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=5201 get_severity_tag /src/htslib/hts.c linenumber=5205 fprintf linenumber=5205 vfprintf linenumber=5208 fprintf linenumber=5211 __errno_location linenumber=5213 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=1473 strdup linenumber=1480 ed_is_big /src/htslib/./htslib/hts.h linenumber=1481 strchr linenumber=1484 strncpy linenumber=1485 strncpy linenumber=1489 strchr linenumber=1493 hts_detect_format2 /src/htslib/hts.c linenumber=1496 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=1506 hopen_htsget_redirect /src/htslib/multipart.c linenumber=1511 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=5064 realloc linenumber=5068 __errno_location linenumber=5082 strerror linenumber=5082 hts_log /src/htslib/hts.c linenumber=5082 exit linenumber=5083 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=1516 __errno_location linenumber=522 hfile_destroy /src/htslib/hfile.c linenumber=526 __errno_location linenumber=527 hts_crypt4gh_redirect /src/htslib/hts.c linenumber=1524 strlen linenumber=1443 snprintf linenumber=1454 strchr linenumber=1455 snprintf linenumber=1455 hopen /src/htslib/hfile.c linenumber=1456 hts_detect_format2 /src/htslib/hts.c linenumber=1541 strchr linenumber=1544 strchr linenumber=1548 strchr linenumber=1549 strchr linenumber=1550 strchr linenumber=1551 strchr linenumber=1554 strchr linenumber=1555 strchr linenumber=1556 abort linenumber=1565 format_category /src/htslib/hts.c linenumber=1570 __errno_location linenumber=1576 bgzf_hopen /src/htslib/bgzf.c linenumber=1582 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=1588 calloc linenumber=5030 cram_read_file_def /src/htslib/cram/cram_io.c linenumber=5050 hread /src/htslib/cram/../htslib/hfile.h linenumber=4417 memcmp linenumber=4422 hts_log /src/htslib/hts.c linenumber=4428 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5056 cram_init_varint /src/htslib/cram/cram_io.c linenumber=4988 cram_read_SAM_hdr /src/htslib/cram/cram_io.c linenumber=5058 int32_decode /src/htslib/cram/cram_io.c linenumber=4475 hread /src/htslib/cram/../htslib/hfile.h linenumber=769 hread /src/htslib/cram/../htslib/hfile.h linenumber=4487 cram_read_container /src/htslib/cram/cram_io.c linenumber=4495 int32_decode /src/htslib/cram/cram_io.c linenumber=3568 crc32 linenumber=3579 calloc linenumber=3624 __errno_location linenumber=3630 cram_free_container /src/htslib/cram/cram_io.c linenumber=3631 cram_free_compression_header /src/htslib/cram/cram_io.c linenumber=3480 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=4110 cram_free_block /src/htslib/cram/cram_io.c linenumber=4140 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4142 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4144 cram_free_block /src/htslib/cram/cram_io.c linenumber=3483 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3489 free_bam_list /src/htslib/cram/cram_io.c linenumber=4171 bam_destroy1 /src/htslib/sam.c linenumber=3461 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=474 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=476 bam_get_mempolicy /src/htslib/./htslib/sam.h linenumber=484 cram_free_block /src/htslib/cram/cram_io.c linenumber=4176 cram_free_block /src/htslib/cram/cram_io.c linenumber=4185 cram_free_block /src/htslib/cram/cram_io.c linenumber=4196 cram_free_slice_header /src/htslib/cram/cram_io.c linenumber=4203 cram_free_block /src/htslib/cram/cram_io.c linenumber=4206 cram_free_block /src/htslib/cram/cram_io.c linenumber=4209 cram_free_block /src/htslib/cram/cram_io.c linenumber=4212 cram_free_block /src/htslib/cram/cram_io.c linenumber=4215 cram_free_block /src/htslib/cram/cram_io.c linenumber=4218 cram_free_block /src/htslib/cram/cram_io.c linenumber=4221 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=4236 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4239 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4241 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3498 cram_stats_free /src/htslib/cram/cram_stats.c linenumber=3503 kh_destroy_m_i2i /src/htslib/cram/cram_structs.h linenumber=214 cram_free_block /src/htslib/cram/cram_io.c linenumber=3525 cram_free_block /src/htslib/cram/cram_io.c linenumber=3526 kh_destroy_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3531 free_bam_list /src/htslib/cram/cram_io.c linenumber=3538 cram_free_container /src/htslib/cram/cram_io.c linenumber=3641 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=3644 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=3645 cram_free_container /src/htslib/cram/cram_io.c linenumber=3646 cram_free_container /src/htslib/cram/cram_io.c linenumber=3651 int32_decode /src/htslib/cram/cram_io.c linenumber=3659 cram_free_container /src/htslib/cram/cram_io.c linenumber=3660 hts_log /src/htslib/hts.c linenumber=3672 cram_free_container /src/htslib/cram/cram_io.c linenumber=3673 cram_free_container /src/htslib/cram/cram_io.c linenumber=4507 cram_read_block /src/htslib/cram/cram_io.c linenumber=4511 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1185 hts_log /src/htslib/hts.c linenumber=1187 crc32 linenumber=1190 hgetc /src/htslib/cram/../htslib/hfile.h linenumber=1191 crc32 linenumber=1192 hread /src/htslib/cram/../htslib/hfile.h linenumber=1207 hread /src/htslib/cram/../htslib/hfile.h linenumber=1219 int32_decode /src/htslib/cram/cram_io.c linenumber=1227 cram_free_container /src/htslib/cram/cram_io.c linenumber=4512 cram_uncompress_block /src/htslib/cram/cram_io.c linenumber=4515 crc32 linenumber=1348 hts_log /src/htslib/hts.c linenumber=1351 __assert_fail linenumber=1361 zlib_mem_inflate /src/htslib/cram/cram_io.c linenumber=1369 inflateInit2_ linenumber=942 hts_log /src/htslib/hts.c linenumber=944 inflate linenumber=955 hts_log /src/htslib/hts.c linenumber=960 inflateEnd linenumber=962 realloc linenumber=968 inflateEnd linenumber=971 inflateEnd linenumber=976 BZ2_bzBuffToBuffDecompress linenumber=1388 lzma_mem_inflate /src/htslib/cram/cram_io.c linenumber=1409 lzma_easy_decoder_memusage linenumber=1082 lzma_stream_decoder linenumber=1082 realloc linenumber=1092 lzma_code linenumber=1100 hts_log /src/htslib/hts.c linenumber=1102 lzma_code linenumber=1113 hts_log /src/htslib/hts.c linenumber=1115 realloc linenumber=1119 lzma_end linenumber=1124 lzma_end linenumber=1129 rans_uncompress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1430 rans_uncompress_O1 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=848 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=635 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=177 pthread_once linenumber=122 htscodecs_tls_init /src/htslib/htscodecs/htscodecs/utils.c linenumber=122 pthread_key_create linenumber=104 htscodecs_tls_free_all /src/htslib/htscodecs/htscodecs/utils.c linenumber=104 fprintf linenumber=95 strerror linenumber=125 fprintf linenumber=124 pthread_getspecific linenumber=130 calloc linenumber=132 pthread_setspecific linenumber=134 fprintf linenumber=156 calloc linenumber=162 RansDecSymbolInit32 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=683 __assert_fail linenumber=558 __assert_fail linenumber=559 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=730 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=731 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=732 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=733 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=779 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=780 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=781 RansDecAdvanceStep /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=782 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=787 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=788 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=790 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=791 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=792 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=793 RansDecGet /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=809 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=814 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=821 pthread_getspecific linenumber=187 fprintf linenumber=199 fprintf linenumber=204 rans_uncompress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=849 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=314 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=315 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=316 RansDecInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=317 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=348 RansDecRenorm2 /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=349 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=351 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=352 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=353 RansDecRenormSafe /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=354 fqz_decompress /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1448 uncompress_block_fqz2f /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1628 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1470 fqz_read_parameters 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/src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=333 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=335 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1503 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1504 realloc linenumber=1536 realloc linenumber=1537 decompress_new_read /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1543 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1395 RC_GetFreq /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=142 RC_Decode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=155 SIMPLE_MODEL256_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=160 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1409 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1410 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1411 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1412 SIMPLE_MODEL2_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1423 SIMPLE_MODEL2_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=160 SIMPLE_MODEL2_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1429 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=1556 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1559 realloc linenumber=1567 realloc linenumber=1568 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1591 fqz_destroy_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1594 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=341 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1597 fqz_destroy_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1606 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1609 rans_uncompress_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1461 rans_uncompress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1877 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1600 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1627 rans_uncompress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1659 unstripe /src/htslib/htscodecs/htscodecs/utils.h linenumber=1668 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1686 hts_unpack_meta /src/htslib/htscodecs/htscodecs/pack.c linenumber=1768 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1779 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1792 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1793 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1801 rans_dec_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1804 pthread_once linenumber=1025 htscodecs_tls_cpu_init /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1025 __get_cpuid_max /usr/local/lib/clang/22/include/cpuid.h linenumber=878 not_ancient_darwin /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=926 strerror linenumber=1028 fprintf linenumber=1027 fprintf linenumber=1029 rans_dec_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1826 hts_rle_decode /src/htslib/htscodecs/htscodecs/rle.c linenumber=1843 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=169 hts_unpack /src/htslib/htscodecs/htscodecs/pack.c linenumber=1857 arith_uncompress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1480 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1048 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1071 arith_uncompress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1103 unstripe /src/htslib/htscodecs/htscodecs/utils.h linenumber=1112 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1130 hts_unpack_meta /src/htslib/htscodecs/htscodecs/pack.c linenumber=1190 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1201 BZ2_bzBuffToBuffDecompress linenumber=1227 arith_uncompress_O1_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1238 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=673 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=679 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=682 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=684 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=689 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=691 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=692 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=696 SIMPLE_MODEL258_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=702 SIMPLE_MODEL258_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=160 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=713 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=714 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=715 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=720 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=721 arith_uncompress_O0_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1239 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=531 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=534 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=541 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=543 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=544 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=548 SIMPLE_MODEL258_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=552 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=564 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=565 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=570 arith_uncompress_O1 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1245 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=239 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=247 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=249 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=250 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=254 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=258 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=259 