Call tree LLVMFuzzerTestOneInput /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=-1 abort linenumber=176 hopen /src/htslib/hfile.c linenumber=180 find_scheme_handler /src/htslib/hfile.c linenumber=1319 isalnum_c /src/htslib/./textutils_internal.h linenumber=1185 __ctype_b_loc linenumber=169 tolower_c /src/htslib/./textutils_internal.h linenumber=1186 tolower linenumber=179 pthread_mutex_lock linenumber=1194 load_hfile_plugins /src/htslib/hfile.c linenumber=1195 kh_init_scheme_string /src/htslib/hfile.c linenumber=1118 calloc linenumber=972 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1122 hts_log /src/htslib/hts.c linenumber=1059 __errno_location linenumber=5296 get_severity_tag /src/htslib/hts.c linenumber=5300 fprintf linenumber=5300 vfprintf linenumber=5303 fprintf linenumber=5306 __errno_location linenumber=5308 try_exe_add_scheme_handler /src/htslib/hfile.c linenumber=1063 hts_log /src/htslib/hts.c linenumber=1064 kh_put_scheme_string /src/htslib/hfile.c linenumber=1068 kh_resize_scheme_string /src/htslib/hfile.c linenumber=972 __errno_location linenumber=972 realloc linenumber=972 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=972 strcmp linenumber=972 __errno_location linenumber=1070 strerror linenumber=1070 hts_log /src/htslib/hts.c linenumber=1070 priority /src/htslib/hfile.c linenumber=1074 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1123 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=1124 init_add_plugin /src/htslib/hfile.c linenumber=1125 hts_log /src/htslib/hts.c linenumber=1084 hts_log /src/htslib/hts.c linenumber=1096 hts_log /src/htslib/hts.c linenumber=1101 hfile_plugin_init_mem /src/htslib/hfile.c linenumber=1125 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=926 init_add_plugin /src/htslib/hfile.c linenumber=1126 hfile_plugin_init_crypt4gh_needed /src/htslib/hfile.c linenumber=1126 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=961 init_add_plugin /src/htslib/hfile.c linenumber=1145 hfile_plugin_init_libcurl /src/htslib/hfile_libcurl.c linenumber=1145 hts_version /src/htslib/hts.c linenumber=1698 curl_global_init linenumber=1706 __errno_location linenumber=1707 curl_share_init linenumber=1709 curl_global_cleanup linenumber=1710 __errno_location linenumber=1710 curl_share_setopt linenumber=1711 share_lock /src/htslib/hfile_libcurl.c linenumber=1711 pthread_mutex_lock linenumber=312 curl_share_setopt linenumber=1712 share_unlock /src/htslib/hfile_libcurl.c linenumber=1712 pthread_mutex_unlock linenumber=316 curl_share_setopt linenumber=1713 curl_share_cleanup linenumber=1715 curl_global_cleanup linenumber=1716 __errno_location linenumber=1717 getenv linenumber=1721 strdup linenumber=1722 kh_init_auth_map /src/htslib/hfile_libcurl.c linenumber=1723 calloc linenumber=70 __errno_location linenumber=1725 kh_destroy_auth_map /src/htslib/hfile_libcurl.c linenumber=1727 curl_share_cleanup linenumber=1728 curl_global_cleanup linenumber=1729 __errno_location linenumber=1730 getenv linenumber=1734 strcmp linenumber=1735 getenv linenumber=1741 atoi linenumber=1742 getenv linenumber=1743 atol linenumber=1744 getenv linenumber=1745 atol linenumber=1746 getenv linenumber=1747 atol linenumber=1748 getenv linenumber=1749 atol linenumber=1750 curl_version_info linenumber=1753 ksprintf /src/htslib/kstring.c linenumber=1754 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=1760 init_add_plugin /src/htslib/hfile.c linenumber=1148 hfile_plugin_init_gcs /src/htslib/hfile_gcs.c linenumber=1148 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=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=1151 hfile_plugin_init_s3 /src/htslib/hfile_s3.c linenumber=1151 hts_version /src/htslib/hts.c linenumber=2595 curl_global_init linenumber=2602 __errno_location linenumber=2606 curl_share_init linenumber=2610 curl_global_cleanup linenumber=2613 __errno_location linenumber=2614 curl_share_setopt linenumber=2618 share_lock /src/htslib/hfile_s3.c linenumber=2618 pthread_mutex_lock linenumber=1136 curl_share_setopt linenumber=2619 share_unlock /src/htslib/hfile_s3.c linenumber=2619 pthread_mutex_unlock linenumber=1140 curl_share_setopt linenumber=2620 curl_share_cleanup linenumber=2623 curl_global_cleanup linenumber=2624 __errno_location linenumber=2625 curl_version_info linenumber=2629 ksprintf /src/htslib/kstring.c linenumber=2630 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2635 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2636 hfile_add_scheme_handler /src/htslib/hfile.c linenumber=2637 atexit linenumber=1159 hfile_exit /src/htslib/hfile.c linenumber=1159 hfile_shutdown /src/htslib/hfile.c linenumber=1007 pthread_mutex_lock linenumber=985 kh_destroy_scheme_string /src/htslib/hfile.c linenumber=988 pthread_mutex_unlock linenumber=1002 pthread_mutex_destroy linenumber=1008 pthread_mutex_unlock linenumber=1196 pthread_mutex_unlock linenumber=1199 kh_get_scheme_string /src/htslib/hfile.c linenumber=1201 strchr linenumber=1321 strcmp linenumber=1335 hopen_fd_stdinout /src/htslib/hfile.c linenumber=1335 strchr linenumber=763 snprintf linenumber=765 hdopen /src/htslib/hfile.c linenumber=769 blksize /src/htslib/hfile.c linenumber=737 fstat linenumber=652 hfile_init /src/htslib/hfile.c linenumber=737 strchr linenumber=114 posix_memalign linenumber=118 strchr linenumber=131 hfile_destroy /src/htslib/hfile.c linenumber=137 __errno_location linenumber=165 __errno_location linenumber=168 strchr linenumber=741 strchr linenumber=742 hopen_fd /src/htslib/hfile.c linenumber=1336 hfile_oflags /src/htslib/hfile.c linenumber=667 open linenumber=667 blksize /src/htslib/hfile.c linenumber=670 hfile_init /src/htslib/hfile.c linenumber=670 __errno_location linenumber=680 close linenumber=680 hfile_destroy /src/htslib/hfile.c linenumber=681 hts_hopen /src/htslib/hts.c linenumber=186 calloc linenumber=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=5159 realloc linenumber=5163 __errno_location linenumber=5177 strerror linenumber=5177 hts_log /src/htslib/hts.c linenumber=5177 exit linenumber=5178 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=1617 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=1677 sam_hrecs_new /src/htslib/header.c linenumber=1297 calloc linenumber=2744 kh_init_sam_hrecs_t /src/htslib/./header.h linenumber=2749 calloc linenumber=168 kh_init_m_s2i /src/htslib/./header.h linenumber=2758 calloc linenumber=169 kh_init_m_s2i /src/htslib/./header.h linenumber=2765 kh_init_m_s2i /src/htslib/./header.h linenumber=2773 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2776 next_power_2 /src/htslib/cram/pooled_alloc.c linenumber=76 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2779 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2782 sam_hrecs_init_type_order /src/htslib/header.c linenumber=2785 calloc linenumber=76 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2792 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2795 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2798 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2801 sam_hrecs_refs_from_targets_array /src/htslib/header.c linenumber=1303 hts_log /src/htslib/hts.c linenumber=1199 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1204 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=1213 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=1219 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=1225 __ac_FNV1a_hash_string /src/htslib/./cram/../htslib/khash.h linenumber=80 strcmp linenumber=80 kh_put_m_s2i /src/htslib/./header.h linenumber=1233 strcmp linenumber=169 hts_log /src/htslib/hts.c linenumber=1236 __errno_location linenumber=1248 strerror linenumber=1248 hts_log /src/htslib/hts.c linenumber=1248 kh_get_m_s2i /src/htslib/./header.h linenumber=1252 kh_del_m_s2i /src/htslib/./header.h linenumber=1253 sam_hrecs_free /src/htslib/header.c linenumber=1304 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2828 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2831 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2837 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2843 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2852 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2855 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2858 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1311 strlen linenumber=1009 sam_hrecs_error /src/htslib/header.c linenumber=1013 hts_log /src/htslib/hts.c linenumber=65 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1024 sam_hrecs_error /src/htslib/header.c linenumber=926 isalpha_c /src/htslib/./textutils_internal.h linenumber=931 __ctype_b_loc linenumber=170 sam_hrecs_error /src/htslib/header.c linenumber=932 TYPEKEY /src/htslib/./header.h linenumber=936 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=942 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=947 kh_resize_sam_hrecs_t /src/htslib/./header.h linenumber=168 realloc linenumber=168 TYPEKEY /src/htslib/./header.h linenumber=954 parse_comment_line /src/htslib/header.c linenumber=956 sam_hrecs_error /src/htslib/header.c linenumber=813 warn_if_known_stderr /src/htslib/header.c linenumber=814 kmemmem /src/htslib/kstring.c linenumber=797 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=798 hts_log /src/htslib/hts.c linenumber=788 hts_log /src/htslib/hts.c linenumber=789 kmemmem /src/htslib/kstring.c linenumber=799 known_stderr /src/htslib/header.c linenumber=800 kmemmem /src/htslib/kstring.c linenumber=801 known_stderr /src/htslib/header.c linenumber=802 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=821 string_ndup /src/htslib/cram/string_alloc.c linenumber=823 parse_noncomment_line /src/htslib/header.c linenumber=963 TYPEKEY /src/htslib/./header.h linenumber=838 sam_hrecs_error /src/htslib/header.c linenumber=848 warn_if_known_stderr /src/htslib/header.c linenumber=849 sam_hrecs_error /src/htslib/header.c linenumber=859 warn_if_known_stderr /src/htslib/header.c linenumber=860 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=872 string_ndup /src/htslib/cram/string_alloc.c linenumber=874 sam_hrecs_global_list_add /src/htslib/header.c linenumber=971 TYPEKEY /src/htslib/./header.h linenumber=510 __assert_fail linenumber=978 sam_hrecs_free_tags /src/htslib/header.c linenumber=995 sam_hrecs_free_tags /src/htslib/header.c linenumber=705 pool_free /src/htslib/cram/pooled_alloc.c linenumber=707 pool_free /src/htslib/cram/pooled_alloc.c linenumber=996 TYPEKEY /src/htslib/./header.h linenumber=1036 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1051 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1055 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1069 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=3005 sam_hrecs_find_key /src/htslib/header.c linenumber=2963 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=2965 strlen linenumber=2975 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=2976 string_alloc /src/htslib/cram/string_alloc.c linenumber=2976 snprintf linenumber=2980 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=1312 add_stub_ref_sq_lines /src/htslib/header.c linenumber=1317 snprintf linenumber=1279 sam_hrecs_add /src/htslib/header.c linenumber=1280 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=2890 kh_get_m_s2i /src/htslib/./header.h linenumber=2898 kh_get_m_s2i /src/htslib/./header.h linenumber=2906 TYPEKEY /src/htslib/./header.h linenumber=2913 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=2913 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=1287 sam_hrecs_free /src/htslib/header.c linenumber=1318 rebuild_target_arrays /src/htslib/header.c linenumber=1324 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1168 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1090 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1095 strcmp linenumber=1110 strdup linenumber=1113 kh_get_s2i /src/htslib/hts.c linenumber=1124 kh_del_s2i /src/htslib/hts.c linenumber=1126 kh_init_s2i /src/htslib/hts.c linenumber=1132 calloc linenumber=80 kh_put_s2i /src/htslib/hts.c linenumber=1138 kh_resize_s2i /src/htslib/hts.c linenumber=80 __errno_location linenumber=80 realloc linenumber=80 kh_get_s2i /src/htslib/hts.c linenumber=1149 kh_del_s2i /src/htslib/hts.c linenumber=1151 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1682 rebuild_target_arrays /src/htslib/header.c linenumber=1685 redact_header_text /src/htslib/header.c linenumber=1689 __assert_fail linenumber=1541 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=3703 pthread_mutex_lock linenumber=262 pthread_mutex_unlock linenumber=264 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3704 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=3707 cram_free_container /src/htslib/cram/cram_io.c linenumber=3716 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3720 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3721 cram_free_container /src/htslib/cram/cram_io.c linenumber=3736 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3740 cram_free_container /src/htslib/cram/cram_io.c linenumber=3750 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=1347 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 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 strcmp linenumber=1112 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=3775 sam_set_thread_pool /src/htslib/sam.c linenumber=3778 sam_state_create /src/htslib/sam.c linenumber=3747 calloc linenumber=3079 pthread_mutex_init linenumber=3751 pthread_mutex_init linenumber=3752 pthread_cond_init linenumber=3753 hts_tpool_size /src/htslib/thread_pool.c linenumber=3757 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=3758 sam_state_destroy /src/htslib/sam.c linenumber=3760 pthread_mutex_lock linenumber=3125 pthread_cond_signal linenumber=3128 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3131 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3138 pthread_mutex_unlock