./htslib/hts.h linenumber=3029 kh_init_bin /src/htslib/hts.c linenumber=3037 bgzf_read /src/htslib/bgzf.c linenumber=3038 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3039 bgzf_read /src/htslib/bgzf.c linenumber=3043 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3044 kh_put_bin /src/htslib/hts.c linenumber=3045 bgzf_read /src/htslib/bgzf.c linenumber=3051 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=3052 bgzf_read /src/htslib/bgzf.c linenumber=3054 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3055 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3059 bgzf_read /src/htslib/bgzf.c linenumber=3061 swap_bins /src/htslib/hts.c linenumber=3062 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2844 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2845 bgzf_read /src/htslib/bgzf.c linenumber=3067 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3068 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3073 bgzf_read /src/htslib/bgzf.c linenumber=3075 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=3076 update_loff /src/htslib/hts.c linenumber=3080 hts_bin_bot /src/htslib/./htslib/hts.h linenumber=2549 hts_bin_level /src/htslib/./htslib/hts.h linenumber=1574 bgzf_read /src/htslib/bgzf.c linenumber=3083 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=3084 memcmp linenumber=3123 bgzf_read /src/htslib/bgzf.c linenumber=3127 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3128 hts_idx_init /src/htslib/hts.c linenumber=3130 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3131 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3134 bgzf_read /src/htslib/bgzf.c linenumber=3139 idx_read_core /src/htslib/hts.c linenumber=3142 memcmp linenumber=3144 bgzf_read /src/htslib/bgzf.c linenumber=3146 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3147 hts_idx_init /src/htslib/hts.c linenumber=3149 idx_read_core /src/htslib/hts.c linenumber=3150 __errno_location linenumber=3152 bgzf_close /src/htslib/bgzf.c linenumber=3154 bgzf_close /src/htslib/bgzf.c linenumber=3158 hts_idx_destroy /src/htslib/hts.c linenumber=3159 __errno_location linenumber=5133 strerror linenumber=5133 hts_log /src/htslib/hts.c linenumber=5133 hts_idx_check_local /src/htslib/hts.c linenumber=5057 hisremote /src/htslib/hfile.c linenumber=4883 strlen linenumber=4884 strncmp linenumber=4891 strncmp linenumber=4892 hts_log /src/htslib/hts.c linenumber=4902 strlen linenumber=4903 calloc linenumber=4904 strcpy linenumber=4910 stat linenumber=4911 strcpy linenumber=4917 stat linenumber=4918 strcpy linenumber=4927 stat linenumber=4928 strcpy linenumber=4934 stat linenumber=4935 strcpy linenumber=4943 stat linenumber=4944 strcpy linenumber=4950 stat linenumber=4951 strcpy linenumber=4959 stat linenumber=4960 strcpy linenumber=4966 stat linenumber=4967 strcpy linenumber=4976 strcmp linenumber=4978 strcmp linenumber=4979 strcpy linenumber=4980 stat linenumber=4981 strcpy linenumber=4986 stat linenumber=4988 hisremote /src/htslib/hfile.c linenumber=5057 idx_filename /src/htslib/hts.c linenumber=5059 haddextension /src/htslib/hfile.c linenumber=5005 find_scheme_handler /src/htslib/hfile.c linenumber=1372 strncmp linenumber=1375 strcspn linenumber=1375 strchr linenumber=1379 strip_extension /src/htslib/hfile.c linenumber=1382 kputsn /src/htslib/./htslib/kstring.h linenumber=1385 kputs /src/htslib/./htslib/kstring.h linenumber=1386 kputs /src/htslib/./htslib/kstring.h linenumber=1387 idx_test_and_fetch /src/htslib/hts.c linenumber=5009 haddextension /src/htslib/hfile.c linenumber=5011 idx_test_and_fetch /src/htslib/hts.c linenumber=5015 idx_filename /src/htslib/hts.c linenumber=5062 idx_filename /src/htslib/hts.c linenumber=5063 idx_filename /src/htslib/hts.c linenumber=5068 idx_filename /src/htslib/hts.c linenumber=5071 idx_filename /src/htslib/hts.c linenumber=5072 hts_log /src/htslib/hts.c linenumber=5080 hts_idx_load3 /src/htslib/hts.c linenumber=5085 idx_read /src/htslib/hts.c linenumber=5087 hts_idx_get_meta /src/htslib/hts.c linenumber=627 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=630 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=631 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=632 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=633 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=634 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=635 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=636 get_tid /src/htslib/tbx.c linenumber=644 