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=264 arith_uncompress_O0 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1246 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=147 RC_SetInput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=155 RC_StartDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=156 SIMPLE_MODEL256_decodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=159 RC_FinishDecode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=161 hts_unpack /src/htslib/htscodecs/htscodecs/pack.c linenumber=1261 tok3_decode_names /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1499 create_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1698 fprintf linenumber=185 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=189 uncompressed_size /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1773 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1421 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1424 uncompress /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1790 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1432 arith_decode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1434 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1230 arith_uncompress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1232 rans_decode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1435 var_get_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1257 rans_uncompress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1259 decode_name /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1816 decode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1022 decode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1032 strlen linenumber=1042 strcpy linenumber=1043 strlen linenumber=1055 decode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1067 decode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1075 decode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1082 decode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1092 decode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1093 append_uint32_fixed /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1095 decode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1104 append_uint32_fixed /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1107 decode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1115 append_uint32_var /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1117 decode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1125 append_uint32_var /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1128 append_uint32_var /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1164 append_uint32_fixed /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1172 realloc linenumber=1194 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1824 pool_destroy /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=218 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=227 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1830 cram_free_container /src/htslib/cram/cram_io.c linenumber=4516 cram_free_block /src/htslib/cram/cram_io.c linenumber=4517 int32_get_blk /src/htslib/cram/cram_io.c linenumber=4527 cram_free_container /src/htslib/cram/cram_io.c linenumber=4530 cram_free_block /src/htslib/cram/cram_io.c linenumber=4531 cram_free_container /src/htslib/cram/cram_io.c linenumber=4535 cram_free_block /src/htslib/cram/cram_io.c linenumber=4536 cram_free_block /src/htslib/cram/cram_io.c linenumber=4541 cram_read_block /src/htslib/cram/cram_io.c linenumber=4545 cram_free_container /src/htslib/cram/cram_io.c linenumber=4546 cram_free_block /src/htslib/cram/cram_io.c linenumber=4554 cram_free_container /src/htslib/cram/cram_io.c linenumber=4561 hread /src/htslib/cram/../htslib/hfile.h linenumber=4566 cram_free_container /src/htslib/cram/cram_io.c linenumber=4567 cram_free_container /src/htslib/cram/cram_io.c linenumber=4575 sam_hdr_init /src/htslib/sam.c linenumber=4579 calloc linenumber=112 sam_hdr_add_lines /src/htslib/header.c linenumber=4585 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1668 sam_hrecs_new /src/htslib/header.c linenumber=1291 calloc linenumber=2735 kh_init_sam_hrecs_t /src/htslib/./header.h linenumber=2740 calloc linenumber=168 kh_init_m_s2i /src/htslib/./header.h linenumber=2749 calloc linenumber=169 kh_init_m_s2i /src/htslib/./header.h linenumber=2756 kh_init_m_s2i /src/htslib/./header.h linenumber=2764 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2767 next_power_2 /src/htslib/cram/pooled_alloc.c linenumber=76 pool_create /src/htslib/cram/pooled_alloc.c linenumber=2770 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2773 sam_hrecs_init_type_order /src/htslib/header.c linenumber=2776 calloc linenumber=76 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2783 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2786 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2789 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2792 sam_hrecs_refs_from_targets_array /src/htslib/header.c linenumber=1297 hts_log /src/htslib/hts.c linenumber=1193 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1198 hts_prod_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=295 hts_realloc /src/htslib/./htslib/hts_alloc.h linenumber=296 __errno_location linenumber=268 realloc linenumber=271 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1207 kh_resize_m_s2i /src/htslib/./header.h linenumber=169 __errno_location linenumber=169 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=169 string_dup /src/htslib/cram/string_alloc.c linenumber=1213 strlen linenumber=154 string_ndup /src/htslib/cram/string_alloc.c linenumber=154 string_alloc /src/htslib/cram/string_alloc.c linenumber=158 new_string_pool /src/htslib/cram/string_alloc.c linenumber=142 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=81 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=295 hts_realloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=296 hts_malloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=94 kh_get_s2i /src/htslib/hts.c linenumber=1219 __ac_FNV1a_hash_string /src/htslib/./cram/../htslib/khash.h linenumber=80 strcmp linenumber=80 kh_put_m_s2i /src/htslib/./header.h linenumber=1227 strcmp linenumber=169 hts_log /src/htslib/hts.c linenumber=1230 __errno_location linenumber=1242 strerror linenumber=1242 hts_log /src/htslib/hts.c linenumber=1242 kh_get_m_s2i /src/htslib/./header.h linenumber=1246 kh_del_m_s2i /src/htslib/./header.h linenumber=1247 sam_hrecs_free /src/htslib/header.c linenumber=1298 kh_destroy_sam_hrecs_t /src/htslib/./header.h linenumber=2819 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2822 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2828 kh_destroy_m_s2i /src/htslib/./header.h linenumber=2834 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2843 pool_destroy /src/htslib/cram/pooled_alloc.c linenumber=2846 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2849 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1305 strlen linenumber=1003 sam_hrecs_error /src/htslib/header.c linenumber=1007 hts_log /src/htslib/hts.c linenumber=65 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1018 sam_hrecs_error /src/htslib/header.c linenumber=920 isalpha_c /src/htslib/./textutils_internal.h linenumber=925 __ctype_b_loc linenumber=170 sam_hrecs_error /src/htslib/header.c linenumber=926 TYPEKEY /src/htslib/./header.h linenumber=930 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=936 new_pool /src/htslib/cram/pooled_alloc.c linenumber=138 hts_realloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=101 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=320 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=321 hts_realloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=322 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=106 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=941 kh_resize_sam_hrecs_t /src/htslib/./header.h linenumber=168 realloc linenumber=168 TYPEKEY /src/htslib/./header.h linenumber=948 parse_comment_line /src/htslib/header.c linenumber=950 sam_hrecs_error /src/htslib/header.c linenumber=807 warn_if_known_stderr /src/htslib/header.c linenumber=808 kmemmem /src/htslib/kstring.c linenumber=791 boyer_moore /src/htslib/kstring.c linenumber=499 memchr linenumber=468 ksBM_prep /src/htslib/kstring.c linenumber=473 hts_calloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=411 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=228 hts_calloc /src/htslib/./htslib/hts_alloc.h linenumber=229 __errno_location linenumber=201 calloc linenumber=204 calloc linenumber=418 karp_rabin /src/htslib/kstring.c linenumber=474 fast_exp /src/htslib/kstring.c linenumber=373 memcmp linenumber=393 known_stderr /src/htslib/header.c linenumber=792 hts_log /src/htslib/hts.c linenumber=782 hts_log /src/htslib/hts.c linenumber=783 kmemmem /src/htslib/kstring.c linenumber=793 known_stderr /src/htslib/header.c linenumber=794 kmemmem /src/htslib/kstring.c linenumber=795 known_stderr /src/htslib/header.c linenumber=796 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=815 string_ndup /src/htslib/cram/string_alloc.c linenumber=817 parse_noncomment_line /src/htslib/header.c linenumber=957 TYPEKEY /src/htslib/./header.h linenumber=832 sam_hrecs_error /src/htslib/header.c linenumber=842 warn_if_known_stderr /src/htslib/header.c linenumber=843 sam_hrecs_error /src/htslib/header.c linenumber=853 warn_if_known_stderr /src/htslib/header.c linenumber=854 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=866 string_ndup /src/htslib/cram/string_alloc.c linenumber=868 sam_hrecs_global_list_add /src/htslib/header.c linenumber=965 TYPEKEY /src/htslib/./header.h linenumber=504 __assert_fail linenumber=972 sam_hrecs_free_tags /src/htslib/header.c linenumber=989 sam_hrecs_free_tags /src/htslib/header.c linenumber=699 pool_free /src/htslib/cram/pooled_alloc.c linenumber=701 pool_free /src/htslib/cram/pooled_alloc.c linenumber=990 TYPEKEY /src/htslib/./header.h linenumber=1030 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1045 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1049 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1063 TYPEKEY /src/htslib/./header.h linenumber=146 __assert_fail linenumber=157 __assert_fail linenumber=160 strtoll linenumber=162 __assert_fail linenumber=167 hts_log /src/htslib/hts.c linenumber=174 hts_log /src/htslib/hts.c linenumber=179 hts_log /src/htslib/hts.c linenumber=185 kh_get_m_s2i /src/htslib/./header.h linenumber=191 snprintf linenumber=203 sam_hrecs_update /src/htslib/header.c linenumber=205 sam_hrecs_vupdate /src/htslib/header.c linenumber=2996 sam_hrecs_find_key /src/htslib/header.c linenumber=2954 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=2956 strlen linenumber=2966 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=2967 string_alloc /src/htslib/cram/string_alloc.c linenumber=2967 snprintf linenumber=2971 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=209 kstrtok /src/htslib/kstring.c linenumber=96 strchr linenumber=216 strlen linenumber=217 string_ndup /src/htslib/cram/string_alloc.c linenumber=100 kh_put_m_s2i /src/htslib/./header.h linenumber=104 hts_log /src/htslib/hts.c linenumber=110 strcmp linenumber=223 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=227 strcmp linenumber=237 hts_log /src/htslib/hts.c linenumber=238 hts_log /src/htslib/hts.c linenumber=246 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=252 kh_put_m_s2i /src/htslib/./header.h linenumber=263 sam_hrecs_add_ref_altnames /src/htslib/header.c linenumber=267 TYPEKEY /src/htslib/./header.h linenumber=276 sam_hrecs_find_key /src/htslib/header.c linenumber=277 hts_log /src/htslib/hts.c linenumber=282 __assert_fail linenumber=285 kh_get_m_s2i /src/htslib/./header.h linenumber=288 __assert_fail linenumber=291 hts_log /src/htslib/hts.c linenumber=293 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=304 kh_put_m_s2i /src/htslib/./header.h linenumber=316 TYPEKEY /src/htslib/./header.h linenumber=324 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=331 __assert_fail linenumber=349 hts_log /src/htslib/hts.c linenumber=353 kh_get_m_s2i /src/htslib/./header.h linenumber=358 kh_put_m_s2i /src/htslib/./header.h linenumber=388 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=400 sam_hrecs_free /src/htslib/header.c linenumber=1306 add_stub_ref_sq_lines /src/htslib/header.c linenumber=1311 snprintf linenumber=1273 sam_hrecs_add /src/htslib/header.c linenumber=1274 sam_hrecs_vadd /src/htslib/header.c linenumber=686 TYPEKEY /src/htslib/./header.h linenumber=558 strncmp linenumber=560 sam_hrecs_find_type_id /src/htslib/header.c linenumber=560 kh_get_m_s2i /src/htslib/./header.h linenumber=2881 kh_get_m_s2i /src/htslib/./header.h linenumber=2889 kh_get_m_s2i /src/htslib/./header.h linenumber=2897 TYPEKEY /src/htslib/./header.h linenumber=2904 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=2904 sam_hrecs_vupdate /src/htslib/header.c linenumber=561 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=563 kh_put_sam_hrecs_t /src/htslib/./header.h linenumber=565 __assert_fail linenumber=576 sam_hrecs_global_list_add /src/htslib/header.c linenumber=590 __assert_fail linenumber=593 __assert_fail linenumber=594 __assert_fail linenumber=595 __assert_fail linenumber=596 strncmp linenumber=605 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=610 strncmp linenumber=613 strlen linenumber=614 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=615 string_alloc /src/htslib/cram/string_alloc.c linenumber=615 snprintf linenumber=616 strlen linenumber=620 string_ndup /src/htslib/cram/string_alloc.c linenumber=621 strncmp linenumber=642 pool_alloc /src/htslib/cram/pooled_alloc.c linenumber=645 strncmp linenumber=648 strlen linenumber=649 hts_add_sat2 /src/htslib/./htslib/hts_alloc.h linenumber=650 string_alloc /src/htslib/cram/string_alloc.c linenumber=650 snprintf linenumber=651 strlen linenumber=655 string_ndup /src/htslib/cram/string_alloc.c linenumber=656 TYPEKEY /src/htslib/./header.h linenumber=670 sam_hrecs_update_hashes /src/htslib/header.c linenumber=670 strncmp linenumber=673 hts_log /src/htslib/hts.c linenumber=1281 sam_hrecs_free /src/htslib/header.c linenumber=1312 rebuild_target_arrays /src/htslib/header.c linenumber=1318 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1162 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1084 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1089 strcmp linenumber=1104 strdup linenumber=1107 kh_get_s2i /src/htslib/hts.c linenumber=1118 kh_del_s2i /src/htslib/hts.c linenumber=1120 kh_init_s2i /src/htslib/hts.c linenumber=1126 calloc linenumber=80 kh_put_s2i /src/htslib/hts.c linenumber=1132 kh_resize_s2i /src/htslib/hts.c linenumber=80 __errno_location linenumber=80 realloc linenumber=80 kh_get_s2i /src/htslib/hts.c