linenumber=3139 hts_usleep /src/htslib/./hts_internal.h linenumber=3140 pthread_mutex_lock linenumber=3141 pthread_mutex_unlock linenumber=3144 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3150 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=832 sam_format_worker /src/htslib/sam.c linenumber=3150 pthread_mutex_lock linenumber=3684 pthread_mutex_unlock linenumber=3689 calloc linenumber=3692 sam_state_err /src/htslib/sam.c linenumber=3694 pthread_mutex_lock linenumber=3093 pthread_mutex_unlock linenumber=3096 sam_format1_append /src/htslib/sam.c linenumber=3706 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4353 __errno_location linenumber=279 ks_resize /src/htslib/./htslib/kstring.h linenumber=280 kputc_ /src/htslib/./htslib/kstring.h linenumber=4354 kputw /src/htslib/./htslib/kstring.h linenumber=4355 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=4355 kputs /src/htslib/./htslib/kstring.h linenumber=4357 kputc_ /src/htslib/./htslib/kstring.h linenumber=4358 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4359 kputll /src/htslib/./htslib/kstring.h linenumber=4360 ks_resize /src/htslib/./htslib/kstring.h linenumber=388 kputuw /src/htslib/./htslib/kstring.h linenumber=398 kputc_ /src/htslib/./htslib/kstring.h linenumber=4360 kputw /src/htslib/./htslib/kstring.h linenumber=4361 kputc_ /src/htslib/./htslib/kstring.h linenumber=4361 kputw /src/htslib/./htslib/kstring.h linenumber=4365 kputc_ /src/htslib/./htslib/kstring.h linenumber=4366 kputc_ /src/htslib/./htslib/kstring.h linenumber=4368 kputc_ /src/htslib/./htslib/kstring.h linenumber=4369 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4370 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4371 kputs /src/htslib/./htslib/kstring.h linenumber=4373 kputc_ /src/htslib/./htslib/kstring.h linenumber=4374 kputll /src/htslib/./htslib/kstring.h linenumber=4376 kputc_ /src/htslib/./htslib/kstring.h linenumber=4376 kputll /src/htslib/./htslib/kstring.h linenumber=4377 kputc_ /src/htslib/./htslib/kstring.h linenumber=4377 ks_resize /src/htslib/./htslib/kstring.h linenumber=4380 nibble2base /src/htslib/./sam_internal.h linenumber=4384 add33 /src/htslib/sam.c linenumber=4394 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4400 kputc_ /src/htslib/./htslib/kstring.h linenumber=4406 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4407 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1482 kputc_ /src/htslib/./htslib/kstring.h linenumber=1483 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1485 kputw /src/htslib/./htslib/kstring.h linenumber=1486 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1489 kputw /src/htslib/./htslib/kstring.h linenumber=1490 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1494 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1495 kputuw /src/htslib/./htslib/kstring.h linenumber=1495 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1500 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1501 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=241 kputw /src/htslib/./htslib/kstring.h linenumber=1501 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1506 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1507 kputuw /src/htslib/./htslib/kstring.h linenumber=1507 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1512 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1513 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=252 kputw /src/htslib/./htslib/kstring.h linenumber=1513 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1517 kputc /src/htslib/./htslib/kstring.h linenumber=1518 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1523 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=314 ksprintf /src/htslib/kstring.c linenumber=1523 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=1533 le_to_u64 /src/htslib/./htslib/hts_endian.h linenumber=330 ksprintf /src/htslib/kstring.c linenumber=1533 kputc_ /src/htslib/./htslib/kstring.h linenumber=1537 kputc_ /src/htslib/./htslib/kstring.h linenumber=1538 kputc_ /src/htslib/./htslib/kstring.h linenumber=1539 kputsn /src/htslib/./htslib/kstring.h linenumber=1540 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1567 kputsn_ /src/htslib/./htslib/kstring.h linenumber=1571 kputc /src/htslib/./htslib/kstring.h linenumber=1572 ks_expand /src/htslib/./htslib/kstring.h linenumber=1575 __errno_location linenumber=183 ks_resize /src/htslib/./htslib/kstring.h linenumber=184 kputw /src/htslib/./htslib/kstring.h linenumber=1578 ks_expand /src/htslib/./htslib/kstring.h linenumber=1583 kputuw /src/htslib/./htslib/kstring.h linenumber=1586 ks_expand /src/htslib/./htslib/kstring.h linenumber=1591 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1594 kputw /src/htslib/./htslib/kstring.h linenumber=1594 ks_expand /src/htslib/./htslib/kstring.h linenumber=1599 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1602 kputuw /src/htslib/./htslib/kstring.h linenumber=1602 ks_expand /src/htslib/./htslib/kstring.h linenumber=1607 le_to_i32 /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_u32 /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_float /src/htslib/./htslib/hts_endian.h linenumber=1627 kputd /src/htslib/kstring.c linenumber=1627 __errno_location linenumber=1640 hts_log /src/htslib/hts.c linenumber=1644 __errno_location linenumber=1645 kputsn /src/htslib/./htslib/kstring.h linenumber=4410 hts_log /src/htslib/hts.c linenumber=4416 __errno_location linenumber=4418 hts_log /src/htslib/hts.c linenumber=4422 __errno_location linenumber=4423 __errno_location linenumber=3707 sam_state_err /src/htslib/sam.c linenumber=3707 kputc /src/htslib/./htslib/kstring.h linenumber=3710 pthread_mutex_lock linenumber=3713 pthread_mutex_unlock linenumber=3727 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3154 pthread_mutex_lock linenumber=3155 pthread_mutex_unlock linenumber=3157 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3159 hts_usleep /src/htslib/./hts_internal.h linenumber=3160 pthread_mutex_lock linenumber=3161 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=3164 pthread_mutex_unlock linenumber=3166 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3169 pthread_join linenumber=3174 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=3180 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3183 pthread_mutex_destroy linenumber=3186 pthread_mutex_destroy linenumber=3187 pthread_cond_destroy linenumber=3188 sam_free_sp_bams /src/htslib/sam.c linenumber=3203 sam_free_sp_bams /src/htslib/sam.c linenumber=3208 bam_hdr_destroy /src/htslib/./htslib/sam.h linenumber=3214 sam_hdr_destroy /src/htslib/sam.c linenumber=404 bgzf_thread_pool /src/htslib/bgzf.c linenumber=3765 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=3781 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=3845 calloc linenumber=3811 strcpy linenumber=3814 regcomp linenumber=3818 strcmp linenumber=3865 kh_init_tag /src/htslib/sam.c linenumber=3867 calloc linenumber=64 strlen linenumber=3870 hts_log /src/htslib/hts.c linenumber=3874 kh_put_tag /src/htslib/sam.c linenumber=3878 kh_resize_tag /src/htslib/sam.c linenumber=64 __errno_location linenumber=64 realloc linenumber=64 strncpy linenumber=3890 strcmp linenumber=3900 isalpha_c /src/htslib/./textutils_internal.h linenumber=3904 isalnum_c /src/htslib/./textutils_internal.h linenumber=3904 strncpy linenumber=3909 hts_log /src/htslib/hts.c linenumber=3923 regfree linenumber=3933 regcomp linenumber=3934 hts_log /src/htslib/hts.c linenumber=3935 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=4866 __errno_location linenumber=4844 skip_aux /src/htslib/sam.c linenumber=4869 aux_type2size /src/htslib/sam.c linenumber=4819 memchr linenumber=4823 aux_type2size /src/htslib/sam.c linenumber=4827 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=4828 bam_aux_next /src/htslib/sam.c linenumber=4866 skip_aux /src/htslib/sam.c linenumber=4851 __errno_location linenumber=4853 hts_log /src/htslib/hts.c linenumber=4857 __errno_location linenumber=4859 hts_log /src/htslib/hts.c linenumber=4880 __errno_location linenumber=4882 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=3322 bam_aux_get /src/htslib/sam.c linenumber=3331 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3338 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=3340 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=3360 block_grow /src/htslib/cram/cram_io.h linenumber=3376 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=3377 nibble2base /src/htslib/cram/../sam_internal.h linenumber=3382 hts_log /src/htslib/hts.c linenumber=3395 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3404 hts_log /src/htslib/hts.c linenumber=3439 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3452 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=3453 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=261 cram_add_substitution /src/htslib/cram/cram_encode.c linenumber=3516 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 /src/htslib/cram/cram_encode.c linenumber=3529 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2580 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3535 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2591 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2592 block_append_char /src/htslib/cram/cram_io.h linenumber=2593 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2594 cram_add_base /src/htslib/cram/cram_encode.c linenumber=3544 kputuw /src/htslib/cram/../htslib/kstring.h linenumber=3560 kputc_ /src/htslib/cram/../htslib/kstring.h linenumber=3562 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=270 kputsn /src/htslib/cram/../htslib/kstring.h linenumber=3563 ks_resize /src/htslib/cram/../htslib/kstring.h linenumber=246 cram_add_deletion /src/htslib/cram/cram_encode.c linenumber=3569 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2621 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2622 cram_add_skip /src/htslib/cram/cram_encode.c linenumber=3576 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2677 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2678 cram_add_insertion /src/htslib/cram/cram_encode.c linenumber=3589 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2699 block_append /src/htslib/cram/cram_io.h linenumber=2705 block_grow /src/htslib/cram/cram_io.h linenumber=241 block_append_char /src/htslib/cram/cram_io.h linenumber=2709 block_append_char /src/htslib/cram/cram_io.h linenumber=2711 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2713 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3594 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2607 block_append_char /src/htslib/cram/cram_io.h linenumber=2608 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2609 cram_add_softclip /src/htslib/cram/cram_encode.c linenumber=3609 block_append /src/htslib/cram/cram_io.h linenumber=2634 block_append_char /src/htslib/cram/cram_io.h linenumber=2635 block_append /src/htslib/cram/cram_io.h linenumber=2642 block_append_char /src/htslib/cram/cram_io.h linenumber=2646 block_append_char /src/htslib/cram/cram_io.h linenumber=2648 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2655 cram_add_quality 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linenumber=228 hts_calloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=229 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1056 cram_new_block /src/htslib/cram/cram_io.c linenumber=1063 cram_new_block /src/htslib/cram/cram_io.c linenumber=1069 cram_new_block /src/htslib/cram/cram_io.c linenumber=1078 block_append /src/htslib/cram/cram_io.h linenumber=1081 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1090 cram_new_block /src/htslib/cram/cram_io.c linenumber=988 cram_new_block /src/htslib/cram/cram_io.c linenumber=995 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1005 cram_allocate_block /src/htslib/cram/cram_encode.c linenumber=1008 cram_encode_slice_read /src/htslib/cram/cram_encode.c linenumber=1110 hts_log /src/htslib/hts.c linenumber=745 cram_free_block /src/htslib/cram/cram_io.c linenumber=1118 cram_free_block /src/htslib/cram/cram_io.c linenumber=1120 cram_free_block /src/htslib/cram/cram_io.c linenumber=1122 cram_free_block 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linenumber=837 rans_compress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=394 hist8 /src/htslib/htscodecs/htscodecs/utils.h linenumber=95 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=148 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=178 __assert_fail linenumber=126 RansEncSymbolInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=154 __assert_fail linenumber=199 __assert_fail linenumber=201 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=163 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=164 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=165 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=166 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=169 __assert_fail linenumber=285 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=171 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=173 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=184 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=185 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=186 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=187 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=190 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=191 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=192 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=193 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=399 hist1_4 /src/htslib/htscodecs/htscodecs/utils.h linenumber=416 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=287 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=322 RansEncSymbolInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=506 __assert_fail