kh_init_s2i /src/htslib/hts.c linenumber=71 kh_put_s2i /src/htslib/hts.c linenumber=76 strdup linenumber=80 kh_del_s2i /src/htslib/hts.c linenumber=85 kh_get_s2i /src/htslib/hts.c linenumber=89 __errno_location linenumber=645 strerror linenumber=645 hts_log /src/htslib/hts.c linenumber=645 strlen linenumber=643 hts_log /src/htslib/hts.c linenumber=652 tbx_destroy /src/htslib/tbx.c linenumber=655 hts_idx_destroy /src/htslib/hts.c linenumber=581 kh_destroy_s2i /src/htslib/hts.c linenumber=582 tbx_seqnames /src/htslib/tbx.c linenumber=2730 calloc linenumber=680 calloc linenumber=683 __assert_fail linenumber=693 __assert_fail linenumber=698 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=2734 add_missing_contig_hrec /src/htslib/vcf.c linenumber=2736 calloc linenumber=2648 strdup linenumber=2652 bcf_hrec_add_key /src/htslib/vcf.c linenumber=2655 strlen linenumber=2656 bcf_hrec_set_val /src/htslib/vcf.c linenumber=2656 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=2658 __errno_location linenumber=2663 __errno_location linenumber=2664 strerror linenumber=2664 hts_log /src/htslib/hts.c linenumber=2664 bcf_hrec_destroy /src/htslib/vcf.c linenumber=2665 __errno_location linenumber=2666 bcf_hdr_sync /src/htslib/vcf.c linenumber=2740 tbx_destroy /src/htslib/tbx.c linenumber=2743 tbx_destroy /src/htslib/tbx.c linenumber=2749 bcf_hdr_destroy /src/htslib/vcf.c linenumber=2752 get_hdr_aux /src/htslib/vcf.c linenumber=1742 kh_destroy_hdict /src/htslib/vcf.c linenumber=1757 kh_destroy_vdict /src/htslib/vcf.c linenumber=1760 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1764 hts_log /src/htslib/hts.c linenumber=1778 __assert_fail linenumber=1782 bcf_hdr_init /src/htslib/vcf.c linenumber=1787 bgzf_read /src/htslib/bgzf.c linenumber=1792 hts_log /src/htslib/hts.c linenumber=1794 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1795 strncmp linenumber=1798 strncmp linenumber=1800 hts_log /src/htslib/hts.c linenumber=1801 hts_log /src/htslib/hts.c linenumber=1803 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1804 bgzf_read /src/htslib/bgzf.c linenumber=1810 __errno_location linenumber=1812 __errno_location linenumber=1814 bgzf_read /src/htslib/bgzf.c linenumber=1818 bcf_hdr_parse /src/htslib/vcf.c linenumber=1820 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1823 get_hdr_aux /src/htslib/vcf.c linenumber=197 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1824 __assert_fail linenumber=53 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1824 bcf_hdr_decr_ref /src/htslib/vcf.c linenumber=214 get_hdr_aux /src/htslib/vcf.c linenumber=203 bcf_hdr_destroy /src/htslib/vcf.c linenumber=208 hts_log /src/htslib/hts.c linenumber=1828 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1830 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=1837 bcf_hdr_sync /src/htslib/vcf.c linenumber=1841 vcf_hdr_write /src/htslib/vcf.c linenumber=1846 bcf_hdr_format /src/htslib/vcf.c linenumber=2890 _bcf_hrec_format /src/htslib/vcf.c linenumber=2820 ksprintf /src/htslib/kstring.c linenumber=2794 strcmp linenumber=2798 kputc /src/htslib/./htslib/kstring.h linenumber=2799 ksprintf /src/htslib/kstring.c linenumber=2800 ksprintf /src/htslib/kstring.c linenumber=2803 ksprintf /src/htslib/kstring.c linenumber=2806 ksprintf /src/htslib/kstring.c linenumber=2822 ksprintf /src/htslib/kstring.c linenumber=2825 ksprintf /src/htslib/kstring.c linenumber=2827 ksprintf /src/htslib/kstring.c linenumber=2829 bgzf_write /src/htslib/bgzf.c linenumber=2897 bgzf_flush /src/htslib/bgzf.c linenumber=2898 hwrite /src/htslib/./htslib/hfile.h linenumber=2900 bcf_hdr_format /src/htslib/vcf.c linenumber=1853 kputc /src/htslib/./htslib/kstring.h linenumber=1857 bgzf_write /src/htslib/bgzf.c linenumber=1860 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1862 bgzf_write /src/htslib/bgzf.c linenumber=1863 bgzf_write /src/htslib/bgzf.c linenumber=1864 bgzf_flush /src/htslib/bgzf.c linenumber=1865 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1867 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1868 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1868 bcf_init /src/htslib/vcf.c linenumber=155 calloc linenumber=1881 bcf_read /src/htslib/vcf.c linenumber=159 vcf_read /src/htslib/vcf.c linenumber=2333 hts_getline /src/htslib/hts.c linenumber=4296 vcf_parse /src/htslib/vcf.c linenumber=4298 ks_resize /src/htslib/./htslib/kstring.h linenumber=4131 bcf_clear /src/htslib/vcf.c linenumber=4144 