linenumber=1143 kh_del_s2i /src/htslib/hts.c linenumber=1145 sam_hrecs_parse_lines /src/htslib/header.c linenumber=1673 rebuild_target_arrays /src/htslib/header.c linenumber=1676 redact_header_text /src/htslib/header.c linenumber=1680 __assert_fail linenumber=1532 sam_hdr_destroy /src/htslib/sam.c linenumber=4587 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=5059 calloc linenumber=5065 strncpy linenumber=5078 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5081 strrchr linenumber=5086 strdup linenumber=5086 refs_create /src/htslib/cram/cram_io.c linenumber=5094 calloc linenumber=2230 string_pool_create /src/htslib/cram/string_alloc.c linenumber=2237 kh_init_refs /src/htslib/cram/cram_structs.h linenumber=2245 calloc linenumber=684 pthread_mutex_init linenumber=2248 refs_free /src/htslib/cram/cram_io.c linenumber=2253 string_pool_destroy /src/htslib/cram/string_alloc.c linenumber=2199 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2211 mfclose /src/htslib/cram/mFILE.c linenumber=2181 mfflush /src/htslib/cram/mFILE.c linenumber=365 fwrite linenumber=615 fflush linenumber=617 fseek linenumber=630 fwrite linenumber=632 fflush linenumber=634 ftell linenumber=637 fileno linenumber=638 ftell linenumber=638 ftruncate linenumber=638 munmap linenumber=370 fclose linenumber=376 mfdestroy /src/htslib/cram/mFILE.c linenumber=378 kh_destroy_refs /src/htslib/cram/cram_structs.h linenumber=2215 bgzf_close /src/htslib/bgzf.c linenumber=2222 bgzf_flush /src/htslib/bgzf.c linenumber=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=2224 pthread_mutex_init linenumber=5130 pthread_mutex_init linenumber=5131 pthread_mutex_init linenumber=5132 pthread_mutex_init linenumber=5133 cram_new_metrics /src/htslib/cram/cram_io.c linenumber=5136 calloc linenumber=2090 kh_init_m_metrics /src/htslib/cram/cram_structs.h linenumber=5141 calloc linenumber=294 refs_from_header /src/htslib/cram/cram_io.c linenumber=5151 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2543 hts_realloc_ps /src/htslib/cram/../htslib/hts_alloc.h linenumber=2553 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2567 __ac_FNV1a_hash_string /src/htslib/cram/../htslib/khash.h linenumber=684 strcmp linenumber=684 calloc linenumber=2572 string_dup /src/htslib/cram/string_alloc.c linenumber=2578 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2583 sam_hrecs_find_key /src/htslib/header.c linenumber=2584 string_dup /src/htslib/cram/string_alloc.c linenumber=2585 sam_hrecs_find_key /src/htslib/header.c linenumber=2587 strtoll linenumber=2589 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2596 kh_resize_refs /src/htslib/cram/cram_structs.h linenumber=684 __errno_location linenumber=684 realloc linenumber=684 cram_set_option /src/htslib/cram/cram_io.c linenumber=1591 cram_set_voption /src/htslib/cram/cram_io.c linenumber=5408 __errno_location linenumber=5425 strdup linenumber=5437 refs_free /src/htslib/cram/cram_io.c linenumber=5513 cram_seek_to_refpos /src/htslib/cram/cram_index.c linenumber=5520 cram_index_query /src/htslib/cram/cram_index.c linenumber=589 cram_seek /src/htslib/cram/cram_io.c linenumber=590 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5172 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=5174 pthread_mutex_lock linenumber=598 pthread_mutex_unlock linenumber=606 cram_free_container /src/htslib/cram/cram_io.c linenumber=609 cram_free_container /src/htslib/cram/cram_io.c linenumber=611 pthread_mutex_lock linenumber=623 pthread_mutex_unlock linenumber=625 pthread_mutex_lock linenumber=5521 pthread_mutex_unlock linenumber=5526 pthread_mutex_lock linenumber=5532 pthread_mutex_unlock linenumber=5545 cram_load_reference /src/htslib/cram/cram_io.c linenumber=5550 refs_load_fai /src/htslib/cram/cram_io.c linenumber=3364 strlen linenumber=2308 refs_create /src/htslib/cram/cram_io.c linenumber=2314 bgzf_close /src/htslib/bgzf.c linenumber=2318 strstr linenumber=2323 string_ndup /src/htslib/cram/string_alloc.c linenumber=2325 snprintf linenumber=2328 strcmp linenumber=2331 string_ndup /src/htslib/cram/string_alloc.c linenumber=2333 snprintf linenumber=2336 string_dup /src/htslib/cram/string_alloc.c linenumber=2339 snprintf linenumber=2341 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=2345 strncmp linenumber=2268 hisremote /src/htslib/hfile.c linenumber=2271 find_scheme_handler /src/htslib/hfile.c linenumber=1347 snprintf linenumber=2274 access linenumber=2275 fai_build /src/htslib/faidx.c linenumber=2276 fai_build3 /src/htslib/faidx.c linenumber=597 fai_build3_core /src/htslib/faidx.c linenumber=592 bgzf_open /src/htslib/bgzf.c linenumber=504 strchr linenumber=515 hopen /src/htslib/hfile.c linenumber=517 bgzf_read_init /src/htslib/bgzf.c linenumber=518 hclose_abruptly /src/htslib/hfile.c linenumber=519 strchr linenumber=521 hopen /src/htslib/hfile.c linenumber=523 bgzf_write_init /src/htslib/bgzf.c linenumber=524 __errno_location linenumber=528 ed_is_big /src/htslib/./htslib/hts.h linenumber=530 __errno_location linenumber=507 strerror linenumber=507 hts_log /src/htslib/hts.c linenumber=507 bgzf_index_build_init /src/htslib/bgzf.c linenumber=512 bgzf_index_destroy /src/htslib/bgzf.c linenumber=2386 calloc linenumber=2387 hts_log /src/htslib/hts.c linenumber=513 fai_build_core /src/htslib/faidx.c linenumber=518 calloc linenumber=171 kh_init_s /src/htslib/faidx.c linenumber=172 bgzf_getc_ /src/htslib/faidx.c linenumber=178 bgzf_getc /src/htslib/bgzf.c linenumber=66 bgzf_read_block /src/htslib/bgzf.c linenumber=2325 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=1034 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=1035 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1039 mt_destroy /src/htslib/bgzf.c linenumber=1043 hts_log /src/htslib/hts.c linenumber=1056 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1059 hts_log /src/htslib/hts.c linenumber=1066 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1076 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1090 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1092 pthread_mutex_lock linenumber=1101 pool_free /src/htslib/cram/pooled_alloc.c linenumber=1102 pthread_mutex_unlock linenumber=1103 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=1112 bgzf_htell /src/htslib/bgzf.c linenumber=1123 pthread_mutex_lock linenumber=1012 pthread_mutex_unlock linenumber=1014 htell /src/htslib/./htslib/hfile.h linenumber=1017 hread /src/htslib/./htslib/hfile.h linenumber=1128 __errno_location linenumber=1131 strerror linenumber=1131 hts_log /src/htslib/hts.c linenumber=1131 inflate_gzip_block /src/htslib/bgzf.c linenumber=1151 hread /src/htslib/./htslib/hfile.h linenumber=861 inflate linenumber=875 bgzf_zerr /src/htslib/bgzf.c linenumber=879 hts_log /src/htslib/hts.c linenumber=879 hpeek /src/htslib/hfile.c linenumber=887 inflateReset linenumber=889 bgzf_zerr /src/htslib/bgzf.c linenumber=891 hts_log /src/htslib/hts.c linenumber=891 hts_log /src/htslib/hts.c linenumber=902 hts_log /src/htslib/hts.c linenumber=1154 load_block_from_cache /src/htslib/bgzf.c linenumber=1163 kh_get_bgzf_cache /src/htslib/bgzf.c linenumber=941 hseek /src/htslib/hfile.c linenumber=948 hts_log /src/htslib/hts.c linenumber=951 exit linenumber=952 hread /src/htslib/./htslib/hfile.h linenumber=1168 hts_log /src/htslib/hts.c linenumber=1172 check_header /src/htslib/bgzf.c linenumber=1178 unpackInt16 /src/htslib/bgzf.c linenumber=917 unpackInt16 /src/htslib/bgzf.c linenumber=919 hts_log /src/htslib/hts.c linenumber=1181 hread /src/htslib/./htslib/hfile.h linenumber=1191 calloc linenumber=1194 inflateInit2_ linenumber=1196 bgzf_zerr /src/htslib/bgzf.c linenumber=1199 hts_log /src/htslib/hts.c linenumber=1199 inflate_gzip_block /src/htslib/bgzf.c linenumber=1205 hts_log /src/htslib/hts.c linenumber=1208 unpackInt16 /src/htslib/bgzf.c linenumber=1219 hts_log /src/htslib/hts.c linenumber=1222 hread /src/htslib/./htslib/hfile.h linenumber=1230 hts_log /src/htslib/hts.c linenumber=1232 inflate_block /src/htslib/bgzf.c linenumber=1239 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=828 bgzf_uncompress /src/htslib/bgzf.c linenumber=829 inflateInit2_ linenumber=792 bgzf_zerr /src/htslib/bgzf.c linenumber=794 hts_log /src/htslib/hts.c linenumber=794 inflate linenumber=797 bgzf_zerr /src/htslib/bgzf.c linenumber=798 hts_log /src/htslib/hts.c linenumber=798 inflateEnd linenumber=799 bgzf_zerr /src/htslib/bgzf.c linenumber=800 hts_log /src/htslib/hts.c linenumber=800 inflateEnd linenumber=804 bgzf_zerr /src/htslib/bgzf.c linenumber=805 hts_log /src/htslib/hts.c linenumber=805 crc32 linenumber=810 hts_log /src/htslib/hts.c linenumber=816 bgzf_zerr /src/htslib/bgzf.c linenumber=1240 hts_log /src/htslib/hts.c linenumber=1240 bgzf_htell /src/htslib/bgzf.c linenumber=1248 bgzf_index_add_block /src/htslib/bgzf.c linenumber=1255 cache_block /src/htslib/bgzf.c linenumber=1261 kh_del_bgzf_cache /src/htslib/bgzf.c linenumber=986 kh_put_bgzf_cache /src/htslib/bgzf.c linenumber=992 kh_resize_bgzf_cache /src/htslib/bgzf.c linenumber=87 __errno_location linenumber=87 realloc linenumber=87 bgzf_htell /src/htslib/bgzf.c linenumber=2330 hts_log /src/htslib/hts.c linenumber=184 hts_log /src/htslib/hts.c linenumber=194 bgzf_getc_ /src/htslib/faidx.c linenumber=204 hts_log /src/htslib/hts.c linenumber=207 __ctype_b_loc linenumber=219 hts_log /src/htslib/hts.c linenumber=219 fai_insert_index /src/htslib/faidx.c linenumber=227 hts_log /src/htslib/hts.c linenumber=100 hts_log /src/htslib/hts.c linenumber=104 hts_log /src/htslib/hts.c linenumber=108 hts_log /src/htslib/hts.c linenumber=113 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=122 hts_log /src/htslib/hts.c linenumber=123 strdup linenumber=130 __errno_location linenumber=132 strerror linenumber=132 hts_log /src/htslib/hts.c linenumber=132 kh_put_s /src/htslib/faidx.c linenumber=137 kh_resize_s /src/htslib/faidx.c linenumber=80 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=80 __errno_location linenumber=139 strerror linenumber=139 hts_log /src/htslib/hts.c linenumber=139 hts_log /src/htslib/hts.c linenumber=144 __ctype_b_loc linenumber=236 kputc_ /src/htslib/./htslib/kstring.h linenumber=237 ks_resize /src/htslib/./htslib/kstring.h linenumber=270 bgzf_getc_ /src/htslib/faidx.c linenumber=242 kputsn /src/htslib/./htslib/kstring.h linenumber=244 hts_log /src/htslib/hts.c linenumber=248 bgzf_getc_ /src/htslib/faidx.c linenumber=253 bgzf_utell /src/htslib/bgzf.c linenumber=256 bgzf_getc_ /src/htslib/faidx.c linenumber=273 bgzf_utell /src/htslib/bgzf.c linenumber=274 hts_log /src/htslib/hts.c linenumber=278 isgraph_ /src/htslib/faidx.c linenumber=289 bgzf_getc_ /src/htslib/faidx.c linenumber=290 hts_log /src/htslib/hts.c linenumber=305 bgzf_getc_ /src/htslib/faidx.c linenumber=315 bgzf_utell /src/htslib/bgzf.c linenumber=316 hts_log /src/htslib/hts.c linenumber=319 hts_log /src/htslib/hts.c linenumber=327 isgraph_ /src/htslib/faidx.c linenumber=343 bgzf_getc_ /src/htslib/faidx.c linenumber=344 hts_log /src/htslib/hts.c linenumber=349 hts_log /src/htslib/hts.c linenumber=354 hts_log /src/htslib/hts.c linenumber=357 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=2280 perror linenumber=2281 bgzf_index_load /src/htslib/bgzf.c linenumber=2285 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=2286 bgzf_close /src/htslib/bgzf.c linenumber=2287 hts_log /src/htslib/hts.c linenumber=2346 hopen /src/htslib/hfile.c linenumber=2350 hts_log /src/htslib/hts.c linenumber=2351 perror linenumber=2353 hgets /src/htslib/hfile.c linenumber=2356 __errno_location linenumber=294 hgetln /src/htslib/./htslib/hfile.h linenumber=297 hgetdelim /src/htslib/hfile.c linenumber=198 __errno_location linenumber=248 writebuffer_is_nonempty /src/htslib/hfile.c linenumber=251 __errno_location linenumber=252 memchr linenumber=263 refill_buffer /src/htslib/hfile.c linenumber=282 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2366 string_dup /src/htslib/cram/string_alloc.c linenumber=2369 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2372 strtoll linenumber=2374 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2377 strtoll linenumber=2379 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2382 strtol linenumber=2384 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=2387 strtol linenumber=2389 kh_put_refs /src/htslib/cram/cram_structs.h linenumber=2400 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=2426 hclose /src/htslib/hfile.c linenumber=2438 hclose_abruptly /src/htslib/hfile.c linenumber=2444 refs_free /src/htslib/cram/cram_io.c linenumber=2447 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=3369 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2466 strcmp linenumber=2478 __assert_fail linenumber=2478 hts_log /src/htslib/hts.c linenumber=2482 refs_free /src/htslib/cram/cram_io.c linenumber=3375 refs_create /src/htslib/cram/cram_io.c linenumber=3376 refs_from_header /src/htslib/cram/cram_io.c linenumber=3378 refs2id /src/htslib/cram/cram_io.c linenumber=3383 kh_get_refs /src/htslib/cram/cram_structs.h linenumber=2514 hts_log /src/htslib/hts.c linenumber=2518 __isoc99_sscanf linenumber=5555 hts_log /src/htslib/hts.c linenumber=5556 hts_log /src/htslib/hts.c linenumber=5562 __errno_location linenumber=5564 cram_init_tables /src/htslib/cram/cram_io.c linenumber=5574 hts_tpool_init /src/htslib/thread_pool.c linenumber=5588 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=5591 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=5605 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=5604 hts_log /src/htslib/hts.c linenumber=5675 __errno_location linenumber=5676 bgzf_hopen /src/htslib/bgzf.c linenumber=1603 __errno_location linenumber=1612 hts_process_opts /src/htslib/hts.c linenumber=1617 hts_parse_opt_list /src/htslib/hts.c linenumber=1423 strncpy linenumber=1319 hts_opt_add /src/htslib/hts.c linenumber=1322 strdup linenumber=1039 strchr linenumber=1044 strcmp linenumber=1049 strcmp linenumber=1050 atoi linenumber=1051 strcmp linenumber=1053 strcmp linenumber=1054 atoi linenumber=1055 strcmp linenumber=1057 strcmp linenumber=1058 atoi linenumber=1059 strcmp linenumber=1061 strcmp linenumber=1062 atoi linenumber=1063 strcmp linenumber=1065 strcmp linenumber=1066 atoi linenumber=1067 strcmp linenumber=1069 strcmp linenumber=1070 atoi linenumber=1071 strcmp linenumber=1073 strcmp linenumber=1074 atoi linenumber=1075 strcmp linenumber=1077 strcmp linenumber=1078 atoi linenumber=1079 strcmp linenumber=1081 strcmp linenumber=1082 atoi linenumber=1083 strcmp linenumber=1085 strcmp linenumber=1086 atoi linenumber=1087 strcmp linenumber=1089 strcmp linenumber=1090 atoi linenumber=1091 strcmp linenumber=1093 strcmp linenumber=1094 atoi linenumber=1095 strcmp linenumber=1097 strcmp linenumber=1098 atoi linenumber=1099 strcmp linenumber=1101 strcmp linenumber=1102 atoi linenumber=1103 strcmp linenumber=1105 strcmp linenumber=1106 atoi linenumber=1107 