linenumber=516 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=519 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=520 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=521 RansEncInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=522 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=541 RansEncPutSymbol4 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=556 __assert_fail linenumber=333 __assert_fail linenumber=334 __assert_fail linenumber=335 __assert_fail linenumber=336 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=565 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=566 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=567 RansEncPutSymbol /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=568 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=570 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=571 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=572 RansEncFlush /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=573 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=593 rans_compress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=838 rans_compress_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=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 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1324 realloc linenumber=1332 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1363 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1377 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1399 hts_pack 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linenumber=443 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=461 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=464 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=471 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=474 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=475 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=476 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=481 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=490 SIMPLE_MODEL258_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=498 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=502 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=503 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=509 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=513 arith_compress_O1_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=987 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=577 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=595 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=601 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=604 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=606 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=611 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=614 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=615 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=616 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=621 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=630 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=638 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=642 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=643 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=644 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=650 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=654 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=655 arith_compress_O1 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=993 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=174 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=185 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=200 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=203 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=204 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=205 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=209 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=213 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=215 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=220 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=222 arith_compress_O0 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=995 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=100 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=118 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=121 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=122 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=123 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=126 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=128 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=134 tok3_encode_names /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=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 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=387 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=870 encode_token_int1_ /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=877 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=878 __ctype_b_loc linenumber=887 __ctype_b_loc linenumber=893 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=923 encode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=933 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=940 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=948 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=965 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=970 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=976 encode_token_end /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=998 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=328 realloc linenumber=1007 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1503 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1565 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1568 compress /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1572 arith_encode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1380 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1214 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1217 rans_encode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1383 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1241 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1244 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1574 memcmp linenumber=1592 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1618 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1659 pthread_mutex_lock linenumber=1845 pthread_mutex_unlock linenumber=1980 pthread_mutex_unlock linenumber=1992 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=1993 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2001 hts_log /src/htslib/hts.c linenumber=2001 pthread_mutex_lock linenumber=2004 pthread_mutex_unlock linenumber=2008 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2009 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2027 hts_log /src/htslib/hts.c linenumber=2030 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2045 hts_log /src/htslib/hts.c linenumber=2045 pthread_mutex_lock linenumber=843 pthread_mutex_unlock linenumber=847 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=850 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=857 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=862 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=867 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=870 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=874 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=879 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=884 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=887 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=891 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=896 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=906 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=912 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=929 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=947 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1150 cram_free_block /src/htslib/cram/cram_io.c linenumber=1161 cram_encode_slice_header /src/htslib/cram/cram_encode.c linenumber=1172 cram_new_block /src/htslib/cram/cram_io.c linenumber=509 hts_malloc_pse /src/htslib/cram/../htslib/hts_alloc.h linenumber=515 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=173 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=174 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=175 hts_malloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=176 cram_free_block /src/htslib/cram/cram_io.c linenumber=517 hts_log /src/htslib/hts.c linenumber=523 cram_free_block /src/htslib/cram/cram_io.c linenumber=524 __assert_fail linenumber=547 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=2410 cram_new_block /src/htslib/cram/cram_io.c linenumber=87 cram_new_block /src/htslib/cram/cram_io.c linenumber=88 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=107 itf8_put /src/htslib/cram/cram_io.c linenumber=624 block_append /src/htslib/cram/cram_io.h linenumber=625 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=108 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=109 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=110 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=111 itf8_put_blk /src/htslib/cram/cram_io.c linenumber=113 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=118 kh_init_map /src/htslib/cram/cram_structs.h linenumber=128 calloc linenumber=83 kh_put_map /src/htslib/cram/cram_structs.h linenumber=131 kh_resize_map /src/htslib/cram/cram_structs.h linenumber=83 __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 /src/htslib/cram/cram_structs.h linenumber=154 kh_put_map /src/htslib/cram/cram_structs.h linenumber=158 kh_put_map /src/htslib/cram/cram_structs.h linenumber=164 block_append /src/htslib/cram/cram_io.h linenumber=188 block_append_char /src/htslib/cram/cram_io.h linenumber=198 sub_idx /src/htslib/cram/cram_encode.c linenumber=211 sub_idx /src/htslib/cram/cram_encode.c linenumber=212 sub_idx /src/htslib/cram/cram_encode.c linenumber=213 sub_idx /src/htslib/cram/cram_encode.c linenumber=214 sub_idx /src/htslib/cram/cram_encode.c linenumber=216 sub_idx /src/htslib/cram/cram_encode.c linenumber=217 sub_idx /src/htslib/cram/cram_encode.c linenumber=218 sub_idx /src/htslib/cram/cram_encode.c linenumber=219 sub_idx /src/htslib/cram/cram_encode.c linenumber=221 sub_idx /src/htslib/cram/cram_encode.c linenumber=222 sub_idx /src/htslib/cram/cram_encode.c linenumber=223 sub_idx /src/htslib/cram/cram_encode.c linenumber=224 sub_idx /src/htslib/cram/cram_encode.c linenumber=226 sub_idx /src/htslib/cram/cram_encode.c linenumber=227 sub_idx /src/htslib/cram/cram_encode.c linenumber=228 sub_idx /src/htslib/cram/cram_encode.c linenumber=229 sub_idx /src/htslib/cram/cram_encode.c linenumber=231 sub_idx /src/htslib/cram/cram_encode.c linenumber=232 sub_idx /src/htslib/cram/cram_encode.c linenumber=233 sub_idx /src/htslib/cram/cram_encode.c linenumber=234 block_append /src/htslib/cram/cram_io.h linenumber=235 block_append /src/htslib/cram/cram_io.h linenumber=241 block_append /src/htslib/cram/cram_io.h linenumber=257 block_append /src/htslib/cram/cram_io.h linenumber=458 block_append /src/htslib/cram/cram_io.h linenumber=484 hts_log /src/htslib/hts.c linenumber=486 cram_free_block /src/htslib/cram/cram_io.c linenumber=490 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2417 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2486 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2494 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=3875 htell /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=2378 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=2333 cram_codec_to_id /src/htslib/cram/cram_codecs.c linenumber=2334 hts_log /src/htslib/hts.c linenumber=2346 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=2399 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2400 block_resize_exact /src/htslib/cram/cram_io.h linenumber=2401 strcmp linenumber=2413 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2421 hts_log /src/htslib/hts.c linenumber=2431 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2436 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=2439 hts_log /src/htslib/hts.c linenumber=2445 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2456 hts_log /src/htslib/hts.c linenumber=2465 pthread_mutex_lock linenumber=2470 pthread_mutex_lock linenumber=2471 pthread_mutex_unlock linenumber=2477 pthread_mutex_unlock linenumber=2478 hts_log /src/htslib/hts.c linenumber=2484 memcmp linenumber=2497 hts_log /src/htslib/hts.c linenumber=2507 hts_log /src/htslib/hts.c linenumber=2515 hts_md5_init /src/htslib/md5.c linenumber=2520 hts_md5_update /src/htslib/md5.c linenumber=2525 hts_md5_final /src/htslib/md5.c linenumber=2526 hts_md5_destroy /src/htslib/md5.c linenumber=2527 cram_get_block_by_id /src/htslib/cram/cram_io.h linenumber=2529 hts_md5_init /src/htslib/md5.c linenumber=2531 hts_md5_update /src/htslib/md5.c linenumber=2533 hts_md5_final /src/htslib/md5.c linenumber=2534 hts_md5_destroy /src/htslib/md5.c linenumber=2535 memcmp linenumber=2541 sam_hdr_tid2name /src/htslib/header.c linenumber=2543 hts_log /src/htslib/hts.c linenumber=2545 md5_print /src/htslib/cram/cram_decode.c linenumber=2547 hts_log /src/htslib/hts.c linenumber=2547 md5_print /src/htslib/cram/cram_decode.c linenumber=2548 hts_log /src/htslib/hts.c linenumber=2548 sam_hdr_find_tag_id /src/htslib/header.c linenumber=2550 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2303 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2308 sam_hrecs_find_key /src/htslib/header.c linenumber=2312 kputsn /src/htslib/./htslib/kstring.h linenumber=2317 hts_log /src/htslib/hts.c linenumber=2551 hts_log /src/htslib/hts.c