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=1905 kstrtok /src/htslib/kstring.c linenumber=4149 kh_get_vdict /src/htslib/vcf.c linenumber=4154 hts_log /src/htslib/hts.c linenumber=4156 hts_log /src/htslib/hts.c linenumber=4158 fix_chromosome /src/htslib/vcf.c linenumber=4160 ksprintf /src/htslib/kstring.c linenumber=3866 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3868 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3870 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3871 bcf_hdr_sync /src/htslib/vcf.c linenumber=3872 kh_get_vdict /src/htslib/vcf.c linenumber=3873 hts_log /src/htslib/hts.c linenumber=4161 kstrtok /src/htslib/kstring.c linenumber=4169 hts_str2uint /src/htslib/./textutils_internal.h linenumber=4175 hts_log /src/htslib/hts.c linenumber=4177 hts_log /src/htslib/hts.c linenumber=4180 kstrtok /src/htslib/kstring.c linenumber=4189 memcmp linenumber=4193 bcf_enc_vchar /src/htslib/vcf.c linenumber=4193 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3048 ks_resize /src/htslib/./htslib/kstring.h linenumber=1595 ks_resize /src/htslib/./htslib/kstring.h linenumber=1603 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1615 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1619 kputsn /src/htslib/./htslib/kstring.h linenumber=3049 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=4194 kstrtok /src/htslib/kstring.c linenumber=4197 bcf_enc_vchar /src/htslib/vcf.c linenumber=4201 kstrtok /src/htslib/kstring.c linenumber=4205 memcmp linenumber=4209 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4213 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=4213 bcf_enc_vchar /src/htslib/vcf.c linenumber=4218 kstrtok /src/htslib/kstring.c linenumber=4227 memcmp linenumber=4231 atof linenumber=4231 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4232 kstrtok /src/htslib/kstring.c linenumber=4236 memcmp linenumber=4240 vcf_parse_filter /src/htslib/vcf.c linenumber=4241 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3890 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3892 hts_log /src/htslib/hts.c linenumber=3892 kstrtok /src/htslib/kstring.c linenumber=3899 kh_get_vdict /src/htslib/vcf.c linenumber=3901 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3906 hts_log /src/htslib/hts.c linenumber=3906 hts_log /src/htslib/hts.c linenumber=3909 ksprintf /src/htslib/kstring.c linenumber=3912 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3913 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3915 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3916 bcf_hdr_sync /src/htslib/vcf.c linenumber=3917 kh_get_vdict /src/htslib/vcf.c linenumber=3918 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3921 hts_log /src/htslib/hts.c linenumber=3921 bcf_enc_vint /src/htslib/vcf.c linenumber=3930 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2915 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=2917 ks_resize /src/htslib/./htslib/kstring.h linenumber=1635 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=1655 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1659 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2957 ks_resize /src/htslib/./htslib/kstring.h linenumber=2958 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2969 ks_resize /src/htslib/./htslib/kstring.h linenumber=2970 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2979 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2985 ks_resize /src/htslib/./htslib/kstring.h linenumber=2986 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2990 bcf_enc_vint /src/htslib/vcf.c linenumber=4244 kstrtok /src/htslib/kstring.c linenumber=4248 memcmp linenumber=4252 vcf_parse_info /src/htslib/vcf.c linenumber=4253 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3951 hts_log /src/htslib/hts.c linenumber=3951 kh_get_vdict /src/htslib/vcf.c linenumber=3965 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3968 hts_log /src/htslib/hts.c linenumber=3968 ksprintf /src/htslib/kstring.c linenumber=3974 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3975 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3977 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3978 bcf_hdr_sync /src/htslib/vcf.c linenumber=3979 kh_get_vdict /src/htslib/vcf.c linenumber=3980 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3983 hts_log /src/htslib/hts.c linenumber=3983 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3990 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3992 