strcmp linenumber=1109 strcmp linenumber=1110 strcmp linenumber=1113 strcmp linenumber=1114 strcmp linenumber=1117 strcmp linenumber=1118 strcmp linenumber=1121 strcmp linenumber=1122 strcmp linenumber=1125 strcmp linenumber=1126 strcmp linenumber=1129 strcmp linenumber=1130 strcmp linenumber=1133 strcmp linenumber=1134 atoi linenumber=1135 strcmp linenumber=1137 strcmp linenumber=1138 atoi linenumber=1139 strcmp linenumber=1141 strcmp linenumber=1142 strtol linenumber=1145 strcmp linenumber=1161 strcmp linenumber=1162 strtol linenumber=1163 strcmp linenumber=1165 strcmp linenumber=1166 strtol linenumber=1167 strcmp linenumber=1169 strcmp linenumber=1170 strcmp linenumber=1173 strcmp linenumber=1174 atoi linenumber=1175 strcmp linenumber=1177 strcmp linenumber=1178 atoi linenumber=1179 strcmp linenumber=1181 strcmp linenumber=1182 strtol linenumber=1183 strcmp linenumber=1185 strcmp linenumber=1186 strtol linenumber=1187 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 strcmp linenumber=1217 strcmp linenumber=1218 strcmp linenumber=1221 strcmp linenumber=1222 atoi linenumber=1223 hts_log /src/htslib/hts.c linenumber=1226 hts_opt_apply /src/htslib/hts.c linenumber=1426 strdup linenumber=1259 hts_set_opt /src/htslib/hts.c linenumber=1269 hts_set_threads /src/htslib/hts.c linenumber=1807 sam_set_threads /src/htslib/sam.c linenumber=1932 hts_tpool_init /src/htslib/thread_pool.c linenumber=3745 sam_set_thread_pool /src/htslib/sam.c linenumber=3748 sam_state_create /src/htslib/sam.c linenumber=3717 calloc linenumber=3049 pthread_mutex_init linenumber=3721 pthread_mutex_init linenumber=3722 pthread_cond_init linenumber=3723 hts_tpool_size /src/htslib/thread_pool.c linenumber=3727 hts_tpool_process_init /src/htslib/thread_pool.c linenumber=3728 sam_state_destroy /src/htslib/sam.c linenumber=3730 pthread_mutex_lock linenumber=3095 pthread_cond_signal linenumber=3098 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3101 hts_tpool_wake_dispatch /src/htslib/thread_pool.c linenumber=3108 pthread_mutex_unlock linenumber=3109 hts_usleep /src/htslib/./hts_internal.h linenumber=3110 pthread_mutex_lock linenumber=3111 pthread_mutex_unlock linenumber=3114 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3120 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=832 sam_format_worker /src/htslib/sam.c linenumber=3120 pthread_mutex_lock linenumber=3654 pthread_mutex_unlock linenumber=3659 calloc linenumber=3662 sam_state_err /src/htslib/sam.c linenumber=3664 pthread_mutex_lock linenumber=3063 pthread_mutex_unlock linenumber=3066 sam_format1_append /src/htslib/sam.c linenumber=3676 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4323 __errno_location linenumber=279 ks_resize /src/htslib/./htslib/kstring.h linenumber=280 kputc_ /src/htslib/./htslib/kstring.h linenumber=4324 kputw /src/htslib/./htslib/kstring.h linenumber=4325 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=4325 kputs /src/htslib/./htslib/kstring.h linenumber=4327 kputc_ /src/htslib/./htslib/kstring.h linenumber=4328 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4329 kputll /src/htslib/./htslib/kstring.h linenumber=4330 ks_resize /src/htslib/./htslib/kstring.h linenumber=388 kputuw /src/htslib/./htslib/kstring.h linenumber=398 kputc_ /src/htslib/./htslib/kstring.h linenumber=4330 kputw /src/htslib/./htslib/kstring.h linenumber=4331 kputc_ /src/htslib/./htslib/kstring.h linenumber=4331 kputw /src/htslib/./htslib/kstring.h linenumber=4335 kputc_ /src/htslib/./htslib/kstring.h linenumber=4336 kputc_ /src/htslib/./htslib/kstring.h linenumber=4338 kputc_ /src/htslib/./htslib/kstring.h linenumber=4339 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4340 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4341 kputs /src/htslib/./htslib/kstring.h linenumber=4343 kputc_ /src/htslib/./htslib/kstring.h linenumber=4344 kputll /src/htslib/./htslib/kstring.h linenumber=4346 kputc_ /src/htslib/./htslib/kstring.h linenumber=4346 kputll /src/htslib/./htslib/kstring.h linenumber=4347 kputc_ /src/htslib/./htslib/kstring.h linenumber=4347 ks_resize /src/htslib/./htslib/kstring.h linenumber=4350 nibble2base /src/htslib/./sam_internal.h linenumber=4354 add33 /src/htslib/sam.c linenumber=4364 kputsn_ /src/htslib/./htslib/kstring.h linenumber=4370 kputc_ /src/htslib/./htslib/kstring.h linenumber=4376 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4377 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=4380 hts_log /src/htslib/hts.c linenumber=4386 __errno_location linenumber=4388 hts_log /src/htslib/hts.c linenumber=4392 __errno_location linenumber=4393 __errno_location linenumber=3677 sam_state_err /src/htslib/sam.c linenumber=3677 kputc /src/htslib/./htslib/kstring.h linenumber=3680 pthread_mutex_lock linenumber=3683 pthread_mutex_unlock linenumber=3697 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=3124 pthread_mutex_lock linenumber=3125 pthread_mutex_unlock linenumber=3127 hts_tpool_process_empty /src/htslib/thread_pool.c linenumber=3129 hts_usleep /src/htslib/./hts_internal.h linenumber=3130 pthread_mutex_lock linenumber=3131 hts_tpool_process_is_shutdown /src/htslib/thread_pool.c linenumber=3134 pthread_mutex_unlock linenumber=3136 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3139 pthread_join linenumber=3144 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=3150 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=3153 pthread_mutex_destroy linenumber=3156 pthread_mutex_destroy linenumber=3157 pthread_cond_destroy linenumber=3158 sam_free_sp_bams /src/htslib/sam.c linenumber=3173 sam_free_sp_bams /src/htslib/sam.c linenumber=3178 bam_hdr_destroy /src/htslib/./htslib/sam.h linenumber=3184 sam_hdr_destroy /src/htslib/sam.c linenumber=404 bgzf_thread_pool /src/htslib/bgzf.c linenumber=3735 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=3751 hts_get_bgzfp /src/htslib/hts.c linenumber=1934 bgzf_mt /src/htslib/bgzf.c linenumber=1934 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=1936 hts_hfile /src/htslib/hts.c linenumber=1811 bgzf_hfile /src/htslib/bgzf.c linenumber=1785 cram_hfile /src/htslib/./cram/cram_io.h linenumber=1786 bgzf_hfile /src/htslib/bgzf.c linenumber=1792 hfile_set_blksize /src/htslib/hfile.c linenumber=1815 hts_log /src/htslib/hts.c linenumber=1816 hts_log /src/htslib/hts.c linenumber=1821 hts_set_thread_pool /src/htslib/hts.c linenumber=1831 sam_set_thread_pool /src/htslib/sam.c linenumber=1943 hts_get_bgzfp /src/htslib/hts.c linenumber=1945 bgzf_thread_pool /src/htslib/bgzf.c linenumber=1945 hts_set_opt /src/htslib/hts.c linenumber=1947 hts_set_cache_size /src/htslib/hts.c linenumber=1838 hts_get_bgzfp /src/htslib/hts.c linenumber=1955 bgzf_set_cache_size /src/htslib/bgzf.c linenumber=1955 fastq_state_set /src/htslib/sam.c linenumber=1847 fastq_state_init /src/htslib/sam.c linenumber=3815 calloc linenumber=3781 strcpy linenumber=3784 regcomp linenumber=3788 strcmp linenumber=3835 kh_init_tag /src/htslib/sam.c linenumber=3837 calloc linenumber=64 strlen linenumber=3840 hts_log /src/htslib/hts.c linenumber=3844 kh_put_tag /src/htslib/sam.c linenumber=3848 kh_resize_tag /src/htslib/sam.c linenumber=64 __errno_location linenumber=64 realloc linenumber=64 strncpy linenumber=3860 strcmp linenumber=3870 isalpha_c /src/htslib/./textutils_internal.h linenumber=3874 isalnum_c /src/htslib/./textutils_internal.h linenumber=3874 strncpy linenumber=3879 hts_log /src/htslib/hts.c linenumber=3893 regfree linenumber=3903 regcomp linenumber=3904 hts_log /src/htslib/hts.c linenumber=3905 fastq_state_set /src/htslib/sam.c linenumber=1856 fastq_state_set /src/htslib/sam.c linenumber=1868 cram_set_option /src/htslib/cram/cram_io.c linenumber=1880 hts_set_filter_expression /src/htslib/hts.c linenumber=1888 hts_filter_free /src/htslib/hts_expr.c linenumber=1977 regfree linenumber=951 hts_filter_init /src/htslib/hts_expr.c linenumber=1982 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=1921 hts_set_opt /src/htslib/hts.c linenumber=1273 hts_opt_free /src/htslib/hts.c linenumber=1427 hts_opt_free /src/htslib/hts.c linenumber=1431 hclose_abruptly /src/htslib/hfile.c linenumber=1625 hts_log /src/htslib/hts.c linenumber=1630 hclose_abruptly /src/htslib/hfile.c linenumber=1633 hclose /src/htslib/hfile.c linenumber=188 abort linenumber=189 hts_close /src/htslib/hts.c linenumber=194 __errno_location linenumber=1650 bgzf_close /src/htslib/bgzf.c linenumber=1658 cram_eof /src/htslib/cram/cram_io.c linenumber=1663 hts_log /src/htslib/hts.c linenumber=1665 cram_close /src/htslib/cram/cram_io.c linenumber=1672 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=5296 cram_flush_container_mt /src/htslib/cram/cram_io.c linenumber=5298 pthread_mutex_lock linenumber=4033 reset_metrics /src/htslib/cram/cram_io.c linenumber=4036 pthread_mutex_unlock linenumber=4001 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=4002 pthread_mutex_lock linenumber=4003 pthread_mutex_unlock linenumber=4039 cram_flush_container /src/htslib/cram/cram_io.c linenumber=4042 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=3890 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=3186 hts_log /src/htslib/hts.c linenumber=3201 pthread_mutex_unlock linenumber=3202 pthread_mutex_lock linenumber=3219 hts_log /src/htslib/hts.c linenumber=3222 cram_populate_ref /src/htslib/cram/cram_io.c linenumber=3224 getenv linenumber=2741 getenv linenumber=2746 hts_log /src/htslib/hts.c linenumber=2750 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2755 sam_hrecs_find_key /src/htslib/header.c linenumber=2758 hts_log /src/htslib/hts.c linenumber=2761 expand_cache_path /src/htslib/cram/cram_io.c linenumber=2766 strchr linenumber=2652 strncpy linenumber=2654 strlen linenumber=2659 strcpy linenumber=2661 strtol linenumber=2670 strlen linenumber=2671 strncpy linenumber=2674 strlen linenumber=2693 strcpy linenumber=2695 strlen linenumber=2699 strcpy linenumber=2703 stat linenumber=2767 stat linenumber=2788 bgzf_open /src/htslib/bgzf.c linenumber=2790 string_dup /src/htslib/cram/string_alloc.c linenumber=2794 bgzf_close /src/htslib/bgzf.c linenumber=2797 open_path_mfile /src/htslib/cram/open_trace_file.c linenumber=2813 getenv linenumber=363 tokenise_search_path /src/htslib/cram/open_trace_file.c linenumber=364 strlen linenumber=117 strncmp linenumber=132 strncmp linenumber=133 strncmp linenumber=134 strncmp linenumber=135 strncmp linenumber=136 strncmp linenumber=137 strncmp linenumber=138 strncmp linenumber=139 strncmp linenumber=140 strncmp linenumber=388 find_file_url /src/htslib/cram/open_trace_file.c linenumber=389 expand_path /src/htslib/cram/open_trace_file.c linenumber=191 strlen linenumber=232 strlen linenumber=233 hts_log /src/htslib/hts.c linenumber=239 strchr linenumber=256 strtol linenumber=259 hopen /src/htslib/hfile.c linenumber=195 __errno_location linenumber=196 __errno_location linenumber=197 strerror linenumber=197 hts_log /src/htslib/hts.c linenumber=197 mfcreate /src/htslib/cram/mFILE.c linenumber=201 hread /src/htslib/cram/../htslib/hfile.h linenumber=203 mfwrite /src/htslib/cram/mFILE.c linenumber=204 realloc linenumber=538 hclose_abruptly /src/htslib/hfile.c linenumber=205 hclose /src/htslib/hfile.c linenumber=209 __errno_location linenumber=210 strerror linenumber=210 hts_log /src/htslib/hts.c linenumber=210 mrewind /src/htslib/cram/mFILE.c linenumber=215 mfdestroy /src/htslib/cram/mFILE.c linenumber=219 strncmp linenumber=391 hisremote /src/htslib/hfile.c linenumber=395 find_file_url /src/htslib/cram/open_trace_file.c linenumber=396 find_file_dir /src/htslib/cram/open_trace_file.c linenumber=402 expand_path /src/htslib/cram/open_trace_file.c linenumber=318 is_file /src/htslib/cram/open_trace_file.c linenumber=322 stat linenumber=92 mfopen /src/htslib/cram/mFILE.c linenumber=323 fopen linenumber=350 mfreopen /src/htslib/cram/mFILE.c linenumber=352 strchr linenumber=276 strchr linenumber=278 strchr linenumber=280 strchr linenumber=282 strchr linenumber=284 strchr linenumber=286 strchr linenumber=292 mfcreate /src/htslib/cram/mFILE.c linenumber=297 mfmmap /src/htslib/cram/mFILE.c linenumber=302 stat linenumber=130 fileno linenumber=135 mmap linenumber=134 mfload /src/htslib/cram/mFILE.c linenumber=309 stat linenumber=88 realloc linenumber=101 fread linenumber=109 feof linenumber=112 fseek linenumber=316 mfcreate /src/htslib/cram/mFILE.c linenumber=321 hts_log /src/htslib/hts.c linenumber=324 fseek linenumber=336 strlen linenumber=372 strcpy linenumber=414 strrchr linenumber=415 find_file_dir /src/htslib/cram/open_trace_file.c linenumber=417 mfsteal /src/htslib/cram/mFILE.c linenumber=2815 mfdetach /src/htslib/cram/mFILE.c linenumber=437 mfflush /src/htslib/cram/mFILE.c linenumber=393 fclose linenumber=398 mfdestroy /src/htslib/cram/mFILE.c linenumber=441 sam_hrecs_find_key /src/htslib/header.c linenumber=2833 strstr linenumber=2836 strncmp linenumber=2837 hts_log /src/htslib/hts.c linenumber=2839 strncmp linenumber=2843 bgzf_close /src/htslib/bgzf.c linenumber=2848 refs_load_fai /src/htslib/cram/cram_io.c linenumber=2852 sanitise_SQ_lines /src/htslib/cram/cram_io.c linenumber=2854 bgzf_close /src/htslib/bgzf.c linenumber=2858 refs2id /src/htslib/cram/cram_io.c linenumber=2866 expand_cache_path /src/htslib/cram/cram_io.c linenumber=2879 hts_log /src/htslib/hts.c linenumber=2882 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2883 strrchr linenumber=2711 is_directory /src/htslib/cram/cram_io.c linenumber=2716 stat linenumber=2638 mkdir linenumber=2721 chmod linenumber=2722 mkdir_prefix /src/htslib/cram/cram_io.c linenumber=2727 mkdir linenumber=2728 chmod linenumber=2729 hts_open_tmpfile /src/htslib/hts.c linenumber=2885 getpid linenumber=1988 time linenumber=1995 clock linenumber=1995 ks_clear /src/htslib/./htslib/kstring.h linenumber=1998 ksprintf /src/htslib/kstring.c linenumber=1999 hopen /src/htslib/hfile.c linenumber=2001 __errno_location linenumber=2002 perror linenumber=2887 hts_md5_init /src/htslib/md5.c linenumber=2899 hts_md5_reset /src/htslib/md5.c linenumber=329 hclose_abruptly /src/htslib/hfile.c linenumber=2900 unlink linenumber=2901 hts_md5_update /src/htslib/md5.c linenumber=2905 body /src/htslib/md5.c linenumber=260 body /src/htslib/md5.c linenumber=264 hts_md5_final /src/htslib/md5.c linenumber=2906 body /src/htslib/md5.c linenumber=283 body /src/htslib/md5.c linenumber=300 hts_md5_destroy /src/htslib/md5.c linenumber=2907 hts_md5_hex /src/htslib/md5.c linenumber=2908 strncmp linenumber=2910 hts_log /src/htslib/hts.c linenumber=2911 hclose_abruptly /src/htslib/hfile.c linenumber=2912 unlink linenumber=2913 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=2918 hclose /src/htslib/hfile.c linenumber=2919 chmod linenumber=2920 rename linenumber=2921 __errno_location linenumber=2922 strerror linenumber=2922 hts_log /src/htslib/hts.c linenumber=2922 unlink linenumber=2924 hts_log /src/htslib/hts.c linenumber=3225 hts_log /src/htslib/hts.c