linenumber=2552 ks_free /src/htslib/cram/../htslib/kstring.h linenumber=2553 ks_initialize /src/htslib/cram/../htslib/kstring.h linenumber=238 pthread_mutex_lock linenumber=2559 pthread_mutex_lock linenumber=2560 calloc linenumber=2561 pthread_mutex_unlock linenumber=2562 pthread_mutex_unlock linenumber=2563 hts_log /src/htslib/hts.c linenumber=2621 pthread_mutex_lock linenumber=2632 pthread_mutex_unlock linenumber=2634 cram_get_ref /src/htslib/cram/cram_io.c linenumber=2637 pthread_mutex_lock linenumber=2646 pthread_mutex_unlock linenumber=2651 pthread_mutex_lock linenumber=2653 pthread_mutex_unlock linenumber=2655 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2658 pthread_mutex_lock linenumber=2663 pthread_mutex_lock linenumber=2664 pthread_mutex_unlock linenumber=2666 pthread_mutex_unlock linenumber=2667 hts_log /src/htslib/hts.c linenumber=2678 hts_log /src/htslib/hts.c linenumber=2689 pthread_mutex_lock linenumber=2706 pthread_mutex_unlock linenumber=2708 hts_log /src/htslib/hts.c linenumber=2746 hts_log /src/htslib/hts.c linenumber=2794 hts_log /src/htslib/hts.c linenumber=2809 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2835 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2863 cram_decode_tlen /src/htslib/cram/cram_decode.c linenumber=2872 cram_decode_aux_1_0 /src/htslib/cram/cram_decode.c linenumber=2899 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=2901 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=2907 block_resize /src/htslib/cram/cram_io.h linenumber=2915 hts_log /src/htslib/hts.c linenumber=2925 cram_decode_seq /src/htslib/cram/cram_decode.c linenumber=2932 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=264 append_uint32 /src/htslib/cram/cram_io.h linenumber=268 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=2984 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2989 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=2994 pthread_mutex_unlock linenumber=2996 cram_decode_slice_xref /src/htslib/cram/cram_decode.c linenumber=2999 hts_log /src/htslib/hts.c linenumber=2235 cram_free_block /src/htslib/cram/cram_io.c linenumber=3006 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3020 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3021 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3022 block_resize_exact /src/htslib/cram/cram_io.h linenumber=3023 bulk_cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3034 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 calloc linenumber=2335 calloc linenumber=2340 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=2347 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=2352 hts_log /src/htslib/hts.c linenumber=3147 strlen linenumber=3155 append_uint64 /src/htslib/cram/cram_io.h linenumber=3164 append_uint32 /src/htslib/cram/cram_io.h linenumber=336 append_uint32 /src/htslib/cram/cram_io.h linenumber=339 append_sub32 /src/htslib/cram/cram_io.h linenumber=341 append_uint32 /src/htslib/cram/cram_io.h linenumber=343 append_sub32 /src/htslib/cram/cram_io.h linenumber=345 append_uint64 /src/htslib/cram/cram_io.h linenumber=3168 bam_set1 /src/htslib/sam.c linenumber=3203 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=3234 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=3041 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=3044 pthread_mutex_unlock linenumber=3047 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=3830 ks_free /src/htslib/./htslib/kstring.h linenumber=3831 ks_initialize /src/htslib/./htslib/kstring.h linenumber=238 ks_free /src/htslib/./htslib/kstring.h linenumber=3832 ks_free /src/htslib/./htslib/kstring.h linenumber=3833 regfree linenumber=3834 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=1938 bam_hdr_read /src/htslib/sam.c linenumber=1944 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=1606 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=1944 sam_hdr_destroy /src/htslib/sam.c linenumber=1872 hts_log /src/htslib/hts.c linenumber=1884 hts_log /src/htslib/hts.c linenumber=1889 hts_log /src/htslib/hts.c linenumber=1893 sam_hdr_destroy /src/htslib/sam.c linenumber=1894 realloc linenumber=1898 sam_hdr_destroy /src/htslib/sam.c linenumber=1900 sam_hdr_dup /src/htslib/sam.c linenumber=1948 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=2390 sam_hrecs_rebuild_lines /src/htslib/header.c linenumber=2392 kputsn /src/htslib/./htslib/kstring.h linenumber=769 build_header_line /src/htslib/header.c linenumber=773 kputc_ /src/htslib/./htslib/kstring.h linenumber=755 kputsn /src/htslib/./htslib/kstring.h linenumber=756 kputc_ /src/htslib/./htslib/kstring.h linenumber=758 kputsn /src/htslib/./htslib/kstring.h linenumber=759 kputc /src/htslib/./htslib/kstring.h linenumber=775 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=1948 sam_hdr_create /src/htslib/sam.c linenumber=1952 sam_hdr_init /src/htslib/sam.c linenumber=1917 sam_hdr_build_from_sam_file /src/htslib/header.c linenumber=1921 sam_hrecs_new /src/htslib/header.c linenumber=1366 hts_getline /src/htslib/hts.c linenumber=1375 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=1383 sam_hrecs_error /src/htslib/header.c linenumber=1384 strncmp linenumber=1389 kputc /src/htslib/./htslib/kstring.h linenumber=1392 valid_sam_header_type /src/htslib/header.c linenumber=1396 hts_log /src/htslib/hts.c linenumber=1397 warn_if_known_stderr /src/htslib/header.c linenumber=1398 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1402 TYPEKEY /src/htslib/./header.h linenumber=1407 kputsn /src/htslib/./htslib/kstring.h linenumber=1413 kputc /src/htslib/./htslib/kstring.h linenumber=1416 bgzf_peek /src/htslib/bgzf.c linenumber=1420 bgzf_read_block /src/htslib/bgzf.c linenumber=1321 hts_log /src/htslib/hts.c linenumber=1322 hpeek /src/htslib/hfile.c linenumber=1423 strstr linenumber=1441 hopen /src/htslib/hfile.c linenumber=1445 khgetline /src/htslib/hfile.c linenumber=1450 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=1451 strtoll linenumber=1459 kputs /src/htslib/./htslib/kstring.h linenumber=1461 kputsn /src/htslib/./htslib/kstring.h linenumber=1462 kputs /src/htslib/./htslib/kstring.h linenumber=1463 kputll /src/htslib/./htslib/kstring.h linenumber=1464 kputc /src/htslib/./htslib/kstring.h linenumber=1465 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1469 ks_free /src/htslib/./htslib/kstring.h linenumber=1481 hclose /src/htslib/hfile.c linenumber=1482 hts_log /src/htslib/hts.c linenumber=1483 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1493 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1497 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1511 kputsn /src/htslib/./htslib/kstring.h linenumber=1517 ks_release /src/htslib/./htslib/kstring.h linenumber=1521 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1523 ks_free /src/htslib/./htslib/kstring.h linenumber=1529 sam_hdr_destroy /src/htslib/sam.c linenumber=1922 sam_hdr_destroy /src/htslib/sam.c linenumber=1927 sam_hdr_sanitise /src/htslib/sam.c linenumber=1928 sam_hdr_init /src/htslib/sam.c linenumber=1957 __errno_location linenumber=1960 __errno_location linenumber=1964 sam_hdr_incr_ref /src/htslib/header.c linenumber=1971 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=2160 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2182 sam_hdr_write /src/htslib/sam.c linenumber=99 __errno_location linenumber=1979 bam_hdr_write /src/htslib/sam.c linenumber=1989 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=1994 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=1996 cram_write_SAM_hdr /src/htslib/cram/cram_io.c linenumber=1997 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=1710 sam_hrecs_vadd /src/htslib/header.c linenumber=1716 rebuild_target_arrays /src/htslib/header.c linenumber=1720 redact_header_text /src/htslib/header.c linenumber=1724 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=1926 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1932 check_for_name_update /src/htslib/header.c linenumber=1941 TYPEKEY /src/htslib/./header.h linenumber=1888 TYPEKEY /src/htslib/./header.h linenumber=1890 TYPEKEY /src/htslib/./header.h linenumber=1892 sam_hrecs_find_key /src/htslib/header.c linenumber=1901 __assert_fail linenumber=1904 strcmp linenumber=1910 strcmp linenumber=1911 kh_get_m_s2i /src/htslib/./header.h linenumber=1912 hts_log /src/htslib/hts.c linenumber=1945 TYPEKEY /src/htslib/./header.h linenumber=1949 hts_log /src/htslib/hts.c linenumber=1951 sam_hrecs_vupdate /src/htslib/header.c linenumber=1955 kh_get_m_s2i /src/htslib/./header.h linenumber=1966 sam_hrecs_find_key /src/htslib/header.c linenumber=1967 __assert_fail linenumber=1969 __assert_fail linenumber=1970 __assert_fail linenumber=1971 kh_del_m_s2i /src/htslib/./header.h linenumber=1973 kh_put_m_s2i /src/htslib/./header.h linenumber=1974 hts_log /src/htslib/hts.c linenumber=1976 TYPEKEY /src/htslib/./header.h linenumber=1982 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1982 rebuild_target_arrays /src/htslib/header.c linenumber=1985 redact_header_text /src/htslib/header.c linenumber=1988 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 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=3207 TYPEKEY /src/htslib/./header.h linenumber=3212 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3212 sam_hrecs_remove_key /src/htslib/header.c linenumber=3220 sam_hrecs_find_key /src/htslib/header.c linenumber=3047 TYPEKEY /src/htslib/./header.h linenumber=3051 __assert_fail linenumber=3052 sam_hrecs_find_key /src/htslib/header.c linenumber=3053 __assert_fail linenumber=3055 kh_get_m_s2i /src/htslib/./header.h linenumber=3056 sam_hrecs_remove_ref_altnames /src/htslib/header.c linenumber=3058 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=3069 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=1589 rebuild_target_arrays /src/htslib/header.c linenumber=1623 hts_log /src/htslib/hts.c linenumber=1624 sam_hdr_link_pg /src/htslib/header.c linenumber=1633 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2486 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2495 calloc linenumber=2499 __assert_fail linenumber=2510 kh_get_m_s2i /src/htslib/./header.h linenumber=2520 hts_log /src/htslib/hts.c linenumber=2523 hts_log /src/htslib/hts.c linenumber=2530 redact_header_text /src/htslib/header.c linenumber=2559 hts_log /src/htslib/hts.c linenumber=1634 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1639 ks_free /src/htslib/./htslib/kstring.h linenumber=1640 hts_log /src/htslib/hts.c linenumber=1641 ks_len /src/htslib/./htslib/kstring.h linenumber=1649 ks_release /src/htslib/./htslib/kstring.h linenumber=1650 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=1596 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=2015 strstr linenumber=2023 bgzf_write /src/htslib/bgzf.c linenumber=2031 hwrite /src/htslib/./htslib/hfile.h linenumber=2033 kputsn /src/htslib/./htslib/kstring.h linenumber=2043 kputs /src/htslib/./htslib/kstring.h linenumber=2044 kputsn /src/htslib/./htslib/kstring.h linenumber=2045 kputw /src/htslib/./htslib/kstring.h linenumber=2046 kputc /src/htslib/./htslib/kstring.h linenumber=2047 bgzf_write /src/htslib/bgzf.c linenumber=2052 hwrite /src/htslib/./htslib/hfile.h linenumber=2054 bgzf_flush /src/htslib/bgzf.c linenumber=2061 hflush /src/htslib/hfile.c linenumber=2063 __errno_location linenumber=2075 sam_hdr_dup /src/htslib/sam.c linenumber=2081 sam_hdr_destroy /src/htslib/sam.c linenumber=2082 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=4295 bam_read1 /src/htslib/sam.c linenumber=4157 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=4161 sam_read1_cram /src/htslib/sam.c linenumber=4299 cram_get_bam_seq /src/htslib/cram/cram_decode.c linenumber=4170 cram_get_seq /src/htslib/cram/cram_decode.c linenumber=3667 pthread_mutex_lock linenumber=3599 pthread_mutex_unlock linenumber=3602 cram_next_slice /src/htslib/cram/cram_decode.c linenumber=3605 cram_first_slice /src/htslib/cram/cram_decode.c linenumber=3313 cram_free_container /src/htslib/cram/cram_io.c linenumber=3256 cram_read_container /src/htslib/cram/cram_io.c linenumber=3258 cram_seek /src/htslib/cram/cram_io.c linenumber=3274 cram_free_container /src/htslib/cram/cram_io.c linenumber=3276 cram_read_container /src/htslib/cram/cram_io.c linenumber=3278 cram_read_block /src/htslib/cram/cram_io.c linenumber=3289 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3294 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=2259 hts_log /src/htslib/hts.c linenumber=2259 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=3298 TYPEKEY /src/htslib/./header.h linenumber=3146 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3146 strcmp linenumber=3152 strcmp linenumber=3154 strcmp linenumber=3156 strcmp linenumber=3158 hts_log /src/htslib/hts.c linenumber=3159 pthread_mutex_lock linenumber=3299 pthread_mutex_unlock linenumber=3301 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3320 cram_free_container /src/htslib/cram/cram_io.c linenumber=3331 cram_read_container /src/htslib/cram/cram_io.c linenumber=3364 cram_free_container /src/htslib/cram/cram_io.c linenumber=3377 cram_free_container /src/htslib/cram/cram_io.c linenumber=3390 cram_free_container /src/htslib/cram/cram_io.c linenumber=3399 cram_free_container /src/htslib/cram/cram_io.c linenumber=3412 hseek /src/htslib/hfile.c linenumber=3415 cram_read_block /src/htslib/cram/cram_io.c linenumber=3425 cram_decode_compression_header /src/htslib/cram/cram_decode.c linenumber=3431 sam_hrecs_sort_order /src/htslib/header.c linenumber=3436 pthread_mutex_lock linenumber=3437 pthread_mutex_unlock linenumber=3439 cram_free_container /src/htslib/cram/cram_io.c linenumber=3450 cram_read_slice /src/htslib/cram/cram_io.c linenumber=3455 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=3470 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3479 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3488 