bcf_enc_vchar /src/htslib/vcf.c linenumber=3994 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=4002 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4004 hts_log /src/htslib/hts.c linenumber=4004 hts_str2int /src/htslib/./textutils_internal.h linenumber=4040 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4046 hts_log /src/htslib/hts.c linenumber=4046 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=4065 bcf_enc_vint /src/htslib/vcf.c linenumber=4068 memcmp linenumber=4071 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4077 hts_log /src/htslib/hts.c linenumber=4077 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=4087 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4089 bcf_enc_vfloat /src/htslib/vcf.c linenumber=4092 __assert_fail linenumber=3040 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3041 serialize_float_array /src/htslib/vcf.c linenumber=3042 ks_resize /src/htslib/./htslib/kstring.h linenumber=3026 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=3030 kstrtok /src/htslib/kstring.c linenumber=4260 vcf_parse_format /src/htslib/vcf.c linenumber=4264 vcf_parse_format_empty1 /src/htslib/vcf.c linenumber=3812 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3218 hts_log /src/htslib/hts.c linenumber=3218 memchr linenumber=3232 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3236 hts_log /src/htslib/hts.c linenumber=3236 vcf_parse_format_dict2 /src/htslib/vcf.c linenumber=3816 kstrtok /src/htslib/kstring.c linenumber=3258 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3261 hts_log /src/htslib/hts.c linenumber=3261 kh_get_vdict /src/htslib/vcf.c linenumber=3267 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3271 hts_log /src/htslib/hts.c linenumber=3271 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3275 hts_log /src/htslib/hts.c linenumber=3275 hts_log /src/htslib/hts.c linenumber=3277 ksprintf /src/htslib/kstring.c linenumber=3280 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3281 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3283 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3284 bcf_hdr_sync /src/htslib/vcf.c linenumber=3285 kh_get_vdict /src/htslib/vcf.c linenumber=3287 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3290 hts_log /src/htslib/hts.c linenumber=3290 vcf_parse_format_max3 /src/htslib/vcf.c linenumber=3837 hts_log /src/htslib/hts.c linenumber=3381 hts_log /src/htslib/hts.c linenumber=3401 vcf_parse_format_alloc4 /src/htslib/vcf.c linenumber=3841 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3423 hts_log /src/htslib/hts.c linenumber=3423 align_mem /src/htslib/vcf.c linenumber=3428 kputsn /src/htslib/./htslib/kstring.h linenumber=3205 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3429 hts_log /src/htslib/hts.c linenumber=3429 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3439 hts_log /src/htslib/hts.c linenumber=3439 ks_resize /src/htslib/./htslib/kstring.h linenumber=3448 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3449 hts_log /src/htslib/hts.c linenumber=3449 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3474 hts_log /src/htslib/hts.c linenumber=3474 vcf_parse_format_fill5 /src/htslib/vcf.c linenumber=3845 bcf_get_version /src/htslib/vcf.c linenumber=3496 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3523 hts_log /src/htslib/hts.c linenumber=3523 hts_str2uint /src/htslib/./textutils_internal.h linenumber=3571 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3596 hts_log /src/htslib/hts.c linenumber=3596 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3600 hts_log /src/htslib/hts.c linenumber=3600 hts_str2int /src/htslib/./textutils_internal.h linenumber=3626 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3631 hts_log /src/htslib/hts.c linenumber=3631 isdigit_c /src/htslib/./textutils_internal.h linenumber=3652 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3653 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3657 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=3660 hts_log /src/htslib/hts.c linenumber=3660 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3670 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3672 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3674 hts_log /src/htslib/hts.c linenumber=3674 hts_strprint /src/htslib/textutils.c linenumber=3687 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3687 hts_log /src/htslib/hts.c linenumber=3687 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3722 