linenumber=3227 pthread_mutex_unlock linenumber=3228 pthread_mutex_unlock linenumber=3229 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3234 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3266 cram_ref_load /src/htslib/cram/cram_io.c linenumber=3269 __assert_fail linenumber=3095 __assert_fail linenumber=3105 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=3109 strcmp linenumber=3117 bgzf_close /src/htslib/bgzf.c linenumber=3119 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3122 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3128 bgzf_useek /src/htslib/bgzf.c linenumber=3017 hseek /src/htslib/hfile.c linenumber=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=3018 bgzf_read /src/htslib/bgzf.c linenumber=3026 __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=3027 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3044 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3049 isspace_c /src/htslib/cram/../textutils_internal.h linenumber=3058 hts_log /src/htslib/hts.c linenumber=3065 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=3072 toupper linenumber=180 pthread_mutex_unlock linenumber=3270 pthread_mutex_unlock linenumber=3271 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=3279 pthread_mutex_unlock linenumber=3295 pthread_mutex_unlock linenumber=3296 pthread_mutex_unlock linenumber=3316 pthread_mutex_unlock linenumber=3317 strcmp linenumber=3322 bgzf_close /src/htslib/bgzf.c linenumber=3324 bgzf_open_ref /src/htslib/cram/cram_io.c linenumber=3327 pthread_mutex_unlock linenumber=3328 pthread_mutex_unlock linenumber=3329 load_ref_portion /src/htslib/cram/cram_io.c linenumber=3334 pthread_mutex_unlock linenumber=3335 pthread_mutex_unlock linenumber=3336 pthread_mutex_unlock linenumber=3349 pthread_mutex_unlock linenumber=3350 hts_log /src/htslib/hts.c linenumber=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=2947 cram_ref_incr_locked /src/htslib/cram/cram_io.c linenumber=2948 pthread_mutex_unlock linenumber=2949 cram_get_ref /src/htslib/cram/cram_io.c linenumber=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=4836 __errno_location linenumber=4814 skip_aux /src/htslib/sam.c linenumber=4839 aux_type2size /src/htslib/sam.c linenumber=4789 memchr linenumber=4793 aux_type2size /src/htslib/sam.c linenumber=4797 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=4798 bam_aux_next /src/htslib/sam.c linenumber=4836 skip_aux /src/htslib/sam.c linenumber=4821 __errno_location linenumber=4823 hts_log /src/htslib/hts.c linenumber=4827 __errno_location linenumber=4829 hts_log /src/htslib/hts.c linenumber=4850 __errno_location linenumber=4852 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=2977 cram_ref_decr_locked /src/htslib/cram/cram_io.c linenumber=2978 __assert_fail linenumber=2962 ref_entry_free_seq /src/htslib/cram/cram_io.c linenumber=2968 pthread_mutex_unlock linenumber=2979 cram_get_ref /src/htslib/cram/cram_io.c linenumber=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=244 block_resize_exact /src/htslib/cram/cram_io.h linenumber=233 realloc linenumber=217 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=262 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=3583 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=249 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=3588 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=3597 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 /src/htslib/cram/cram_encode.c linenumber=3606 cram_add_quality /src/htslib/cram/cram_encode.c linenumber=3610 cram_add_hardclip /src/htslib/cram/cram_encode.c linenumber=3619 cram_stats_add /src/htslib/cram/cram_stats.c linenumber=2667 cram_add_feature /src/htslib/cram/cram_encode.c linenumber=2668 cram_add_pad /src/htslib/cram/cram_encode.c linenumber=3624 cram_stats_add 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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 /src/htslib/cram/cram_io.c linenumber=1124 cram_compress_slice /src/htslib/cram/cram_encode.c linenumber=1143 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=776 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2081 pthread_mutex_lock linenumber=1741 pthread_mutex_unlock linenumber=1818 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=1836 zlib_mem_deflate /src/htslib/cram/cram_io.c linenumber=1540 deflateInit2_ linenumber=1009 hts_log /src/htslib/hts.c linenumber=1011 hts_log /src/htslib/hts.c linenumber=1020 deflate linenumber=1023 hts_log /src/htslib/hts.c linenumber=1026 deflate linenumber=1030 hts_log /src/htslib/hts.c linenumber=1031 deflateEnd linenumber=1035 hts_log /src/htslib/hts.c linenumber=1036 BZ2_bzBuffToBuffCompress linenumber=1550 fqz_compress /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1583 compress_block_fqz2f /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1622 fqz_pick_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1024 calloc linenumber=758 fqz_qual_stats /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=798 calloc linenumber=428 memcmp linenumber=443 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=564 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=565 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=566 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=567 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=568 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=569 fast_log /src/htslib/htscodecs/htscodecs/utils.h linenumber=570 log linenumber=573 log linenumber=574 log linenumber=575 log linenumber=633 log linenumber=635 log linenumber=637 log linenumber=640 log linenumber=641 log linenumber=815 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1060 var_put_u32_safe /src/htslib/htscodecs/htscodecs/varint.h linenumber=208 fqz_store_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1061 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=722 fqz_store_parameters1 /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=727 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=697 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=701 store_array /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=705 fqz_create_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1078 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1081 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1082 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1083 compress_new_read /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1126 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=945 RC_Encode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=125 RC_ShiftLowCheck /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=143 SIMPLE_MODEL256_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=954 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=955 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=956 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=957 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=965 SIMPLE_MODEL2_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=967 memcmp linenumber=985 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=986 SIMPLE_MODEL2_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=992 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1153 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1155 mm_prefetch /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1157 fqz_update_ctx /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1159 mm_prefetch 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RC_ShiftLowCheck /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=125 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=1223 fqz_destroy_models /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1227 fqz_free_parameters /src/htslib/htscodecs/htscodecs/fqzcomp_qual.c linenumber=1229 lzma_mem_deflate /src/htslib/cram/cram_io.c linenumber=1591 lzma_stream_buffer_bound linenumber=1060 lzma_easy_buffer_encode linenumber=1066 rans_compress /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=1600 rans_compress_O1 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=837 rans_compress_O0 /src/htslib/htscodecs/htscodecs/rANS_static.c linenumber=394 hist8 /src/htslib/htscodecs/htscodecs/utils.h linenumber=95 htscodecs_tls_calloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=148 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=178 __assert_fail linenumber=126 RansEncSymbolInit /src/htslib/htscodecs/htscodecs/rANS_byte.h linenumber=154 __assert_fail linenumber=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 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 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/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=1621 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1583 rans_compress_bound_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1222 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1294 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1324 realloc linenumber=1332 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1363 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1377 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1399 hts_pack /src/htslib/htscodecs/htscodecs/pack.c linenumber=1417 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1430 hts_rle_encode /src/htslib/htscodecs/htscodecs/rle.c linenumber=1457 rle_find_syms /src/htslib/htscodecs/htscodecs/rle.c linenumber=117 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=131 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1472 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1473 rans_enc_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1487 pthread_once linenumber=951 htscodecs_tls_cpu_init /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=951 strerror linenumber=954 fprintf linenumber=953 fprintf linenumber=955 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1496 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1500 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1501 rans_enc_func /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1531 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1641 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=742 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=755 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=799 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=870 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=885 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=895 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=912 hts_pack /src/htslib/htscodecs/htscodecs/pack.c linenumber=929 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=942 BZ2_bzBuffToBuffCompress linenumber=964 arith_compress_O0_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=985 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=443 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=461 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=464 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=471 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=474 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=475 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=476 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=481 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=490 SIMPLE_MODEL258_normalize /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=130 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=498 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=502 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=503 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=509 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=513 arith_compress_O1_RLE /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=987 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=577 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=595 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=601 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=604 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=606 SIMPLE_MODEL258_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=611 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=614 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=615 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=616 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=621 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=630 SIMPLE_MODEL258_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=638 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=642 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=643 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=644 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=650 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=654 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=655 arith_compress_O1 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=993 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=174 htscodecs_tls_alloc /src/htslib/htscodecs/htscodecs/utils.c linenumber=185 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=200 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=203 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=204 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=205 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=209 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=213 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=215 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=220 htscodecs_tls_free /src/htslib/htscodecs/htscodecs/utils.c linenumber=222 arith_compress_O0 /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=995 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=100 SIMPLE_MODEL256_init /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=118 RC_SetOutput /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=121 RC_SetOutputEnd /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=122 RC_StartEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=123 SIMPLE_MODEL256_encodeSymbol /src/htslib/htscodecs/htscodecs/c_simple_model.h linenumber=126 RC_FinishEncode /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=128 RC_OutSize /src/htslib/htscodecs/htscodecs/c_range_coder.h linenumber=134 tok3_encode_names /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1653 create_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1463 build_trie /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1477 calloc linenumber=482 pool_create /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=505 pool_alloc /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=506 new_pool /src/htslib/htscodecs/htscodecs/pooled_alloc.h linenumber=133 realloc linenumber=86 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1478 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1496 encode_name /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1502 