cram_decode_slice_mt /src/htslib/cram/cram_decode.c linenumber=3500 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3078 hts_tpool_process_sz /src/htslib/thread_pool.c linenumber=3088 pthread_mutex_lock linenumber=307 pthread_mutex_unlock linenumber=309 __errno_location linenumber=3090 __errno_location linenumber=3091 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=3092 cram_decode_slice_thread /src/htslib/cram/cram_decode.c linenumber=3092 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=3064 __errno_location linenumber=3095 __errno_location linenumber=3101 hts_log /src/htslib/hts.c linenumber=3501 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3502 hts_tpool_process_len /src/htslib/thread_pool.c linenumber=3523 pthread_mutex_lock linenumber=293 pthread_mutex_unlock linenumber=295 hts_tpool_process_qsize /src/htslib/thread_pool.c linenumber=3524 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3535 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3540 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3542 hts_log /src/htslib/hts.c linenumber=3543 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3547 hts_log /src/htslib/hts.c linenumber=3552 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3554 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3558 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3630 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3637 bam_get_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3673 bam_copy1 /src/htslib/sam.c linenumber=3677 realloc_bam_data /src/htslib/./sam_internal.h linenumber=490 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=3684 cram_to_bam /src/htslib/cram/cram_decode.c linenumber=3690 cram_eof /src/htslib/cram/cram_io.c linenumber=4172 sam_read1_sam /src/htslib/sam.c linenumber=4303 sam_parse1 /src/htslib/sam.c linenumber=4183 strchr linenumber=2725 hts_log /src/htslib/hts.c linenumber=2727 hts_log /src/htslib/hts.c linenumber=2728 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2730 parse_sam_flag /src/htslib/sam.c linenumber=2740 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2509 strtoul linenumber=2515 strchr linenumber=2744 strcmp linenumber=2745 bam_name2id /src/htslib/./htslib/sam.h linenumber=2747 sam_hdr_name2tid /src/htslib/header.c linenumber=783 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2410 kh_get_m_s2i /src/htslib/./header.h linenumber=2418 hts_log /src/htslib/hts.c linenumber=2748 hts_strprint /src/htslib/textutils.c linenumber=2749 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=2749 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2753 hts_log /src/htslib/hts.c linenumber=2756 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2762 bam_parse_cigar /src/htslib/sam.c linenumber=2768 hts_log /src/htslib/hts.c linenumber=2956 read_ncigar /src/htslib/sam.c linenumber=2961 isdigit_c /src/htslib/./textutils_internal.h linenumber=2870 hts_log /src/htslib/hts.c linenumber=2872 hts_log /src/htslib/hts.c linenumber=2876 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2969 hts_log /src/htslib/hts.c linenumber=2970 parse_cigar /src/htslib/sam.c linenumber=2982 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2896 hts_log /src/htslib/hts.c linenumber=2898 hts_log /src/htslib/hts.c linenumber=2902 hts_log /src/htslib/hts.c linenumber=2908 bam_cigar2rlen /src/htslib/sam.c linenumber=2773 hts_log /src/htslib/hts.c linenumber=2776 strchr linenumber=2778 hts_log /src/htslib/hts.c linenumber=2781 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2783 strchr linenumber=2786 strcmp linenumber=2787 strcmp linenumber=2789 bam_name2id /src/htslib/./htslib/sam.h linenumber=2792 hts_log /src/htslib/hts.c linenumber=2793 hts_strprint /src/htslib/textutils.c linenumber=2794 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2798 hts_log /src/htslib/hts.c linenumber=2801 hts_str2int /src/htslib/./textutils_internal.h linenumber=2806 hts_log /src/htslib/hts.c linenumber=2808 strchr linenumber=2811 strcmp linenumber=2812 hts_log /src/htslib/hts.c linenumber=2813 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2816 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2826 hts_log /src/htslib/hts.c linenumber=2832 hts_log /src/htslib/hts.c linenumber=2836 aux_parse /src/htslib/sam.c linenumber=2841 hts_log /src/htslib/hts.c linenumber=2564 isspace_c /src/htslib/./textutils_internal.h linenumber=2568 hts_log /src/htslib/hts.c linenumber=2568 isspace_c /src/htslib/./textutils_internal.h linenumber=2571 isspace_c /src/htslib/./textutils_internal.h linenumber=2573 kh_get_tag /src/htslib/sam.c linenumber=2580 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2588 isspace_c /src/htslib/./textutils_internal.h linenumber=2592 hts_log /src/htslib/hts.c linenumber=2592 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2595 hts_str2int /src/htslib/./textutils_internal.h linenumber=2602 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2608 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=275 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2612 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=283 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2616 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2622 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2626 strtod linenumber=2632 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2632 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=345 strtod linenumber=2636 double_to_le /src/htslib/./htslib/hts_endian.h linenumber=2636 u64_to_le /src/htslib/./htslib/hts_endian.h linenumber=359 strchr linenumber=2639 strlen linenumber=2640 isspace_c /src/htslib/./textutils_internal.h linenumber=2641 hts_log /src/htslib/hts.c linenumber=2641 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2644 isspace_c /src/htslib/./textutils_internal.h linenumber=2651 hts_log /src/htslib/hts.c linenumber=2651 sam_parse_B_vals /src/htslib/sam.c linenumber=2654 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2504 hts_log /src/htslib/hts.c linenumber=2384 aux_type2size /src/htslib/sam.c linenumber=2394 hts_log /src/htslib/hts.c linenumber=2396 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2413 hts_log /src/htslib/hts.c linenumber=2414 sam_parse_Bc_vals /src/htslib/sam.c linenumber=2427 grow_B_array /src/htslib/sam.c linenumber=2258 __errno_location linenumber=2233 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2238 hts_log /src/htslib/hts.c linenumber=2239 hts_str2int /src/htslib/./textutils_internal.h linenumber=2261 sam_parse_BC_vals /src/htslib/sam.c linenumber=2430 grow_B_array /src/htslib/sam.c linenumber=2272 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2276 sam_parse_Bs_vals /src/htslib/sam.c linenumber=2433 grow_B_array /src/htslib/sam.c linenumber=2292 hts_str2int /src/htslib/./textutils_internal.h linenumber=2295 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2295 sam_parse_BS_vals /src/htslib/sam.c linenumber=2436 grow_B_array /src/htslib/sam.c linenumber=2307 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2311 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2311 sam_parse_Bi_vals /src/htslib/sam.c linenumber=2439 grow_B_array /src/htslib/sam.c linenumber=2328 hts_str2int /src/htslib/./textutils_internal.h linenumber=2331 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2331 sam_parse_BI_vals /src/htslib/sam.c linenumber=2442 grow_B_array /src/htslib/sam.c linenumber=2343 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2347 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2347 sam_parse_Bf_vals /src/htslib/sam.c linenumber=2445 grow_B_array /src/htslib/sam.c linenumber=2364 strtod linenumber=2367 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2367 hts_log /src/htslib/hts.c linenumber=2450 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2453 hts_str2int /src/htslib/./textutils_internal.h linenumber=2467 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2476 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2478 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2480 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2484 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2486 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2488 hts_log /src/htslib/hts.c linenumber=2493 isspace_c /src/htslib/./textutils_internal.h linenumber=2656 hts_strprint /src/htslib/textutils.c linenumber=2656 hts_log /src/htslib/hts.c linenumber=2656 isspace_c /src/htslib/./textutils_internal.h linenumber=2662 hts_log /src/htslib/hts.c linenumber=2662 bam_tag2cigar /src/htslib/sam.c linenumber=2844 bam_cigar2qlen /src/htslib/sam.c linenumber=2848 hts_log /src/htslib/hts.c linenumber=2850 sam_state_destroy /src/htslib/sam.c linenumber=4194 __errno_location linenumber=4195 bgzf_seek /src/htslib/bgzf.c linenumber=4198 bgzf_seek_common /src/htslib/bgzf.c linenumber=2278 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=4209 pthread_create linenumber=4213 sam_dispatcher_read /src/htslib/sam.c linenumber=4213 ks_resize /src/htslib/./htslib/kstring.h linenumber=3357 pthread_mutex_lock linenumber=3362 pthread_cond_signal linenumber=3366 pthread_mutex_unlock linenumber=3367 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3368 pthread_mutex_unlock linenumber=3374 pthread_mutex_lock linenumber=3376 pthread_mutex_unlock linenumber=3382 calloc linenumber=3386 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3390 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3401 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=3414 hread /src/htslib/./htslib/hfile.h linenumber=3416 __errno_location linenumber=3418 sam_state_err /src/htslib/sam.c linenumber=3418 hts_realloc_pse /src/htslib/./htslib/hts_alloc.h linenumber=3435 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=3440 __assert_fail linenumber=3441 __assert_fail linenumber=3442 ks_resize /src/htslib/./htslib/kstring.h linenumber=3448 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=3460 sam_parse_worker /src/htslib/sam.c linenumber=3460 pthread_mutex_lock linenumber=3247 calloc linenumber=3255 calloc linenumber=3260 sam_state_err /src/htslib/sam.c linenumber=3262 sam_state_err /src/htslib/sam.c linenumber=3273 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3283 sam_state_err /src/htslib/sam.c linenumber=3286 strchr linenumber=3302 sam_parse1 /src/htslib/sam.c linenumber=3314 __errno_location linenumber=3315 sam_state_err /src/htslib/sam.c linenumber=3315 cleanup_sp_lines /src/htslib/sam.c linenumber=3316 __assert_fail linenumber=3228 sam_free_sp_bams /src/htslib/sam.c linenumber=3231 pthread_mutex_lock linenumber=3325 pthread_mutex_unlock linenumber=3328 sam_free_sp_bams /src/htslib/sam.c linenumber=3332 cleanup_sp_lines /src/htslib/sam.c linenumber=3460 cleanup_sp_bams /src/htslib/sam.c linenumber=3460 sam_free_sp_bams /src/htslib/sam.c linenumber=3342 pthread_mutex_lock linenumber=3463 pthread_mutex_unlock linenumber=3465 pthread_mutex_unlock linenumber=3470 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3474 sam_parse_eof /src/htslib/sam.c linenumber=3474 pthread_mutex_lock linenumber=3480 pthread_cond_wait linenumber=3482 pthread_cond_signal linenumber=3485 pthread_mutex_unlock linenumber=3486 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3487 pthread_mutex_unlock linenumber=3491 pthread_mutex_lock linenumber=3497 pthread_cond_signal linenumber=3499 pthread_mutex_unlock linenumber=3500 pthread_mutex_lock linenumber=3503 pthread_mutex_unlock linenumber=3506 __errno_location linenumber=3513 sam_state_err /src/htslib/sam.c linenumber=3513 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3514 hts_log /src/htslib/hts.c linenumber=4220 __errno_location linenumber=4228 pthread_mutex_lock linenumber=4232 pthread_mutex_unlock linenumber=4234 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=4238 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4241 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4242 pthread_mutex_lock linenumber=4245 pthread_mutex_unlock linenumber=4247 bam_copy1 /src/htslib/sam.c linenumber=4252 pthread_mutex_lock linenumber=4255 pthread_mutex_unlock linenumber=4258 hts_getline /src/htslib/hts.c linenumber=4271 sam_parse1 /src/htslib/sam.c linenumber=4274 hts_log /src/htslib/hts.c linenumber=4277 fastq_state_init /src/htslib/sam.c linenumber=4310 fastq_parse1 /src/htslib/sam.c linenumber=4315 hts_getline /src/htslib/hts.c linenumber=3968 strpbrk linenumber=3984 isspace_c /src/htslib/./textutils_internal.h linenumber=3996 isspace_c /src/htslib/./textutils_internal.h linenumber=4004 hts_getline /src/htslib/hts.c linenumber=4012 kputsn /src/htslib/./htslib/kstring.h linenumber=4018 hts_getline /src/htslib/hts.c linenumber=4027 kputsn /src/htslib/./htslib/kstring.h linenumber=4031 isdigit_c /src/htslib/./textutils_internal.h linenumber=4044 regexec linenumber=4058 hts_log /src/htslib/hts.c linenumber=4063 isalpha_c /src/htslib/./textutils_internal.h linenumber=4071 bam_set1 /src/htslib/sam.c linenumber=4091 bam_aux_append /src/htslib/sam.c linenumber=4103 __assert_fail linenumber=4786 realloc_bam_data /src/htslib/./sam_internal.h linenumber=4790 __errno_location linenumber=4810 isdigit_c /src/htslib/./textutils_internal.h linenumber=4115 strtol linenumber=4116 isdigit_c /src/htslib/./textutils_internal.h linenumber=4130 isspace_c /src/htslib/./textutils_internal.h linenumber=4133 bam_aux_append /src/htslib/sam.c linenumber=4142 aux_parse /src/htslib/sam.c linenumber=4149 __errno_location linenumber=4319 __errno_location linenumber=4323 sam_passes_filter /src/htslib/sam.c linenumber=4328 hts_filter_eval2 /src/htslib/hts_expr.c linenumber=1568 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=1568 memcmp linenumber=1246 ks_clear /src/htslib/./htslib/kstring.h linenumber=1249 kputw /src/htslib/./htslib/kstring.h linenumber=1254 kputc_ /src/htslib/./htslib/kstring.h linenumber=1255 kputs /src/htslib/./htslib/kstring.h linenumber=1257 kputs /src/htslib/./htslib/kstring.h linenumber=1259 memcmp linenumber=1266 bam_endpos /src/htslib/sam.c linenumber=1268 memcmp linenumber=1274 memcmp linenumber=1281 memcmp linenumber=1285 memcmp linenumber=1289 memcmp linenumber=1293 memcmp linenumber=1297 memcmp linenumber=1301 memcmp linenumber=1305 memcmp linenumber=1309 memcmp linenumber=1313 memcmp linenumber=1317 memcmp linenumber=1321 memcmp linenumber=1325 hts_log /src/htslib/hts.c linenumber=1330 memcmp linenumber=1338 memcmp linenumber=1358 bam_get_library /src/htslib/sam.c linenumber=1361 bam_aux_get /src/htslib/sam.c linenumber=1205 sam_hdr_find_tag_id /src/htslib/header.c linenumber=1212 ks_clear /src/htslib/./htslib/kstring.h linenumber=1362 kputs /src/htslib/./htslib/kstring.h linenumber=1362 memcmp linenumber=1368 memcmp linenumber=1372 memcmp linenumber=1376 sam_hdr_tid2name /src/htslib/header.c linenumber=1379 ks_clear /src/htslib/./htslib/kstring.h linenumber=1380 kputs /src/htslib/./htslib/kstring.h linenumber=1380 memcmp linenumber=1382 memcmp linenumber=1390 memcmp linenumber=1398 memcmp linenumber=1402 memcmp linenumber=1410 bam_cigar2qlen /src/htslib/sam.c linenumber=1412 memcmp linenumber=1414 ks_clear /src/htslib/./htslib/kstring.h linenumber=1417 kputs /src/htslib/./htslib/kstring.h linenumber=1417 memcmp linenumber=1419 ks_clear /src/htslib/./htslib/kstring.h linenumber=1421 ks_resize /src/htslib/./htslib/kstring.h linenumber=1422 memcmp linenumber=1433 bam_cigar2rlen /src/htslib/sam.c linenumber=1435 memcmp linenumber=1437 sam_hdr_tid2name /src/htslib/header.c linenumber=1440 ks_clear /src/htslib/./htslib/kstring.h linenumber=1441 kputs /src/htslib/./htslib/kstring.h linenumber=1441 memcmp linenumber=1443 sam_hdr_tid2name /src/htslib/header.c linenumber=1446 ks_clear /src/htslib/./htslib/kstring.h linenumber=1447 kputs /src/htslib/./htslib/kstring.h linenumber=1447 memcmp linenumber=1449 memcmp linenumber=1457 ks_clear /src/htslib/./htslib/kstring.h linenumber=1459 ks_resize /src/htslib/./htslib/kstring.h linenumber=1460 nibble2base /src/htslib/./sam_internal.h linenumber=1462 memcmp linenumber=1467 memcmp linenumber=1498 bam_aux_get /src/htslib/sam.c linenumber=1510 ks_clear /src/htslib/./htslib/kstring.h linenumber=1518 kputs /src/htslib/./htslib/kstring.h linenumber=1518 ks_clear /src/htslib/./htslib/kstring.h linenumber=1523 kputsn /src/htslib/./htslib/kstring.h linenumber=1523 bam_aux2i /src/htslib/sam.c linenumber=1530 get_int_aux_val /src/htslib/sam.c linenumber=5142 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=5126 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=5128 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=5129 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=5130 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=5131 __errno_location linenumber=5133 bam_aux2f /src/htslib/sam.c linenumber=1536 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=5149 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=5150 get_int_aux_val /src/htslib/sam.c linenumber=5151 hts_log /src/htslib/hts.c linenumber=1540 hts_log /src/htslib/hts.c linenumber=1569 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1570 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1575 sam_write1 /src/htslib/sam.c linenumber=107 bam_write_idx1 /src/htslib/sam.c linenumber=4582 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 __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=2452 hts_log /src/htslib/hts.c linenumber=977 cram_put_bam_seq /src/htslib/cram/cram_encode.c linenumber=4585 hts_log /src/htslib/hts.c linenumber=3974 __errno_location linenumber=3975 cram_new_container /src/htslib/cram/cram_io.c linenumber=3980 pthread_mutex_lock linenumber=3986 pthread_mutex_unlock linenumber=3989 hts_log /src/htslib/hts.c linenumber=4014 pthread_mutex_lock linenumber=4017 hts_log /src/htslib/hts.c linenumber=4020 pthread_mutex_unlock linenumber=4022 cram_next_container /src/htslib/cram/cram_encode.c linenumber=4031 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=3219 hts_log /src/htslib/hts.c linenumber=3225 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=3230 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3236 cram_free_container /src/htslib/cram/cram_io.c linenumber=3244 cram_new_container /src/htslib/cram/cram_io.c linenumber=3247 pthread_mutex_lock linenumber=3252 pthread_mutex_unlock linenumber=3256 cram_new_slice /src/htslib/cram/cram_io.c linenumber=3264 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=4063 hts_log /src/htslib/hts.c linenumber=4065 pthread_mutex_unlock linenumber=4076 pthread_mutex_lock linenumber=4079 calloc linenumber=4080 pthread_mutex_unlock linenumber=4081 pthread_mutex_lock linenumber=4095 calloc linenumber=4096 pthread_mutex_unlock linenumber=4097 pthread_mutex_lock linenumber=4101 pthread_mutex_unlock linenumber=4104 pthread_mutex_lock linenumber=4114 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4119 pthread_mutex_unlock linenumber=4122 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4128 calloc linenumber=4136 pthread_mutex_unlock linenumber=4139 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4144 pthread_mutex_unlock linenumber=4146 bam_copy1 /src/htslib/sam.c linenumber=4153 bam_cigar2qlen /src/htslib/sam.c linenumber=4163 hts_log /src/htslib/hts.c linenumber=4165 pthread_create linenumber=4608 sam_dispatcher_write /src/htslib/sam.c linenumber=4608 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3527 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3528 sam_state_err /src/htslib/sam.c linenumber=3530 bgzf_flush_try /src/htslib/bgzf.c linenumber=3545 bgzf_write /src/htslib/bgzf.c linenumber=3547 hwrite /src/htslib/./htslib/hfile.h linenumber=3550 bam_endpos /src/htslib/sam.c linenumber=3557 bgzf_idx_push /src/htslib/bgzf.c linenumber=3556 __errno_location linenumber=3560 sam_state_err /src/htslib/sam.c linenumber=3560 sam_hdr_tid2name /src/htslib/header.c linenumber=3561 sam_hdr_tid2len /src/htslib/header.c linenumber=3561 hts_log /src/htslib/hts.c linenumber=3561 bam_endpos /src/htslib/sam.c linenumber=3566 hts_idx_push /src/htslib/hts.c linenumber=3566 __errno_location linenumber=3568 sam_state_err /src/htslib/sam.c linenumber=3568 sam_hdr_tid2name /src/htslib/header.c linenumber=3569 sam_hdr_tid2len /src/htslib/header.c linenumber=3569 hts_log /src/htslib/hts.c linenumber=3569 __assert_fail linenumber=3576 pthread_mutex_lock linenumber=3579 pthread_mutex_unlock linenumber=3583 bgzf_write /src/htslib/bgzf.c linenumber=3630 bgzf_flush_try /src/htslib/bgzf.c linenumber=3638 bgzf_write /src/htslib/bgzf.c linenumber=3643 hwrite /src/htslib/./htslib/hfile.h linenumber=3650 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3655 pthread_mutex_lock linenumber=3658 pthread_mutex_unlock linenumber=3661 sam_state_err /src/htslib/sam.c linenumber=3664 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3665 __errno_location linenumber=3669 sam_state_err /src/htslib/sam.c linenumber=3669 hts_log /src/htslib/hts.c linenumber=4615 pthread_mutex_lock linenumber=4622 pthread_mutex_unlock linenumber=4629 pthread_mutex_unlock linenumber=4631 calloc linenumber=4632 calloc linenumber=4633 bam_copy1 /src/htslib/sam.c linenumber=4646 pthread_mutex_lock linenumber=4653 pthread_mutex_unlock linenumber=4655 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=4658 sam_format_worker /src/htslib/sam.c linenumber=4658 cleanup_sp_bams /src/htslib/sam.c linenumber=4658 cleanup_sp_lines /src/htslib/sam.c linenumber=4658 pthread_mutex_unlock linenumber=4661 pthread_mutex_unlock linenumber=4664 sam_format1 /src/htslib/sam.c linenumber=4673 sam_format1_append /src/htslib/sam.c linenumber=4430 kputc /src/htslib/./htslib/kstring.h linenumber=4674 bgzf_flush_try /src/htslib/bgzf.c linenumber=4676 bgzf_write /src/htslib/bgzf.c linenumber=4678 hwrite /src/htslib/./htslib/hfile.h linenumber=4680 bam_endpos /src/htslib/sam.c linenumber=4685 bgzf_idx_push /src/htslib/bgzf.c linenumber=4685 sam_hdr_tid2name /src/htslib/header.c linenumber=4687 sam_hdr_tid2len /src/htslib/header.c linenumber=4687 hts_log /src/htslib/hts.c linenumber=4687 bam_endpos /src/htslib/sam.c linenumber=4692 hts_idx_push /src/htslib/hts.c linenumber=4692 sam_hdr_tid2name /src/htslib/header.c linenumber=4694 sam_hdr_tid2len /src/htslib/header.c linenumber=4694 hts_log /src/htslib/hts.c linenumber=4694 fastq_state_init /src/htslib/sam.c linenumber=4709 fastq_format1 /src/htslib/sam.c linenumber=4714 kputc /src/htslib/./htslib/kstring.h linenumber=4443 kputs /src/htslib/./htslib/kstring.h linenumber=4443 bam_aux_get /src/htslib/sam.c linenumber=4465 kputc /src/htslib/./htslib/kstring.h linenumber=4467 isalpha_c /src/htslib/./textutils_internal.h linenumber=4470 toupper_c /src/htslib/./textutils_internal.h linenumber=4470 kputc /src/htslib/./htslib/kstring.h linenumber=4470 kputs /src/htslib/./htslib/kstring.h linenumber=4475 kputs /src/htslib/./htslib/kstring.h linenumber=4483 kputs /src/htslib/./htslib/kstring.h linenumber=4486 bam_aux_get /src/htslib/sam.c linenumber=4496 ksprintf /src/htslib/kstring.c linenumber=4497 isupper_c /src/htslib/./textutils_internal.h linenumber=4501 __ctype_b_loc linenumber=177 islower_c /src/htslib/./textutils_internal.h linenumber=4501 __ctype_b_loc linenumber=173 hts_log /src/htslib/hts.c linenumber=4502 strlen linenumber=4503 strlen linenumber=4511 isalpha_c /src/htslib/./textutils_internal.h linenumber=4514 islower_c /src/htslib/./textutils_internal.h linenumber=4516 toupper_c /src/htslib/./textutils_internal.h linenumber=4517 kh_get_tag /src/htslib/sam.c linenumber=4528 kputc_ /src/htslib/./htslib/kstring.h linenumber=4529 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4530 skip_aux /src/htslib/sam.c linenumber=4533 kputsn /src/htslib/./htslib/kstring.h linenumber=4536 ks_resize /src/htslib/./htslib/kstring.h linenumber=4539 kputc_ /src/htslib/./htslib/kstring.h linenumber=4540 kputc_ /src/htslib/./htslib/kstring.h linenumber=4546 kputc_ /src/htslib/./htslib/kstring.h linenumber=4549 kputsn /src/htslib/./htslib/kstring.h linenumber=4554 kputc_ /src/htslib/./htslib/kstring.h linenumber=4558 kputc_ /src/htslib/./htslib/kstring.h linenumber=4561 kputc_ /src/htslib/./htslib/kstring.h linenumber=4564 kputc /src/htslib/./htslib/kstring.h linenumber=4567 bgzf_flush_try /src/htslib/bgzf.c linenumber=4717 bgzf_write /src/htslib/bgzf.c linenumber=4719 hwrite /src/htslib/./htslib/hfile.h linenumber=4722 __errno_location linenumber=4729 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=2676 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 hts_log /src/htslib/hts.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=5219 __errno_location linenumber=5220 realloc linenumber=5224 __errno_location linenumber=5226 __errno_location linenumber=5227 strerror linenumber=5227 hts_log /src/htslib/hts.c linenumber=5227 __errno_location linenumber=5228 abort linenumber=5237 abort linenumber=5248 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_getline /src/htslib/hts.c linenumber=2682 hts_log /src/htslib/hts.c linenumber=2686 hopen /src/htslib/hfile.c linenumber=2691 hts_log /src/htslib/hts.c linenumber=2693 khgetline /src/htslib/hfile.c linenumber=2696 strchr linenumber=2697 kputs /src/htslib/./htslib/kstring.h linenumber=2699 kputsn /src/htslib/./htslib/kstring.h linenumber=2700 kputs /src/htslib/./htslib/kstring.h linenumber=2701 atol linenumber=2702 kputl /src/htslib/./htslib/kstring.h linenumber=2702 kputll /src/htslib/./htslib/kstring.h linenumber=446 kputsn /src/htslib/./htslib/kstring.h linenumber=2703 hclose /src/htslib/hfile.c linenumber=2706 hts_log /src/htslib/hts.c linenumber=2707 kputsn /src/htslib/./htslib/kstring.h linenumber=2712 kputc /src/htslib/./htslib/kstring.h linenumber=2713 hts_log /src/htslib/hts.c linenumber=2719 bcf_hdr_parse /src/htslib/vcf.c linenumber=2722 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 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=4710 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=2725 index_load /src/htslib/tbx.c linenumber=642 calloc linenumber=599 hts_idx_load3 /src/htslib/hts.c linenumber=602 idx_find_and_load /src/htslib/hts.c linenumber=5097 strstr linenumber=5030 strdup linenumber=5035 __errno_location linenumber=5037 strerror linenumber=5037 hts_log /src/htslib/hts.c linenumber=5037 hts_idx_load3 /src/htslib/hts.c linenumber=5042 hisremote /src/htslib/hfile.c linenumber=5101 stat linenumber=5103 hts_log /src/htslib/hts.c linenumber=5106 idx_test_and_fetch /src/htslib/hts.c linenumber=5111 hisremote /src/htslib/hfile.c linenumber=4735 strncmp linenumber=4740 strcspn linenumber=4740 kputsn /src/htslib/./htslib/kstring.h linenumber=4747 access linenumber=4748 hopen /src/htslib/hfile.c linenumber=4757 hts_log /src/htslib/hts.c linenumber=4758 hts_detect_format2 /src/htslib/hts.c linenumber=4762 hts_log /src/htslib/hts.c linenumber=4763 hts_log /src/htslib/hts.c linenumber=4768 hts_open_tmpfile /src/htslib/hts.c linenumber=4773 hts_log /src/htslib/hts.c linenumber=4774 hts_log /src/htslib/hts.c linenumber=4777 calloc linenumber=4778 __errno_location linenumber=4780 strerror linenumber=4780 hts_log /src/htslib/hts.c linenumber=4780 hread /src/htslib/./htslib/hfile.h linenumber=4783 hwrite /src/htslib/./htslib/hfile.h linenumber=4784 __errno_location linenumber=4785 strerror linenumber=4785 hts_log /src/htslib/hts.c linenumber=4785 hts_log /src/htslib/hts.c linenumber=4793 hclose /src/htslib/hfile.c linenumber=4796 __errno_location linenumber=4797 strerror linenumber=4797 hts_log /src/htslib/hts.c linenumber=4797 rename linenumber=4802 __errno_location linenumber=4803 strerror linenumber=4803 hts_log /src/htslib/hts.c linenumber=4803 ks_clear /src/htslib/./htslib/kstring.h linenumber=4806 hclose /src/htslib/hfile.c linenumber=4815 hts_log /src/htslib/hts.c linenumber=4816 hopen /src/htslib/hfile.c linenumber=4824 