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3723 vcf_parse_format_gt6 /src/htslib/vcf.c linenumber=3849 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3745 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3747 kputsn /src/htslib/./htslib/kstring.h linenumber=3748 bcf_enc_vint /src/htslib/vcf.c linenumber=3750 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3752 serialize_float_array /src/htslib/vcf.c linenumber=3753 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3756 hts_log /src/htslib/hts.c linenumber=3756 vcf_parse_format_check7 /src/htslib/vcf.c linenumber=3853 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3782 hts_log /src/htslib/hts.c linenumber=3782 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3789 hts_log /src/htslib/hts.c linenumber=3789 get_rlen /src/htslib/vcf.c linenumber=4270 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6585 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6596 strlen linenumber=186 memcmp linenumber=191 memcmp linenumber=192 memcmp linenumber=193 memcmp linenumber=194 strcmp linenumber=6600 strcmp linenumber=6601 strlen linenumber=6606 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6609 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=1727 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=1718 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=1685 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1688 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1691 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=1694 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=263 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6614 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6618 strncmp linenumber=6622 strncmp linenumber=6623 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6634 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6639 bcf_get_info /src/htslib/vcf.c linenumber=6644 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6191 bcf_get_info_id /src/htslib/vcf.c linenumber=6193 bcf_unpack /src/htslib/vcf.c linenumber=6210 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4372 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=3160 bcf_fmt_array /src/htslib/vcf.c linenumber=3161 kputc_ /src/htslib/./htslib/kstring.h linenumber=3117 memchr linenumber=3126 kputsn /src/htslib/./htslib/kstring.h linenumber=3127 kputc /src/htslib/./htslib/kstring.h linenumber=3130 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=3146 kputc_ /src/htslib/./htslib/kstring.h linenumber=3146 kputc /src/htslib/./htslib/kstring.h linenumber=3146 kputw /src/htslib/./htslib/kstring.h linenumber=3146 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3147 kputc_ /src/htslib/./htslib/kstring.h linenumber=3147 kputc /src/htslib/./htslib/kstring.h linenumber=3147 kputw /src/htslib/./htslib/kstring.h linenumber=3147 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3148 kputc_ /src/htslib/./htslib/kstring.h linenumber=3148 kputc /src/htslib/./htslib/kstring.h linenumber=3148 kputw /src/htslib/./htslib/kstring.h linenumber=3148 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3149 kputc_ /src/htslib/./htslib/kstring.h linenumber=3149 kputc /src/htslib/./htslib/kstring.h linenumber=3149 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3149 kputd /src/htslib/kstring.c linenumber=3149 hts_log /src/htslib/hts.c linenumber=3150 exit linenumber=3150 kputc_ /src/htslib/./htslib/kstring.h linenumber=4374 hts_realloc_or_die /src/htslib/hts.c linenumber=4378 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4384 kputc_ /src/htslib/./htslib/kstring.h linenumber=4385 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4400 hts_realloc_or_die /src/htslib/hts.c linenumber=4401 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=4403 hts_realloc_or_die /src/htslib/hts.c linenumber=4410 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=4413 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4319 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4320 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=4332 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=4336 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=4340 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=4344 hts_realloc_or_die /src/htslib/hts.c linenumber=4418 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=4421 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4304 