search_trie /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=700 __ctype_b_loc linenumber=613 __ctype_b_loc linenumber=614 __ctype_b_loc linenumber=615 __ctype_b_loc linenumber=616 __ctype_b_loc linenumber=617 calloc linenumber=645 __ctype_b_loc linenumber=667 strlen linenumber=711 encode_token_dup /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=712 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=465 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=342 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=316 realloc linenumber=302 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=343 encode_token_diff /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=727 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=470 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=743 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=443 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=444 memcmp linenumber=758 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=759 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=324 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=761 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=415 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=416 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=764 __ctype_b_loc linenumber=785 __ctype_b_loc linenumber=791 __ctype_b_loc linenumber=792 memcmp linenumber=809 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=815 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=822 encode_token_alpha /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=828 __ctype_b_loc linenumber=842 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=856 encode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=863 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=375 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=376 encode_token_int1_ /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=869 descriptor_grow /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=387 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=870 encode_token_int1_ /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=877 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=878 __ctype_b_loc linenumber=887 __ctype_b_loc linenumber=893 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=923 encode_token_int1 /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=933 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=940 encode_token_int /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=948 encode_token_match /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=965 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=970 encode_token_char /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=976 encode_token_end /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=998 encode_token_type /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=328 realloc linenumber=1007 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1503 arith_compress_bound /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1565 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1568 compress /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1572 arith_encode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1380 arith_compress_to /src/htslib/htscodecs/htscodecs/arith_dynamic.c linenumber=1214 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1217 rans_encode /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1383 rans_compress_to_4x16 /src/htslib/htscodecs/htscodecs/rANS_static4x16pr.c linenumber=1241 var_put_u32 /src/htslib/htscodecs/htscodecs/varint.h linenumber=1244 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1574 memcmp linenumber=1592 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1618 free_context /src/htslib/htscodecs/htscodecs/tokenise_name3.c linenumber=1659 pthread_mutex_lock linenumber=1863 pthread_mutex_unlock linenumber=1998 pthread_mutex_unlock linenumber=2010 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2011 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2019 hts_log /src/htslib/hts.c linenumber=2019 pthread_mutex_lock linenumber=2022 pthread_mutex_unlock linenumber=2026 cram_compress_block3 /src/htslib/cram/cram_io.c linenumber=2027 cram_compress_by_method /src/htslib/cram/cram_io.c linenumber=2045 hts_log /src/htslib/hts.c linenumber=2048 cram_block_method2str /src/htslib/cram/cram_io.c linenumber=2063 hts_log /src/htslib/hts.c linenumber=2063 pthread_mutex_lock linenumber=843 pthread_mutex_unlock linenumber=847 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=850 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=857 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=862 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=867 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=870 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=874 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=879 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=884 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=887 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=891 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=896 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=906 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=912 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=929 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=947 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=1150 cram_free_block /src/htslib/cram/cram_io.c linenumber=1161 cram_encode_slice_header /src/htslib/cram/cram_encode.c linenumber=1172 cram_new_block /src/htslib/cram/cram_io.c linenumber=509 hts_malloc_pse /src/htslib/cram/../htslib/hts_alloc.h linenumber=515 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=173 hts_prod_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=174 hts_add_sat2 /src/htslib/cram/../htslib/hts_alloc.h linenumber=175 hts_malloc /src/htslib/cram/../htslib/hts_alloc.h linenumber=176 cram_free_block /src/htslib/cram/cram_io.c linenumber=517 hts_log /src/htslib/hts.c linenumber=523 cram_free_block /src/htslib/cram/cram_io.c linenumber=524 __assert_fail linenumber=547 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=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=3893 htell /src/htslib/cram/../htslib/hfile.h linenumber=3842 cram_write_container /src/htslib/cram/cram_io.c linenumber=3845 itf8_put /src/htslib/cram/cram_io.c linenumber=3785 crc32 linenumber=3813 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=3821 htell /src/htslib/cram/../htslib/hfile.h linenumber=3848 cram_write_block /src/htslib/cram/cram_io.c linenumber=3851 __assert_fail linenumber=1277 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1279 hputc2 /src/htslib/hfile.c linenumber=268 flush_buffer /src/htslib/hfile.c linenumber=403 hputc /src/htslib/cram/../htslib/hfile.h linenumber=1280 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1284 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1289 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=1292 __assert_fail linenumber=1297 crc32 linenumber=1309 crc32 linenumber=1312 crc32 linenumber=1314 int32_encode /src/htslib/cram/cram_io.c linenumber=1317 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=784 htell /src/htslib/cram/../htslib/hfile.h linenumber=3855 cram_write_block /src/htslib/cram/cram_io.c linenumber=3860 cram_write_block /src/htslib/cram/cram_io.c linenumber=3864 htell /src/htslib/cram/../htslib/hfile.h linenumber=3868 cram_index_slice /src/htslib/cram/cram_index.c linenumber=3872 cram_index_build_multiref /src/htslib/cram/cram_index.c linenumber=720 cram_decode_slice /src/htslib/cram/cram_decode.c linenumber=652 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 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=2294 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2299 sam_hrecs_find_key /src/htslib/header.c linenumber=2303 kputsn /src/htslib/./htslib/kstring.h linenumber=2308 hts_log /src/htslib/hts.c linenumber=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=272 append_uint32 /src/htslib/cram/cram_io.h linenumber=276 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=344 append_uint32 /src/htslib/cram/cram_io.h linenumber=347 append_sub32 /src/htslib/cram/cram_io.h linenumber=349 append_uint32 /src/htslib/cram/cram_io.h linenumber=351 append_sub32 /src/htslib/cram/cram_io.h linenumber=353 append_uint64 /src/htslib/cram/cram_io.h linenumber=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=706 __errno_location linenumber=707 __errno_location linenumber=709 __errno_location linenumber=710 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=721 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=731 __errno_location linenumber=57 sam_realloc_bam_data /src/htslib/sam.c linenumber=61 bam_endpos /src/htslib/sam.c linenumber=742 bam_cigar2rlen /src/htslib/sam.c linenumber=685 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=742 hts_log /src/htslib/hts.c linenumber=744 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=662 snprintf linenumber=675 strlen linenumber=679 bgzf_write /src/htslib/bgzf.c linenumber=679 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=689 strlen linenumber=693 bgzf_write /src/htslib/bgzf.c linenumber=693 snprintf linenumber=722 strlen linenumber=726 bgzf_write /src/htslib/bgzf.c linenumber=726 __errno_location linenumber=4053 hts_tpool_dispatch2 /src/htslib/thread_pool.c linenumber=4054 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=844 cram_flush_thread /src/htslib/cram/cram_io.c linenumber=4054 cram_encode_container /src/htslib/cram/cram_encode.c linenumber=3905 hts_log /src/htslib/hts.c linenumber=3906 __errno_location linenumber=4055 cram_flush_result /src/htslib/cram/cram_io.c linenumber=4056 hts_tpool_next_result /src/htslib/thread_pool.c linenumber=3921 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=3922 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3926 cram_flush_container2 /src/htslib/cram/cram_io.c linenumber=3934 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3941 cram_free_slice /src/htslib/cram/cram_io.c linenumber=3950 cram_free_container /src/htslib/cram/cram_io.c linenumber=3963 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3968 cram_free_container /src/htslib/cram/cram_io.c linenumber=3975 hts_usleep /src/htslib/cram/../hts_internal.h linenumber=4061 cram_drain_rqueue /src/htslib/cram/cram_decode.c linenumber=5303 hts_tpool_process_flush /src/htslib/thread_pool.c linenumber=5306 cram_flush_result /src/htslib/cram/cram_io.c linenumber=5308 hts_tpool_process_destroy /src/htslib/thread_pool.c linenumber=5316 pthread_mutex_destroy linenumber=5319 pthread_mutex_destroy linenumber=5320 pthread_mutex_destroy linenumber=5321 pthread_mutex_destroy linenumber=5322 cram_write_eof_block /src/htslib/cram/cram_io.c linenumber=5326 cram_encode_compression_header /src/htslib/cram/cram_encode.c linenumber=5247 cram_write_container /src/htslib/cram/cram_io.c linenumber=5252 cram_write_block /src/htslib/cram/cram_io.c linenumber=5253 cram_close /src/htslib/cram/cram_io.c linenumber=5254 free_bam_list /src/htslib/cram/cram_io.c linenumber=5332 hclose /src/htslib/hfile.c linenumber=5336 cram_free_file_def /src/htslib/cram/cram_io.c linenumber=5340 sam_hdr_destroy /src/htslib/sam.c linenumber=5343 cram_free_container /src/htslib/cram/cram_io.c linenumber=5348 cram_free_container /src/htslib/cram/cram_io.c linenumber=5351 refs_free /src/htslib/cram/cram_io.c linenumber=5354 kh_destroy_m_metrics /src/htslib/cram/cram_structs.h linenumber=5370 cram_index_free /src/htslib/cram/cram_index.c linenumber=5374 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=388 cram_index_free_recurse /src/htslib/cram/cram_index.c linenumber=375 hts_tpool_destroy /src/htslib/thread_pool.c linenumber=5377 bgzf_close /src/htslib/bgzf.c linenumber=5380 cram_free_block /src/htslib/cram/cram_io.c linenumber=5255 kh_destroy_map /src/htslib/cram/cram_structs.h linenumber=5259 cram_free_block /src/htslib/cram/cram_io.c linenumber=5260 sam_state_destroy /src/htslib/sam.c linenumber=1683 fastq_state_destroy /src/htslib/sam.c linenumber=1686 kh_destroy_tag /src/htslib/sam.c linenumber=3800 ks_free /src/htslib/./htslib/kstring.h linenumber=3801 ks_initialize /src/htslib/./htslib/kstring.h linenumber=238 ks_free /src/htslib/./htslib/kstring.h linenumber=3802 ks_free /src/htslib/./htslib/kstring.h linenumber=3803 regfree linenumber=3804 bgzf_close /src/htslib/bgzf.c linenumber=1689 hclose /src/htslib/hfile.c linenumber=1691 hts_idx_close_otf_fp /src/htslib/hts.c linenumber=1704 need_idx_ugly_delay_hack /src/htslib/hts.c linenumber=2922 idx_write_uint64 /src/htslib/hts.c linenumber=2924 ed_is_big /src/htslib/./htslib/hts.h linenumber=2743 ed_swap_8 /src/htslib/./htslib/hts.h linenumber=2743 bgzf_write /src/htslib/bgzf.c linenumber=2744 bgzf_close /src/htslib/bgzf.c linenumber=2926 sam_hdr_destroy /src/htslib/sam.c linenumber=1708 hts_idx_destroy /src/htslib/hts.c linenumber=1709 cram_index_free /src/htslib/cram/cram_index.c linenumber=2704 kh_destroy_bin /src/htslib/hts.c linenumber=2716 hts_filter_free /src/htslib/hts_expr.c linenumber=1710 __errno_location linenumber=1715 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=1922 bam_hdr_read /src/htslib/sam.c linenumber=1928 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=1928 hts_log /src/htslib/hts.c linenumber=1855 sam_hdr_destroy /src/htslib/sam.c linenumber=1856 hts_log /src/htslib/hts.c linenumber=1873 hts_log /src/htslib/hts.c linenumber=1877 sam_hdr_destroy /src/htslib/sam.c linenumber=1878 realloc linenumber=1882 sam_hdr_destroy /src/htslib/sam.c linenumber=1884 sam_hdr_dup /src/htslib/sam.c linenumber=1932 sam_hdr_init /src/htslib/sam.c linenumber=175 calloc linenumber=184 calloc linenumber=186 strdup linenumber=192 sam_hdr_dup_sdict /src/htslib/sam.c linenumber=199 kh_init_s2i /src/htslib/hts.c linenumber=149 kh_get_s2i /src/htslib/hts.c linenumber=157 kh_put_s2i /src/htslib/hts.c linenumber=159 kh_destroy_s2i /src/htslib/hts.c linenumber=161 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=205 kputsn /src/htslib/./htslib/kstring.h linenumber=2381 sam_hrecs_rebuild_lines /src/htslib/header.c linenumber=2383 kputsn /src/htslib/./htslib/kstring.h linenumber=763 build_header_line /src/htslib/header.c linenumber=767 kputc_ /src/htslib/./htslib/kstring.h linenumber=749 kputsn /src/htslib/./htslib/kstring.h linenumber=750 kputc_ /src/htslib/./htslib/kstring.h linenumber=752 kputsn /src/htslib/./htslib/kstring.h linenumber=753 kputc /src/htslib/./htslib/kstring.h linenumber=769 ks_release /src/htslib/./htslib/kstring.h linenumber=206 ks_release /src/htslib/./htslib/kstring.h linenumber=211 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=213 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=217 sam_hdr_destroy /src/htslib/sam.c