hclose_abruptly /src/htslib/hfile.c linenumber=4825 strlen linenumber=4827 __errno_location linenumber=4832 hclose_abruptly /src/htslib/hfile.c linenumber=4833 hclose_abruptly /src/htslib/hfile.c linenumber=4834 unlink linenumber=4835 __errno_location linenumber=4838 strdup linenumber=5113 idx_read /src/htslib/hts.c linenumber=5121 bgzf_open /src/htslib/bgzf.c linenumber=3097 ed_is_big /src/htslib/./htslib/hts.h linenumber=3099 bgzf_read /src/htslib/bgzf.c linenumber=3100 memcmp linenumber=3102 bgzf_read /src/htslib/bgzf.c linenumber=3104 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3105 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3108 bgzf_read /src/htslib/bgzf.c linenumber=3109 bgzf_read /src/htslib/bgzf.c linenumber=3113 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3114 hts_idx_init /src/htslib/hts.c linenumber=3116 calloc linenumber=2509 calloc linenumber=2521 calloc linenumber=2523 idx_read_core /src/htslib/hts.c linenumber=3120 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=3050 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=3051 bgzf_read /src/htslib/bgzf.c linenumber=3053 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3054 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3058 bgzf_read /src/htslib/bgzf.c linenumber=3060 swap_bins /src/htslib/hts.c linenumber=3061 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=3066 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3067 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3072 bgzf_read /src/htslib/bgzf.c linenumber=3074 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=3075 update_loff /src/htslib/hts.c linenumber=3079 hts_bin_bot /src/htslib/./htslib/hts.h linenumber=2549 hts_bin_level /src/htslib/./htslib/hts.h linenumber=1570 bgzf_read /src/htslib/bgzf.c linenumber=3082 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=3083 memcmp linenumber=3122 bgzf_read /src/htslib/bgzf.c linenumber=3126 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3127 hts_idx_init /src/htslib/hts.c linenumber=3129 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3130 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3133 bgzf_read /src/htslib/bgzf.c linenumber=3138 idx_read_core /src/htslib/hts.c linenumber=3141 memcmp linenumber=3143 bgzf_read /src/htslib/bgzf.c linenumber=3145 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3146 hts_idx_init /src/htslib/hts.c linenumber=3148 idx_read_core /src/htslib/hts.c linenumber=3149 __errno_location linenumber=3151 bgzf_close /src/htslib/bgzf.c linenumber=3153 bgzf_close /src/htslib/bgzf.c linenumber=3157 hts_idx_destroy /src/htslib/hts.c linenumber=3158 __errno_location linenumber=5123 strerror linenumber=5123 hts_log /src/htslib/hts.c linenumber=5123 hts_idx_check_local /src/htslib/hts.c linenumber=5047 hisremote /src/htslib/hfile.c linenumber=4873 strlen linenumber=4874 strncmp linenumber=4881 strncmp linenumber=4882 hts_log /src/htslib/hts.c linenumber=4892 strlen linenumber=4893 calloc linenumber=4894 strcpy linenumber=4900 stat linenumber=4901 strcpy linenumber=4907 stat linenumber=4908 strcpy linenumber=4917 stat linenumber=4918 strcpy linenumber=4924 stat linenumber=4925 strcpy linenumber=4933 stat linenumber=4934 strcpy linenumber=4940 stat linenumber=4941 strcpy linenumber=4949 stat linenumber=4950 strcpy linenumber=4956 stat linenumber=4957 strcpy linenumber=4966 strcmp linenumber=4968 strcmp linenumber=4969 strcpy linenumber=4970 stat linenumber=4971 strcpy linenumber=4976 stat linenumber=4978 hisremote /src/htslib/hfile.c linenumber=5047 idx_filename /src/htslib/hts.c linenumber=5049 haddextension /src/htslib/hfile.c linenumber=4995 find_scheme_handler /src/htslib/hfile.c linenumber=1369 strncmp linenumber=1372 strcspn linenumber=1372 strchr linenumber=1376 strip_extension /src/htslib/hfile.c linenumber=1379 kputsn /src/htslib/./htslib/kstring.h linenumber=1382 kputs /src/htslib/./htslib/kstring.h linenumber=1383 kputs /src/htslib/./htslib/kstring.h linenumber=1384 idx_test_and_fetch /src/htslib/hts.c linenumber=4999 haddextension /src/htslib/hfile.c linenumber=5001 idx_test_and_fetch /src/htslib/hts.c linenumber=5005 idx_filename /src/htslib/hts.c linenumber=5052 idx_filename /src/htslib/hts.c linenumber=5053 idx_filename /src/htslib/hts.c linenumber=5058 idx_filename /src/htslib/hts.c linenumber=5061 idx_filename /src/htslib/hts.c linenumber=5062 hts_log /src/htslib/hts.c linenumber=5070 hts_idx_load3 /src/htslib/hts.c linenumber=5075 idx_read /src/htslib/hts.c linenumber=5077 hts_idx_get_meta /src/htslib/hts.c linenumber=608 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=611 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=612 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=613 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=614 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=615 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=616 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=617 get_tid /src/htslib/tbx.c linenumber=625 kh_init_s2i /src/htslib/hts.c linenumber=71 kh_put_s2i /src/htslib/hts.c linenumber=76 strdup linenumber=80 kh_del_s2i /src/htslib/hts.c linenumber=85 kh_get_s2i /src/htslib/hts.c linenumber=89 __errno_location linenumber=626 strerror linenumber=626 hts_log /src/htslib/hts.c linenumber=626 strlen linenumber=624 hts_log /src/htslib/hts.c linenumber=633 tbx_destroy /src/htslib/tbx.c linenumber=636 hts_idx_destroy /src/htslib/hts.c linenumber=562 kh_destroy_s2i /src/htslib/hts.c linenumber=563 tbx_seqnames /src/htslib/tbx.c linenumber=2729 calloc linenumber=661 calloc linenumber=664 __assert_fail linenumber=674 __assert_fail linenumber=679 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=2733 add_missing_contig_hrec /src/htslib/vcf.c linenumber=2735 calloc linenumber=2647 strdup linenumber=2651 bcf_hrec_add_key /src/htslib/vcf.c linenumber=2654 strlen linenumber=2655 bcf_hrec_set_val /src/htslib/vcf.c linenumber=2655 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=2657 __errno_location linenumber=2662 __errno_location linenumber=2663 strerror linenumber=2663 hts_log /src/htslib/hts.c linenumber=2663 bcf_hrec_destroy /src/htslib/vcf.c linenumber=2664 __errno_location linenumber=2665 bcf_hdr_sync /src/htslib/vcf.c linenumber=2739 tbx_destroy /src/htslib/tbx.c linenumber=2742 tbx_destroy /src/htslib/tbx.c linenumber=2748 bcf_hdr_destroy /src/htslib/vcf.c linenumber=2751 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=2889 _bcf_hrec_format /src/htslib/vcf.c linenumber=2819 ksprintf /src/htslib/kstring.c linenumber=2793 strcmp linenumber=2797 kputc /src/htslib/./htslib/kstring.h linenumber=2798 ksprintf /src/htslib/kstring.c linenumber=2799 ksprintf /src/htslib/kstring.c linenumber=2802 ksprintf /src/htslib/kstring.c linenumber=2805 ksprintf /src/htslib/kstring.c linenumber=2821 ksprintf /src/htslib/kstring.c linenumber=2824 ksprintf /src/htslib/kstring.c linenumber=2826 ksprintf /src/htslib/kstring.c linenumber=2828 bgzf_write /src/htslib/bgzf.c linenumber=2896 bgzf_flush /src/htslib/bgzf.c linenumber=2897 hwrite /src/htslib/./htslib/hfile.h linenumber=2899 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=4258 vcf_parse /src/htslib/vcf.c linenumber=4260 ks_resize /src/htslib/./htslib/kstring.h linenumber=4093 bcf_clear /src/htslib/vcf.c linenumber=4106 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=1905 kstrtok /src/htslib/kstring.c linenumber=4111 kh_get_vdict /src/htslib/vcf.c linenumber=4116 hts_log /src/htslib/hts.c linenumber=4118 hts_log /src/htslib/hts.c linenumber=4120 fix_chromosome /src/htslib/vcf.c linenumber=4122 ksprintf /src/htslib/kstring.c linenumber=3828 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3830 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3832 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3833 bcf_hdr_sync /src/htslib/vcf.c linenumber=3834 kh_get_vdict /src/htslib/vcf.c linenumber=3835 hts_log /src/htslib/hts.c linenumber=4123 kstrtok /src/htslib/kstring.c linenumber=4131 hts_str2uint /src/htslib/./textutils_internal.h linenumber=4137 hts_log /src/htslib/hts.c linenumber=4139 hts_log /src/htslib/hts.c linenumber=4142 kstrtok /src/htslib/kstring.c linenumber=4151 memcmp linenumber=4155 bcf_enc_vchar /src/htslib/vcf.c linenumber=4155 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3047 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=3048 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=4156 kstrtok /src/htslib/kstring.c linenumber=4159 bcf_enc_vchar /src/htslib/vcf.c linenumber=4163 kstrtok /src/htslib/kstring.c linenumber=4167 memcmp linenumber=4171 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4175 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=4175 bcf_enc_vchar /src/htslib/vcf.c linenumber=4180 kstrtok /src/htslib/kstring.c linenumber=4189 memcmp linenumber=4193 atof linenumber=4193 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4194 kstrtok /src/htslib/kstring.c linenumber=4198 memcmp linenumber=4202 vcf_parse_filter /src/htslib/vcf.c linenumber=4203 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3852 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3854 hts_log /src/htslib/hts.c linenumber=3854 kstrtok /src/htslib/kstring.c linenumber=3861 kh_get_vdict /src/htslib/vcf.c linenumber=3863 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3868 hts_log /src/htslib/hts.c linenumber=3868 hts_log /src/htslib/hts.c linenumber=3871 ksprintf /src/htslib/kstring.c linenumber=3874 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3875 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3877 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3878 bcf_hdr_sync /src/htslib/vcf.c linenumber=3879 kh_get_vdict /src/htslib/vcf.c linenumber=3880 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3883 hts_log /src/htslib/hts.c linenumber=3883 bcf_enc_vint /src/htslib/vcf.c linenumber=3892 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2914 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=2916 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=2956 ks_resize /src/htslib/./htslib/kstring.h linenumber=2957 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2968 ks_resize /src/htslib/./htslib/kstring.h linenumber=2969 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2978 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2984 ks_resize /src/htslib/./htslib/kstring.h linenumber=2985 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2989 bcf_enc_vint /src/htslib/vcf.c linenumber=4206 kstrtok /src/htslib/kstring.c linenumber=4210 memcmp linenumber=4214 vcf_parse_info /src/htslib/vcf.c linenumber=4215 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3913 hts_log /src/htslib/hts.c linenumber=3913 kh_get_vdict /src/htslib/vcf.c linenumber=3927 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3930 hts_log /src/htslib/hts.c linenumber=3930 hts_log /src/htslib/hts.c linenumber=3933 ksprintf /src/htslib/kstring.c linenumber=3936 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3937 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3939 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3940 bcf_hdr_sync /src/htslib/vcf.c linenumber=3941 kh_get_vdict /src/htslib/vcf.c linenumber=3942 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3945 hts_log /src/htslib/hts.c linenumber=3945 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3952 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3954 bcf_enc_vchar /src/htslib/vcf.c linenumber=3956 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3964 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3966 hts_log /src/htslib/hts.c linenumber=3966 hts_str2int /src/htslib/./textutils_internal.h linenumber=4002 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4008 hts_log /src/htslib/hts.c linenumber=4008 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=4027 bcf_enc_vint /src/htslib/vcf.c linenumber=4030 memcmp linenumber=4033 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4039 hts_log /src/htslib/hts.c linenumber=4039 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=4049 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4051 bcf_enc_vfloat /src/htslib/vcf.c linenumber=4054 __assert_fail linenumber=3039 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3040 serialize_float_array /src/htslib/vcf.c linenumber=3041 ks_resize /src/htslib/./htslib/kstring.h linenumber=3025 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=3029 kstrtok /src/htslib/kstring.c linenumber=4222 vcf_parse_format /src/htslib/vcf.c linenumber=4226 vcf_parse_format_empty1 /src/htslib/vcf.c linenumber=3774 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3217 hts_log /src/htslib/hts.c linenumber=3217 vcf_parse_format_dict2 /src/htslib/vcf.c linenumber=3778 kstrtok /src/htslib/kstring.c linenumber=3240 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3243 hts_log /src/htslib/hts.c linenumber=3243 kh_get_vdict /src/htslib/vcf.c linenumber=3249 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3253 hts_log /src/htslib/hts.c linenumber=3253 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3257 hts_log /src/htslib/hts.c linenumber=3257 hts_log /src/htslib/hts.c linenumber=3259 ksprintf /src/htslib/kstring.c linenumber=3262 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3263 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3265 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3266 bcf_hdr_sync /src/htslib/vcf.c linenumber=3267 kh_get_vdict /src/htslib/vcf.c linenumber=3269 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3272 hts_log /src/htslib/hts.c linenumber=3272 vcf_parse_format_max3 /src/htslib/vcf.c linenumber=3799 hts_log /src/htslib/hts.c linenumber=3353 vcf_parse_format_alloc4 /src/htslib/vcf.c linenumber=3803 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3389 hts_log /src/htslib/hts.c linenumber=3389 