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4305 bcf_get_info /src/htslib/vcf.c linenumber=6645 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6648 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6650 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6656 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6663 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6672 bcf_get_fmt /src/htslib/vcf.c linenumber=6679 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6184 bcf_get_fmt_id /src/htslib/vcf.c linenumber=6186 bcf_unpack /src/htslib/vcf.c linenumber=6199 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6682 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=6684 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6689 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6719 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6723 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6727 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6731 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6763 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6767 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6771 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6775 bgzf_get_private_data /src/htslib/./bgzf_internal.h linenumber=2335 __assert_fail linenumber=68 bcf_read1_core /src/htslib/vcf.c linenumber=2336 bgzf_read /src/htslib/bgzf.c linenumber=1942 bcf_clear /src/htslib/vcf.c linenumber=1946 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1947 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1950 ks_resize /src/htslib/./htslib/kstring.h linenumber=1955 ks_resize /src/htslib/./htslib/kstring.h linenumber=1956 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1957 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1958 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1960 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1961 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1962 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1963 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1964 bgzf_read /src/htslib/bgzf.c linenumber=1971 bgzf_read /src/htslib/bgzf.c linenumber=1972 bcf_record_check /src/htslib/vcf.c linenumber=2337 bcf_get_version /src/htslib/vcf.c linenumber=2125 bcf_hdr_id2int /src/htslib/vcf.c linenumber=2126 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2140 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2023 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1993 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1996 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2142 get_type_name /src/htslib/vcf.c linenumber=2142 hts_log /src/htslib/hts.c linenumber=2142 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2151 hts_log /src/htslib/hts.c linenumber=2151 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2158 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2161 get_type_name /src/htslib/vcf.c linenumber=2161 hts_log /src/htslib/hts.c linenumber=2161 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2171 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2175 get_type_name /src/htslib/vcf.c linenumber=2175 hts_log /src/htslib/hts.c linenumber=2175 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=2182 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2187 hts_log /src/htslib/hts.c linenumber=2187 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2199 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2203 hts_log /src/htslib/hts.c linenumber=2203 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2206 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2210 get_type_name /src/htslib/vcf.c linenumber=2210 hts_log /src/htslib/hts.c linenumber=2210 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2224 bcf_record_check_err /src/htslib/vcf.c linenumber=2228 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2097 hts_log /src/htslib/hts.c linenumber=2097 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2231 bcf_record_check_err /src/htslib/vcf.c linenumber=2234 updatephasing /src/htslib/vcf.c linenumber=2249 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2262 hts_log /src/htslib/hts.c linenumber=2262 get_rlen /src/htslib/vcf.c linenumber=2268 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2277 hts_log /src/htslib/hts.c linenumber=2277 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2281 hts_log /src/htslib/hts.c linenumber=2281 