align_mem /src/htslib/vcf.c linenumber=3394 kputsn /src/htslib/./htslib/kstring.h linenumber=3204 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3395 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3405 hts_log /src/htslib/hts.c linenumber=3405 ks_resize /src/htslib/./htslib/kstring.h linenumber=3414 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3415 hts_log /src/htslib/hts.c linenumber=3415 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3440 hts_log /src/htslib/hts.c linenumber=3440 vcf_parse_format_fill5 /src/htslib/vcf.c linenumber=3807 bcf_get_version /src/htslib/vcf.c linenumber=3462 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3485 hts_log /src/htslib/hts.c linenumber=3485 hts_str2uint /src/htslib/./textutils_internal.h linenumber=3533 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3558 hts_log /src/htslib/hts.c linenumber=3558 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3562 hts_log /src/htslib/hts.c linenumber=3562 hts_str2int /src/htslib/./textutils_internal.h linenumber=3588 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3593 hts_log /src/htslib/hts.c linenumber=3593 isdigit_c /src/htslib/./textutils_internal.h linenumber=3614 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3615 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3619 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=3622 hts_log /src/htslib/hts.c linenumber=3622 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3632 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3634 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3636 hts_log /src/htslib/hts.c linenumber=3636 hts_strprint /src/htslib/textutils.c linenumber=3649 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3649 hts_log /src/htslib/hts.c linenumber=3649 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3684 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3685 vcf_parse_format_gt6 /src/htslib/vcf.c linenumber=3811 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3707 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3709 kputsn /src/htslib/./htslib/kstring.h linenumber=3710 bcf_enc_vint /src/htslib/vcf.c linenumber=3712 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3714 serialize_float_array /src/htslib/vcf.c linenumber=3715 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3718 hts_log /src/htslib/hts.c linenumber=3718 vcf_parse_format_check7 /src/htslib/vcf.c linenumber=3815 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3744 hts_log /src/htslib/hts.c linenumber=3744 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3751 hts_log /src/htslib/hts.c linenumber=3751 get_rlen /src/htslib/vcf.c linenumber=4232 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6545 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6556 strlen linenumber=186 memcmp linenumber=191 memcmp linenumber=192 memcmp linenumber=193 memcmp linenumber=194 strcmp linenumber=6560 strcmp linenumber=6561 strlen linenumber=6566 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6569 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=6574 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6578 strncmp linenumber=6582 strncmp linenumber=6583 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6594 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6599 bcf_get_info /src/htslib/vcf.c linenumber=6604 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6152 bcf_get_info_id /src/htslib/vcf.c linenumber=6154 bcf_unpack /src/htslib/vcf.c linenumber=6171 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4334 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=3159 bcf_fmt_array /src/htslib/vcf.c linenumber=3160 kputc_ /src/htslib/./htslib/kstring.h linenumber=3116 memchr linenumber=3125 kputsn /src/htslib/./htslib/kstring.h linenumber=3126 kputc /src/htslib/./htslib/kstring.h linenumber=3129 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=3145 kputc_ /src/htslib/./htslib/kstring.h linenumber=3145 kputc /src/htslib/./htslib/kstring.h linenumber=3145 kputw /src/htslib/./htslib/kstring.h linenumber=3145 le_to_i16 /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_i32 /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_u32 /src/htslib/./htslib/hts_endian.h linenumber=3148 kputc_ /src/htslib/./htslib/kstring.h linenumber=3148 kputc /src/htslib/./htslib/kstring.h linenumber=3148 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3148 kputd /src/htslib/kstring.c linenumber=3148 hts_log /src/htslib/hts.c linenumber=3149 exit linenumber=3149 kputc_ /src/htslib/./htslib/kstring.h linenumber=4336 hts_realloc_or_die /src/htslib/hts.c linenumber=4340 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4346 kputc_ /src/htslib/./htslib/kstring.h linenumber=4347 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4362 hts_realloc_or_die /src/htslib/hts.c linenumber=4363 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=4365 hts_realloc_or_die /src/htslib/hts.c linenumber=4372 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=4375 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4281 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4282 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=4294 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=4298 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=4302 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=4306 hts_realloc_or_die /src/htslib/hts.c linenumber=4380 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=4383 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4266 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4267 bcf_get_info /src/htslib/vcf.c linenumber=6605 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6608 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6610 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6616 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6623 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6632 bcf_get_fmt /src/htslib/vcf.c linenumber=6639 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6145 bcf_get_fmt_id /src/htslib/vcf.c linenumber=6147 bcf_unpack /src/htslib/vcf.c linenumber=6160 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6642 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=6644 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6649 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6679 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6683 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6687 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6691 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6723 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6727 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6731 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6735 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=2588 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2592 vcf_write /src/htslib/vcf.c linenumber=2598 vcf_format /src/htslib/vcf.c linenumber=4676 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=4393 hts_log /src/htslib/hts.c linenumber=4395 __errno_location linenumber=4397 bcf_unpack /src/htslib/vcf.c linenumber=4401 get_hdr_aux /src/htslib/vcf.c linenumber=4412 calloc linenumber=4414 kputs /src/htslib/./htslib/kstring.h linenumber=4419 kputc_ /src/htslib/./htslib/kstring.h linenumber=4420 kputll /src/htslib/./htslib/kstring.h linenumber=4420 kputc_ /src/htslib/./htslib/kstring.h linenumber=4421 kputs /src/htslib/./htslib/kstring.h linenumber=4421 kputc_ /src/htslib/./htslib/kstring.h linenumber=4422 kputs /src/htslib/./htslib/kstring.h linenumber=4423 kputc_ /src/htslib/./htslib/kstring.h linenumber=4424 kputc_ /src/htslib/./htslib/kstring.h linenumber=4425 kputc_ /src/htslib/./htslib/kstring.h linenumber=4428 kputs /src/htslib/./htslib/kstring.h linenumber=4429 kputc_ /src/htslib/./htslib/kstring.h linenumber=4431 kputc_ /src/htslib/./htslib/kstring.h linenumber=4432 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4433 kputc_ /src/htslib/./htslib/kstring.h linenumber=4433 kputd /src/htslib/kstring.c linenumber=4434 kputc_ /src/htslib/./htslib/kstring.h linenumber=4435 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4441 hts_log /src/htslib/hts.c linenumber=4441 __errno_location linenumber=4443 kputc_ /src/htslib/./htslib/kstring.h linenumber=4446 strlen linenumber=4448 kputsn /src/htslib/./htslib/kstring.h linenumber=4449 kputc_ /src/htslib/./htslib/kstring.h linenumber=4451 kputc_ /src/htslib/./htslib/kstring.h linenumber=4453 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4473 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4474 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4490 hts_log /src/htslib/hts.c linenumber=4490 __errno_location linenumber=4495 strlen linenumber=4501 ks_resize /src/htslib/./htslib/kstring.h linenumber=4503 bcf_fmt_array /src/htslib/vcf.c linenumber=4520 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4525 kputc_ /src/htslib/./htslib/kstring.h linenumber=4526 kputd /src/htslib/kstring.c linenumber=4528 kputc_ /src/htslib/./htslib/kstring.h linenumber=4530 kputc_ /src/htslib/./htslib/kstring.h linenumber=4539 kputw /src/htslib/./htslib/kstring.h linenumber=4541 kputc_ /src/htslib/./htslib/kstring.h linenumber=4544 kputll /src/htslib/./htslib/kstring.h linenumber=4546 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4548 hts_log /src/htslib/hts.c linenumber=4548 __errno_location linenumber=4549 kputc_ /src/htslib/./htslib/kstring.h linenumber=4554 kputc_ /src/htslib/./htslib/kstring.h linenumber=4555 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=4574 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4584 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4585 kputc_ /src/htslib/./htslib/kstring.h linenumber=4591 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4598 hts_log /src/htslib/hts.c linenumber=4598 __errno_location linenumber=4599 kputsn /src/htslib/./htslib/kstring.h linenumber=4608 kputsn /src/htslib/./htslib/kstring.h linenumber=4612 kputc_ /src/htslib/./htslib/kstring.h linenumber=4616 kputc_ /src/htslib/./htslib/kstring.h linenumber=4621 bcf_format_gt_v2 /src/htslib/vcf.c linenumber=4624 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6483 kputc /src/htslib/./htslib/kstring.h linenumber=6483 kputw /src/htslib/./htslib/kstring.h linenumber=6483 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6485 kputc /src/htslib/./htslib/kstring.h linenumber=6485 kputw /src/htslib/./htslib/kstring.h linenumber=6485 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6487 kputc /src/htslib/./htslib/kstring.h linenumber=6487 kputw /src/htslib/./htslib/kstring.h linenumber=6487 kputc /src/htslib/./htslib/kstring.h linenumber=6489 hts_log /src/htslib/hts.c linenumber=6490 get_hdr_aux /src/htslib/vcf.c linenumber=6494 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6504 ks_resize /src/htslib/./htslib/kstring.h linenumber=474 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6506 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6513 hts_log /src/htslib/hts.c linenumber=4625 __errno_location linenumber=4626 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4634 kputc_ /src/htslib/./htslib/kstring.h linenumber=3066 kputc_ /src/htslib/./htslib/kstring.h linenumber=3072 kputw /src/htslib/./htslib/kstring.h linenumber=3073 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3077 kputc_ /src/htslib/./htslib/kstring.h linenumber=3080 kputw /src/htslib/./htslib/kstring.h linenumber=3081 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3086 kputc_ /src/htslib/./htslib/kstring.h linenumber=3089 kputw /src/htslib/./htslib/kstring.h linenumber=3090 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3095 kputc_ /src/htslib/./htslib/kstring.h linenumber=3098 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3099 kputd /src/htslib/kstring.c linenumber=3099 bcf_fmt_array /src/htslib/vcf.c linenumber=4636 kputc_ /src/htslib/./htslib/kstring.h linenumber=4642 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4644 bcf_fmt_array /src/htslib/vcf.c linenumber=4646 kputc_ /src/htslib/./htslib/kstring.h linenumber=4648 kputsn /src/htslib/./htslib/kstring.h linenumber=4655 kputc /src/htslib/./htslib/kstring.h linenumber=4657 bgzf_flush_try /src/htslib/bgzf.c linenumber=4679 hts_idx_amend_last /src/htslib/hts.c linenumber=4682 bgzf_write /src/htslib/bgzf.c linenumber=4683 hwrite /src/htslib/./htslib/hfile.h linenumber=4685 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4690 hts_idx_tbi_name /src/htslib/hts.c linenumber=4690 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=4693 bcf_strerror /src/htslib/vcf.c linenumber=2607 add_desc_to_buffer /src/htslib/vcf.c linenumber=6431 strlen linenumber=6405 snprintf linenumber=6406 snprintf linenumber=6409 add_desc_to_buffer /src/htslib/vcf.c linenumber=6440 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2607 hts_log /src/htslib/hts.c linenumber=2607 bcf1_sync /src/htslib/vcf.c linenumber=2610 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=2614 hts_log /src/htslib/hts.c linenumber=2614 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2620 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2621 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2622 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2623 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2624 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2625 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2626 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2627 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2628 bgzf_write /src/htslib/bgzf.c linenumber=2629 bgzf_write /src/htslib/bgzf.c linenumber=2630 bgzf_write /src/htslib/bgzf.c linenumber=2631 bgzf_idx_push /src/htslib/bgzf.c linenumber=2634 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 ====================================