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2285 hts_log /src/htslib/hts.c linenumber=2285 bcf_subset_format /src/htslib/vcf.c linenumber=2339 hts_realloc_or_die /src/htslib/hts.c linenumber=2302 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=2307 bcf_write /src/htslib/vcf.c linenumber=160 bcf_hdr_sync /src/htslib/vcf.c linenumber=2589 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2593 hts_log /src/htslib/hts.c linenumber=2593 vcf_write /src/htslib/vcf.c linenumber=2599 vcf_format /src/htslib/vcf.c linenumber=4714 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=4431 hts_log /src/htslib/hts.c linenumber=4433 __errno_location linenumber=4435 bcf_unpack /src/htslib/vcf.c linenumber=4439 get_hdr_aux /src/htslib/vcf.c linenumber=4450 calloc linenumber=4452 kputs /src/htslib/./htslib/kstring.h linenumber=4457 kputc_ /src/htslib/./htslib/kstring.h linenumber=4458 kputll /src/htslib/./htslib/kstring.h linenumber=4458 kputc_ /src/htslib/./htslib/kstring.h linenumber=4459 kputs /src/htslib/./htslib/kstring.h linenumber=4459 kputc_ /src/htslib/./htslib/kstring.h linenumber=4460 kputs /src/htslib/./htslib/kstring.h linenumber=4461 kputc_ /src/htslib/./htslib/kstring.h linenumber=4462 kputc_ /src/htslib/./htslib/kstring.h linenumber=4463 kputc_ /src/htslib/./htslib/kstring.h linenumber=4466 kputs /src/htslib/./htslib/kstring.h linenumber=4467 kputc_ /src/htslib/./htslib/kstring.h linenumber=4469 kputc_ /src/htslib/./htslib/kstring.h linenumber=4470 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4471 kputc_ /src/htslib/./htslib/kstring.h linenumber=4471 kputd /src/htslib/kstring.c linenumber=4472 kputc_ /src/htslib/./htslib/kstring.h linenumber=4473 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4479 hts_log /src/htslib/hts.c linenumber=4479 __errno_location linenumber=4481 kputc_ /src/htslib/./htslib/kstring.h linenumber=4484 strlen linenumber=4486 kputsn /src/htslib/./htslib/kstring.h linenumber=4487 kputc_ /src/htslib/./htslib/kstring.h linenumber=4489 kputc_ /src/htslib/./htslib/kstring.h linenumber=4491 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4511 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4512 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4528 hts_log /src/htslib/hts.c linenumber=4528 __errno_location linenumber=4533 strlen linenumber=4539 ks_resize /src/htslib/./htslib/kstring.h linenumber=4541 bcf_fmt_array /src/htslib/vcf.c linenumber=4558 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4563 kputd /src/htslib/kstring.c linenumber=4566 kputc_ /src/htslib/./htslib/kstring.h linenumber=4568 kputc_ /src/htslib/./htslib/kstring.h linenumber=4577 kputw /src/htslib/./htslib/kstring.h linenumber=4579 kputc_ /src/htslib/./htslib/kstring.h linenumber=4582 kputll /src/htslib/./htslib/kstring.h linenumber=4584 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4586 hts_log /src/htslib/hts.c linenumber=4586 __errno_location linenumber=4587 kputc_ /src/htslib/./htslib/kstring.h linenumber=4592 kputc_ /src/htslib/./htslib/kstring.h linenumber=4593 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=4612 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4622 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4623 kputc_ /src/htslib/./htslib/kstring.h linenumber=4629 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4636 hts_log /src/htslib/hts.c linenumber=4636 __errno_location linenumber=4637 strlen linenumber=4644 kputsn /src/htslib/./htslib/kstring.h linenumber=4646 kputsn /src/htslib/./htslib/kstring.h linenumber=4650 kputc_ /src/htslib/./htslib/kstring.h linenumber=4654 kputc_ /src/htslib/./htslib/kstring.h linenumber=4659 bcf_format_gt_v2 /src/htslib/vcf.c linenumber=4662 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6523 kputc /src/htslib/./htslib/kstring.h linenumber=6523 kputw /src/htslib/./htslib/kstring.h linenumber=6523 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6525 kputc /src/htslib/./htslib/kstring.h linenumber=6525 kputw /src/htslib/./htslib/kstring.h linenumber=6525 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6527 kputc /src/htslib/./htslib/kstring.h linenumber=6527 kputw /src/htslib/./htslib/kstring.h linenumber=6527 kputc /src/htslib/./htslib/kstring.h linenumber=6529 hts_log /src/htslib/hts.c linenumber=6530 get_hdr_aux /src/htslib/vcf.c linenumber=6534 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6544 ks_resize /src/htslib/./htslib/kstring.h linenumber=474 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6546 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6553 hts_log /src/htslib/hts.c linenumber=4663 __errno_location linenumber=4664 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4672 kputc_ /src/htslib/./htslib/kstring.h linenumber=3067 kputc_ /src/htslib/./htslib/kstring.h linenumber=3073 kputw /src/htslib/./htslib/kstring.h linenumber=3074 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3078 kputc_ /src/htslib/./htslib/kstring.h linenumber=3081 kputw /src/htslib/./htslib/kstring.h linenumber=3082 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3087 kputc_ /src/htslib/./htslib/kstring.h linenumber=3090 kputw /src/htslib/./htslib/kstring.h linenumber=3091 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3096 kputc_ /src/htslib/./htslib/kstring.h linenumber=3099 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3100 kputd /src/htslib/kstring.c linenumber=3100 hts_log /src/htslib/hts.c linenumber=3105 bcf_fmt_array /src/htslib/vcf.c linenumber=4674 kputc_ /src/htslib/./htslib/kstring.h linenumber=4680 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4682 bcf_fmt_array /src/htslib/vcf.c linenumber=4684 kputc_ /src/htslib/./htslib/kstring.h linenumber=4686 kputsn /src/htslib/./htslib/kstring.h linenumber=4693 kputc /src/htslib/./htslib/kstring.h linenumber=4695 bgzf_flush_try /src/htslib/bgzf.c linenumber=4717 hts_idx_amend_last /src/htslib/hts.c linenumber=4720 bgzf_write /src/htslib/bgzf.c linenumber=4721 hwrite /src/htslib/./htslib/hfile.h linenumber=4723 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4728 hts_idx_tbi_name /src/htslib/hts.c linenumber=4728 strlen linenumber=2756 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=2757 strcpy linenumber=2763 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=2767 u32_to_le /src/htslib/./cram/../htslib/hts_endian.h linenumber=2767 bgzf_idx_push /src/htslib/bgzf.c linenumber=4731 bcf_strerror /src/htslib/vcf.c linenumber=2608 add_desc_to_buffer /src/htslib/vcf.c linenumber=6471 strlen linenumber=6445 snprintf linenumber=6446 snprintf linenumber=6449 add_desc_to_buffer /src/htslib/vcf.c linenumber=6480 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2608 hts_log /src/htslib/hts.c linenumber=2608 bcf1_sync /src/htslib/vcf.c linenumber=2611 bcf1_sync_id /src/htslib/vcf.c linenumber=2417 strcmp linenumber=2356 strlen linenumber=2357 bcf_enc_vchar /src/htslib/vcf.c linenumber=2357 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2359 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2420 strlen linenumber=2367 bcf_enc_vchar /src/htslib/vcf.c linenumber=2367 strlen linenumber=2370 bcf1_sync_filter /src/htslib/vcf.c linenumber=2423 bcf_enc_vint /src/htslib/vcf.c linenumber=2377 bcf_enc_vint /src/htslib/vcf.c linenumber=2379 bcf1_sync_info /src/htslib/vcf.c linenumber=2426 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2396 bcf_unpack /src/htslib/vcf.c linenumber=2433 bcf1_sync_id /src/htslib/vcf.c linenumber=2440 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2442 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2448 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2451 strlen linenumber=2452 bcf1_sync_filter /src/htslib/vcf.c linenumber=2461 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2463 bcf_enc_vint /src/htslib/vcf.c linenumber=2465 bcf1_sync_info /src/htslib/vcf.c linenumber=2474 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2481 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2518 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2615 hts_log /src/htslib/hts.c linenumber=2615 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2621 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2622 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2623 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2624 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2625 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2626 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2627 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2628 bgzf_write /src/htslib/bgzf.c linenumber=2630 bgzf_write /src/htslib/bgzf.c linenumber=2631 bgzf_write /src/htslib/bgzf.c linenumber=2632 bgzf_idx_push /src/htslib/bgzf.c linenumber=2635 bcf_destroy /src/htslib/vcf.c linenumber=163 bcf_empty /src/htslib/vcf.c linenumber=1933 bcf_clear /src/htslib/vcf.c linenumber=1919 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 ====================================