linenumber=227 sam_hdr_sanitise /src/htslib/sam.c linenumber=1932 sam_hdr_create /src/htslib/sam.c linenumber=1936 sam_hdr_init /src/htslib/sam.c linenumber=1901 sam_hdr_build_from_sam_file /src/htslib/header.c linenumber=1905 sam_hrecs_new /src/htslib/header.c linenumber=1360 hts_getline /src/htslib/hts.c linenumber=1369 hts_log /src/htslib/hts.c linenumber=2046 abort linenumber=2047 kgetline2 /src/htslib/kstring.c linenumber=2053 ks_resize /src/htslib/./htslib/kstring.h linenumber=322 hgetln_wrapper /src/htslib/hts.c linenumber=2053 hgetln /src/htslib/./htslib/hfile.h linenumber=2039 herrno /src/htslib/./htslib/hfile.h linenumber=2055 __errno_location linenumber=2055 bgzf_getline /src/htslib/bgzf.c linenumber=2061 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 abort linenumber=2065 isalpha_c /src/htslib/./textutils_internal.h linenumber=1377 sam_hrecs_error /src/htslib/header.c linenumber=1378 strncmp linenumber=1383 kputc /src/htslib/./htslib/kstring.h linenumber=1386 valid_sam_header_type /src/htslib/header.c linenumber=1389 hts_log /src/htslib/hts.c linenumber=1390 warn_if_known_stderr /src/htslib/header.c linenumber=1391 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1395 TYPEKEY /src/htslib/./header.h linenumber=1400 kputsn /src/htslib/./htslib/kstring.h linenumber=1406 kputc /src/htslib/./htslib/kstring.h linenumber=1409 bgzf_peek /src/htslib/bgzf.c linenumber=1413 bgzf_read_block /src/htslib/bgzf.c linenumber=1321 hts_log /src/htslib/hts.c linenumber=1322 hpeek /src/htslib/hfile.c linenumber=1416 strstr linenumber=1434 hopen /src/htslib/hfile.c linenumber=1438 khgetline /src/htslib/hfile.c linenumber=1443 kgetline /src/htslib/kstring.c linenumber=310 ks_resize /src/htslib/./htslib/kstring.h linenumber=277 strlen linenumber=281 hgets_wrapper /src/htslib/hfile.c linenumber=310 hgets /src/htslib/hfile.c linenumber=303 strchr linenumber=1444 strtoll linenumber=1452 kputs /src/htslib/./htslib/kstring.h linenumber=1454 kputsn /src/htslib/./htslib/kstring.h linenumber=1455 kputs /src/htslib/./htslib/kstring.h linenumber=1456 kputll /src/htslib/./htslib/kstring.h linenumber=1457 kputc /src/htslib/./htslib/kstring.h linenumber=1458 sam_hrecs_parse_single_line /src/htslib/header.c linenumber=1462 ks_free /src/htslib/./htslib/kstring.h linenumber=1474 hclose /src/htslib/hfile.c linenumber=1475 hts_log /src/htslib/hts.c linenumber=1476 kh_grow_to_fit_m_s2i /src/htslib/./header.h linenumber=1486 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1490 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1504 kputsn /src/htslib/./htslib/kstring.h linenumber=1510 ks_release /src/htslib/./htslib/kstring.h linenumber=1512 sam_hdr_update_target_arrays /src/htslib/header.c linenumber=1514 ks_free /src/htslib/./htslib/kstring.h linenumber=1520 sam_hdr_destroy /src/htslib/sam.c linenumber=1906 sam_hdr_destroy /src/htslib/sam.c linenumber=1911 sam_hdr_sanitise /src/htslib/sam.c linenumber=1912 sam_hdr_init /src/htslib/sam.c linenumber=1941 __errno_location linenumber=1944 __errno_location linenumber=1948 sam_hdr_incr_ref /src/htslib/header.c linenumber=1955 hts_close_or_abort /src/htslib/test/fuzz/hts_open_fuzzer.c linenumber=89 hts_close /src/htslib/hts.c linenumber=41 abort linenumber=42 hts_close /src/htslib/hts.c linenumber=91 hts_close /src/htslib/hts.c linenumber=92 sam_hdr_count_lines /src/htslib/header.c linenumber=97 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2151 sam_hrecs_find_type_id /src/htslib/header.c linenumber=2173 sam_hdr_write /src/htslib/sam.c linenumber=99 __errno_location linenumber=1963 bam_hdr_write /src/htslib/sam.c linenumber=1973 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=1978 sam_hdr_destroy /src/htslib/sam.c linenumber=2621 sam_hdr_dup /src/htslib/sam.c linenumber=2622 refs_from_header /src/htslib/cram/cram_io.c linenumber=2626 cram_load_reference /src/htslib/cram/cram_io.c linenumber=1980 cram_write_SAM_hdr /src/htslib/cram/cram_io.c linenumber=1981 cram_write_file_def /src/htslib/cram/cram_io.c linenumber=4649 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4447 sam_hrecs_find_rg /src/htslib/header.c linenumber=4655 sam_hdr_add_line /src/htslib/header.c linenumber=4656 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1701 sam_hrecs_vadd /src/htslib/header.c linenumber=1707 rebuild_target_arrays /src/htslib/header.c linenumber=1711 redact_header_text /src/htslib/header.c linenumber=1715 refs_from_header /src/htslib/cram/cram_io.c linenumber=4661 refs2id /src/htslib/cram/cram_io.c linenumber=4663 sam_hrecs_find_type_id /src/htslib/header.c linenumber=4673 sam_hrecs_find_key /src/htslib/header.c linenumber=4676 cram_get_ref /src/htslib/cram/cram_io.c linenumber=4688 hts_log /src/htslib/hts.c linenumber=4692 hts_log /src/htslib/hts.c linenumber=4694 hts_log /src/htslib/hts.c linenumber=4695 pthread_mutex_lock linenumber=4697 pthread_mutex_unlock linenumber=4701 hts_md5_init /src/htslib/md5.c linenumber=4707 hts_md5_update /src/htslib/md5.c linenumber=4711 hts_md5_final /src/htslib/md5.c linenumber=4722 hts_md5_destroy /src/htslib/md5.c linenumber=4723 cram_ref_decr /src/htslib/cram/cram_io.c linenumber=4724 hts_md5_hex /src/htslib/md5.c linenumber=4726 sam_hdr_update_line /src/htslib/header.c linenumber=4728 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=1917 sam_hrecs_find_type_id /src/htslib/header.c linenumber=1923 check_for_name_update /src/htslib/header.c linenumber=1932 TYPEKEY /src/htslib/./header.h linenumber=1879 TYPEKEY /src/htslib/./header.h linenumber=1881 TYPEKEY /src/htslib/./header.h linenumber=1883 sam_hrecs_find_key /src/htslib/header.c linenumber=1892 __assert_fail linenumber=1895 strcmp linenumber=1901 strcmp linenumber=1902 kh_get_m_s2i /src/htslib/./header.h linenumber=1903 hts_log /src/htslib/hts.c linenumber=1936 TYPEKEY /src/htslib/./header.h linenumber=1940 hts_log /src/htslib/hts.c linenumber=1942 sam_hrecs_vupdate /src/htslib/header.c linenumber=1946 kh_get_m_s2i /src/htslib/./header.h linenumber=1957 sam_hrecs_find_key /src/htslib/header.c linenumber=1958 __assert_fail linenumber=1960 __assert_fail linenumber=1961 __assert_fail linenumber=1962 kh_del_m_s2i /src/htslib/./header.h linenumber=1964 kh_put_m_s2i /src/htslib/./header.h linenumber=1965 hts_log /src/htslib/hts.c linenumber=1967 TYPEKEY /src/htslib/./header.h linenumber=1973 sam_hrecs_update_hashes /src/htslib/header.c linenumber=1973 rebuild_target_arrays /src/htslib/header.c linenumber=1976 redact_header_text /src/htslib/header.c linenumber=1979 full_path /src/htslib/cram/cram_io.c linenumber=4734 strlen linenumber=4603 hisremote /src/htslib/hfile.c linenumber=4604 hts_log /src/htslib/hts.c linenumber=4606 strncpy linenumber=4609 toupper_c /src/htslib/cram/../textutils_internal.h linenumber=4615 strncpy linenumber=4617 getcwd linenumber=4623 strlen linenumber=4624 strncpy linenumber=4625 snprintf linenumber=4630 sam_hdr_update_line /src/htslib/header.c linenumber=4735 sam_hdr_remove_tag_all /src/htslib/header.c linenumber=4742 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=3196 TYPEKEY /src/htslib/./header.h linenumber=3201 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3201 sam_hrecs_remove_key /src/htslib/header.c linenumber=3209 sam_hrecs_find_key /src/htslib/header.c linenumber=3038 TYPEKEY /src/htslib/./header.h linenumber=3042 __assert_fail linenumber=3043 sam_hrecs_find_key /src/htslib/header.c linenumber=3044 __assert_fail linenumber=3046 kh_get_m_s2i /src/htslib/./header.h linenumber=3047 sam_hrecs_remove_ref_altnames /src/htslib/header.c linenumber=3049 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=127 strcmp linenumber=130 kh_del_m_s2i /src/htslib/./header.h linenumber=131 pool_free /src/htslib/cram/pooled_alloc.c linenumber=3058 hts_log /src/htslib/hts.c linenumber=4743 sam_hdr_length /src/htslib/header.c linenumber=4749 sam_hdr_rebuild /src/htslib/header.c linenumber=1580 rebuild_target_arrays /src/htslib/header.c linenumber=1614 hts_log /src/htslib/hts.c linenumber=1615 sam_hdr_link_pg /src/htslib/header.c linenumber=1624 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2477 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2486 calloc linenumber=2490 __assert_fail linenumber=2501 kh_get_m_s2i /src/htslib/./header.h linenumber=2511 hts_log /src/htslib/hts.c linenumber=2514 hts_log /src/htslib/hts.c linenumber=2521 redact_header_text /src/htslib/header.c linenumber=2550 hts_log /src/htslib/hts.c linenumber=1625 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1630 ks_free /src/htslib/./htslib/kstring.h linenumber=1631 hts_log /src/htslib/hts.c linenumber=1632 ks_len /src/htslib/./htslib/kstring.h linenumber=1640 ks_release /src/htslib/./htslib/kstring.h linenumber=1641 hts_log /src/htslib/hts.c linenumber=4751 int32_encode /src/htslib/cram/cram_io.c linenumber=4755 sam_hdr_str /src/htslib/header.c linenumber=4759 sam_hdr_rebuild /src/htslib/header.c linenumber=1587 hwrite /src/htslib/cram/../htslib/hfile.h linenumber=4759 cram_new_block /src/htslib/cram/cram_io.c linenumber=4763 cram_new_container /src/htslib/cram/cram_io.c linenumber=4764 calloc linenumber=3401 calloc linenumber=3429 cram_new_compression_header /src/htslib/cram/cram_io.c linenumber=3433 calloc linenumber=4078 cram_new_block /src/htslib/cram/cram_io.c linenumber=4082 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4087 cram_free_block /src/htslib/cram/cram_io.c linenumber=4088 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4093 kh_destroy_m_s2i /src/htslib/cram/../header.h linenumber=4094 cram_free_block /src/htslib/cram/cram_io.c linenumber=4095 cram_stats_create /src/htslib/cram/cram_stats.c linenumber=3438 calloc linenumber=50 kh_init_m_tagmap /src/htslib/cram/cram_structs.h linenumber=3442 calloc linenumber=380 cram_free_block /src/htslib/cram/cram_io.c linenumber=4770 cram_free_container /src/htslib/cram/cram_io.c linenumber=4771 int32_put_blk /src/htslib/cram/cram_io.c linenumber=4775 block_append /src/htslib/cram/cram_io.h linenumber=815 sam_hdr_str /src/htslib/header.c linenumber=4778 block_append /src/htslib/cram/cram_io.h linenumber=4778 cram_compress_block /src/htslib/cram/cram_io.c linenumber=4783 cram_compress_block2 /src/htslib/cram/cram_io.c linenumber=2086 cram_free_block /src/htslib/cram/cram_io.c linenumber=4795 cram_free_container /src/htslib/cram/cram_io.c linenumber=4796 calloc linenumber=4823 cram_free_block /src/htslib/cram/cram_io.c linenumber=4824 cram_free_container /src/htslib/cram/cram_io.c linenumber=4825 block_append /src/htslib/cram/cram_io.h linenumber=4828 cram_write_container /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_write_block /src/htslib/cram/cram_io.c linenumber=4839 cram_free_block /src/htslib/cram/cram_io.c linenumber=4840 cram_free_container /src/htslib/cram/cram_io.c linenumber=4841 block_resize /src/htslib/cram/cram_io.h linenumber=4846 cram_write_block /src/htslib/cram/cram_io.c linenumber=4851 cram_free_block /src/htslib/cram/cram_io.c linenumber=4852 cram_free_container /src/htslib/cram/cram_io.c linenumber=4853 cram_free_block /src/htslib/cram/cram_io.c linenumber=4858 cram_free_container /src/htslib/cram/cram_io.c linenumber=4859 hflush /src/htslib/hfile.c linenumber=4862 sam_hrecs_rebuild_text /src/htslib/header.c linenumber=1999 strstr linenumber=2007 bgzf_write /src/htslib/bgzf.c linenumber=2015 hwrite /src/htslib/./htslib/hfile.h linenumber=2017 kputsn /src/htslib/./htslib/kstring.h linenumber=2027 kputs /src/htslib/./htslib/kstring.h linenumber=2028 kputsn /src/htslib/./htslib/kstring.h linenumber=2029 kputw /src/htslib/./htslib/kstring.h linenumber=2030 kputc /src/htslib/./htslib/kstring.h linenumber=2031 bgzf_write /src/htslib/bgzf.c linenumber=2036 hwrite /src/htslib/./htslib/hfile.h linenumber=2038 bgzf_flush /src/htslib/bgzf.c linenumber=2045 hflush /src/htslib/hfile.c linenumber=2047 __errno_location linenumber=2059 sam_hdr_dup /src/htslib/sam.c linenumber=2065 sam_hdr_destroy /src/htslib/sam.c linenumber=2066 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=4265 bam_read1 /src/htslib/sam.c linenumber=4127 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=804 bgzf_read /src/htslib/bgzf.c linenumber=168 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=809 bgzf_read /src/htslib/bgzf.c linenumber=817 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=820 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=821 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=822 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=827 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=830 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=831 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=832 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=833 realloc_bam_data /src/htslib/./sam_internal.h linenumber=840 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=843 fixup_missing_qname_nul /src/htslib/sam.c linenumber=845 realloc_bam_data /src/htslib/./sam_internal.h linenumber=783 bgzf_read_small /src/htslib/./htslib/bgzf.h linenumber=850 swap_data /src/htslib/sam.c linenumber=852 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=770 bam_tag2cigar /src/htslib/sam.c linenumber=853 bam_cigar2rqlens /src/htslib/sam.c linenumber=859 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=861 hts_log /src/htslib/hts.c linenumber=864 __errno_location linenumber=4131 sam_read1_cram /src/htslib/sam.c linenumber=4269 cram_get_bam_seq /src/htslib/cram/cram_decode.c linenumber=4140 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=3135 kh_get_sam_hrecs_t /src/htslib/./header.h linenumber=3135 strcmp linenumber=3141 strcmp linenumber=3143 strcmp linenumber=3145 strcmp linenumber=3147 hts_log /src/htslib/hts.c linenumber=3148 pthread_mutex_lock linenumber=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=4319 calloc linenumber=4320 cram_decode_slice_header /src/htslib/cram/cram_decode.c linenumber=4330 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=4335 hts_log /src/htslib/hts.c linenumber=4335 hts_log /src/htslib/hts.c linenumber=4341 calloc linenumber=4345 cram_read_block /src/htslib/cram/cram_io.c linenumber=4350 calloc linenumber=4361 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4375 cram_new_block /src/htslib/cram/cram_io.c linenumber=4378 cram_new_block /src/htslib/cram/cram_io.c linenumber=4379 cram_new_block /src/htslib/cram/cram_io.c linenumber=4380 cram_new_block /src/htslib/cram/cram_io.c linenumber=4381 cram_new_block /src/htslib/cram/cram_io.c linenumber=4382 cram_new_block /src/htslib/cram/cram_io.c linenumber=4383 cram_free_block /src/htslib/cram/cram_io.c linenumber=4394 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4397 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=4142 sam_read1_sam /src/htslib/sam.c linenumber=4273 sam_parse1 /src/htslib/sam.c linenumber=4153 strchr linenumber=2709 hts_log /src/htslib/hts.c linenumber=2711 hts_log /src/htslib/hts.c linenumber=2712 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2714 parse_sam_flag /src/htslib/sam.c linenumber=2724 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2493 strtoul linenumber=2499 strchr linenumber=2728 strcmp linenumber=2729 hts_log /src/htslib/hts.c linenumber=2730 bam_name2id /src/htslib/./htslib/sam.h linenumber=2731 sam_hdr_name2tid /src/htslib/header.c linenumber=783 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=2401 kh_get_m_s2i /src/htslib/./header.h linenumber=2409 hts_log /src/htslib/hts.c linenumber=2732 hts_strprint /src/htslib/textutils.c linenumber=2733 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=2733 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2737 hts_log /src/htslib/hts.c linenumber=2740 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2746 bam_parse_cigar /src/htslib/sam.c linenumber=2752 hts_log /src/htslib/hts.c linenumber=2926 read_ncigar /src/htslib/sam.c linenumber=2931 isdigit_c /src/htslib/./textutils_internal.h linenumber=2840 hts_log /src/htslib/hts.c linenumber=2842 hts_log /src/htslib/hts.c linenumber=2846 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2939 hts_log /src/htslib/hts.c linenumber=2940 parse_cigar /src/htslib/sam.c linenumber=2952 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2866 hts_log /src/htslib/hts.c linenumber=2868 hts_log /src/htslib/hts.c linenumber=2872 hts_log /src/htslib/hts.c linenumber=2878 bam_cigar2rlen /src/htslib/sam.c linenumber=2757 hts_log /src/htslib/hts.c linenumber=2760 strchr linenumber=2762 hts_log /src/htslib/hts.c linenumber=2765 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2767 strchr linenumber=2769 strcmp linenumber=2770 strcmp linenumber=2772 bam_name2id /src/htslib/./htslib/sam.h linenumber=2775 hts_log /src/htslib/hts.c linenumber=2776 hts_strprint /src/htslib/textutils.c linenumber=2777 hts_log /src/htslib/hts.c linenumber=2777 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2780 hts_log /src/htslib/hts.c linenumber=2783 hts_str2int /src/htslib/./textutils_internal.h linenumber=2787 hts_log /src/htslib/hts.c linenumber=2789 strchr linenumber=2791 strcmp linenumber=2792 hts_log /src/htslib/hts.c linenumber=2793 bam_cigar2qlen /src/htslib/sam.c linenumber=2795 hts_log /src/htslib/hts.c linenumber=2796 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2798 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2807 hts_log /src/htslib/hts.c linenumber=2813 aux_parse /src/htslib/sam.c linenumber=2822 isspace_c /src/htslib/./textutils_internal.h linenumber=2552 isspace_c /src/htslib/./textutils_internal.h linenumber=2555 isspace_c /src/htslib/./textutils_internal.h linenumber=2557 kh_get_tag /src/htslib/sam.c linenumber=2564 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2572 isspace_c /src/htslib/./textutils_internal.h linenumber=2576 hts_log /src/htslib/hts.c linenumber=2576 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2579 hts_str2int /src/htslib/./textutils_internal.h linenumber=2586 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2592 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=275 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2596 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=283 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2600 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2606 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2610 strtod linenumber=2616 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2616 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=345 strtod linenumber=2620 double_to_le /src/htslib/./htslib/hts_endian.h linenumber=2620 u64_to_le /src/htslib/./htslib/hts_endian.h linenumber=359 strchr linenumber=2623 strlen linenumber=2624 isspace_c /src/htslib/./textutils_internal.h linenumber=2625 hts_log /src/htslib/hts.c linenumber=2625 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2628 isspace_c /src/htslib/./textutils_internal.h linenumber=2635 hts_log /src/htslib/hts.c linenumber=2635 sam_parse_B_vals /src/htslib/sam.c linenumber=2638 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2488 hts_log /src/htslib/hts.c linenumber=2368 aux_type2size /src/htslib/sam.c linenumber=2378 hts_log /src/htslib/hts.c linenumber=2380 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2397 hts_log /src/htslib/hts.c linenumber=2398 sam_parse_Bc_vals /src/htslib/sam.c linenumber=2411 grow_B_array /src/htslib/sam.c linenumber=2242 __errno_location linenumber=2217 possibly_expand_bam_data /src/htslib/./sam_internal.h linenumber=2222 hts_log /src/htslib/hts.c linenumber=2223 hts_str2int /src/htslib/./textutils_internal.h linenumber=2245 sam_parse_BC_vals /src/htslib/sam.c linenumber=2414 grow_B_array /src/htslib/sam.c linenumber=2256 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2260 sam_parse_Bs_vals /src/htslib/sam.c linenumber=2417 grow_B_array /src/htslib/sam.c linenumber=2276 hts_str2int /src/htslib/./textutils_internal.h linenumber=2279 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2279 sam_parse_BS_vals /src/htslib/sam.c linenumber=2420 grow_B_array /src/htslib/sam.c linenumber=2291 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2295 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2295 sam_parse_Bi_vals /src/htslib/sam.c linenumber=2423 grow_B_array /src/htslib/sam.c linenumber=2312 hts_str2int /src/htslib/./textutils_internal.h linenumber=2315 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2315 sam_parse_BI_vals /src/htslib/sam.c linenumber=2426 grow_B_array /src/htslib/sam.c linenumber=2327 hts_str2uint /src/htslib/./textutils_internal.h linenumber=2331 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2331 sam_parse_Bf_vals /src/htslib/sam.c linenumber=2429 grow_B_array /src/htslib/sam.c linenumber=2348 strtod linenumber=2351 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2351 hts_log /src/htslib/hts.c linenumber=2434 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2437 hts_str2int /src/htslib/./textutils_internal.h linenumber=2451 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2460 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2462 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2464 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2468 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2470 sam_parse_B_vals_r /src/htslib/sam.c linenumber=2472 hts_log /src/htslib/hts.c linenumber=2477 isspace_c /src/htslib/./textutils_internal.h linenumber=2640 hts_strprint /src/htslib/textutils.c linenumber=2640 hts_log /src/htslib/hts.c linenumber=2640 isspace_c /src/htslib/./textutils_internal.h linenumber=2646 hts_log /src/htslib/hts.c linenumber=2646 bam_tag2cigar /src/htslib/sam.c linenumber=2825 sam_state_destroy /src/htslib/sam.c linenumber=4164 __errno_location linenumber=4165 bgzf_seek /src/htslib/bgzf.c linenumber=4168 bgzf_seek_common /src/htslib/bgzf.c linenumber=2278 sam_hdr_fill_hrecs /src/htslib/header.c linenumber=4179 pthread_create linenumber=4183 sam_dispatcher_read /src/htslib/sam.c linenumber=4183 ks_resize /src/htslib/./htslib/kstring.h linenumber=3327 pthread_mutex_lock linenumber=3332 pthread_cond_signal linenumber=3336 pthread_mutex_unlock linenumber=3337 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3338 pthread_mutex_unlock linenumber=3344 pthread_mutex_lock linenumber=3346 pthread_mutex_unlock linenumber=3352 calloc linenumber=3356 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3360 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3371 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=3384 hread /src/htslib/./htslib/hfile.h linenumber=3386 __errno_location linenumber=3388 sam_state_err /src/htslib/sam.c linenumber=3388 hts_realloc_pse /src/htslib/./htslib/hts_alloc.h linenumber=3405 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=3410 __assert_fail linenumber=3411 __assert_fail linenumber=3412 ks_resize /src/htslib/./htslib/kstring.h linenumber=3418 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=3430 sam_parse_worker /src/htslib/sam.c linenumber=3430 pthread_mutex_lock linenumber=3217 pthread_mutex_unlock linenumber=3222 calloc linenumber=3225 calloc linenumber=3230 sam_state_err /src/htslib/sam.c linenumber=3232 sam_state_err /src/htslib/sam.c linenumber=3243 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3253 sam_state_err /src/htslib/sam.c linenumber=3256 strchr linenumber=3272 sam_parse1 /src/htslib/sam.c linenumber=3284 __errno_location linenumber=3285 sam_state_err /src/htslib/sam.c linenumber=3285 cleanup_sp_lines /src/htslib/sam.c linenumber=3286 __assert_fail linenumber=3198 sam_free_sp_bams /src/htslib/sam.c linenumber=3201 pthread_mutex_lock linenumber=3295 pthread_mutex_unlock linenumber=3298 sam_free_sp_bams /src/htslib/sam.c linenumber=3302 cleanup_sp_lines /src/htslib/sam.c linenumber=3430 cleanup_sp_bams /src/htslib/sam.c linenumber=3430 sam_free_sp_bams /src/htslib/sam.c linenumber=3312 pthread_mutex_lock linenumber=3433 pthread_mutex_unlock linenumber=3435 pthread_mutex_unlock linenumber=3440 hts_tpool_dispatch /src/htslib/thread_pool.c linenumber=3444 sam_parse_eof /src/htslib/sam.c linenumber=3444 pthread_mutex_lock linenumber=3450 pthread_cond_wait linenumber=3452 pthread_cond_signal linenumber=3455 pthread_mutex_unlock linenumber=3456 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3457 pthread_mutex_unlock linenumber=3461 pthread_mutex_lock linenumber=3467 pthread_cond_signal linenumber=3469 pthread_mutex_unlock linenumber=3470 pthread_mutex_lock linenumber=3473 pthread_mutex_unlock linenumber=3476 __errno_location linenumber=3483 sam_state_err /src/htslib/sam.c linenumber=3483 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3484 hts_log /src/htslib/hts.c linenumber=4190 __errno_location linenumber=4198 pthread_mutex_lock linenumber=4202 pthread_mutex_unlock linenumber=4204 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=4208 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=4211 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=4212 pthread_mutex_lock linenumber=4215 pthread_mutex_unlock linenumber=4217 bam_copy1 /src/htslib/sam.c linenumber=4222 pthread_mutex_lock linenumber=4225 pthread_mutex_unlock linenumber=4228 hts_getline /src/htslib/hts.c linenumber=4241 sam_parse1 /src/htslib/sam.c linenumber=4244 hts_log /src/htslib/hts.c linenumber=4247 fastq_state_init /src/htslib/sam.c linenumber=4280 fastq_parse1 /src/htslib/sam.c linenumber=4285 hts_getline /src/htslib/hts.c linenumber=3938 strpbrk linenumber=3954 isspace_c /src/htslib/./textutils_internal.h linenumber=3966 isspace_c /src/htslib/./textutils_internal.h linenumber=3974 hts_getline /src/htslib/hts.c linenumber=3982 kputsn /src/htslib/./htslib/kstring.h linenumber=3988 hts_getline /src/htslib/hts.c linenumber=3997 kputsn /src/htslib/./htslib/kstring.h linenumber=4001 isdigit_c /src/htslib/./textutils_internal.h linenumber=4014 regexec linenumber=4028 hts_log /src/htslib/hts.c linenumber=4033 isalpha_c /src/htslib/./textutils_internal.h linenumber=4041 bam_set1 /src/htslib/sam.c linenumber=4061 bam_aux_append /src/htslib/sam.c linenumber=4073 __assert_fail linenumber=4756 realloc_bam_data /src/htslib/./sam_internal.h linenumber=4760 __errno_location linenumber=4780 isdigit_c /src/htslib/./textutils_internal.h linenumber=4085 strtol linenumber=4086 isdigit_c /src/htslib/./textutils_internal.h linenumber=4100 isspace_c /src/htslib/./textutils_internal.h linenumber=4103 bam_aux_append /src/htslib/sam.c linenumber=4112 aux_parse /src/htslib/sam.c linenumber=4119 __errno_location linenumber=4289 __errno_location linenumber=4293 sam_passes_filter /src/htslib/sam.c linenumber=4298 hts_filter_eval2 /src/htslib/hts_expr.c linenumber=1552 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=1552 memcmp linenumber=1230 ks_clear /src/htslib/./htslib/kstring.h linenumber=1233 kputw /src/htslib/./htslib/kstring.h linenumber=1238 kputc_ /src/htslib/./htslib/kstring.h linenumber=1239 kputs /src/htslib/./htslib/kstring.h linenumber=1241 kputs /src/htslib/./htslib/kstring.h linenumber=1243 memcmp linenumber=1250 bam_endpos /src/htslib/sam.c linenumber=1252 memcmp linenumber=1258 memcmp linenumber=1265 memcmp linenumber=1269 memcmp linenumber=1273 memcmp linenumber=1277 memcmp linenumber=1281 memcmp linenumber=1285 memcmp linenumber=1289 memcmp linenumber=1293 memcmp linenumber=1297 memcmp linenumber=1301 memcmp linenumber=1305 memcmp linenumber=1309 hts_log /src/htslib/hts.c linenumber=1314 memcmp linenumber=1322 memcmp linenumber=1342 bam_get_library /src/htslib/sam.c linenumber=1345 bam_aux_get /src/htslib/sam.c linenumber=1189 sam_hdr_find_tag_id /src/htslib/header.c linenumber=1196 ks_clear /src/htslib/./htslib/kstring.h linenumber=1346 kputs /src/htslib/./htslib/kstring.h linenumber=1346 memcmp linenumber=1352 memcmp linenumber=1356 memcmp linenumber=1360 sam_hdr_tid2name /src/htslib/header.c linenumber=1363 ks_clear /src/htslib/./htslib/kstring.h linenumber=1364 kputs /src/htslib/./htslib/kstring.h linenumber=1364 memcmp linenumber=1366 memcmp linenumber=1374 memcmp linenumber=1382 memcmp linenumber=1386 memcmp linenumber=1394 bam_cigar2qlen /src/htslib/sam.c linenumber=1396 memcmp linenumber=1398 ks_clear /src/htslib/./htslib/kstring.h linenumber=1401 kputs /src/htslib/./htslib/kstring.h linenumber=1401 memcmp linenumber=1403 ks_clear /src/htslib/./htslib/kstring.h linenumber=1405 ks_resize /src/htslib/./htslib/kstring.h linenumber=1406 memcmp linenumber=1417 bam_cigar2rlen /src/htslib/sam.c linenumber=1419 memcmp linenumber=1421 sam_hdr_tid2name /src/htslib/header.c linenumber=1424 ks_clear /src/htslib/./htslib/kstring.h linenumber=1425 kputs /src/htslib/./htslib/kstring.h linenumber=1425 memcmp linenumber=1427 sam_hdr_tid2name /src/htslib/header.c linenumber=1430 ks_clear /src/htslib/./htslib/kstring.h linenumber=1431 kputs /src/htslib/./htslib/kstring.h linenumber=1431 memcmp linenumber=1433 memcmp linenumber=1441 ks_clear /src/htslib/./htslib/kstring.h linenumber=1443 ks_resize /src/htslib/./htslib/kstring.h linenumber=1444 nibble2base /src/htslib/./sam_internal.h linenumber=1446 memcmp linenumber=1451 memcmp linenumber=1482 bam_aux_get /src/htslib/sam.c linenumber=1494 ks_clear /src/htslib/./htslib/kstring.h linenumber=1502 kputs /src/htslib/./htslib/kstring.h linenumber=1502 ks_clear /src/htslib/./htslib/kstring.h linenumber=1507 kputsn /src/htslib/./htslib/kstring.h linenumber=1507 bam_aux2i /src/htslib/sam.c linenumber=1514 get_int_aux_val /src/htslib/sam.c linenumber=5112 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=5096 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=5098 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=5099 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=5100 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=5101 __errno_location linenumber=5103 bam_aux2f /src/htslib/sam.c linenumber=1520 le_to_double /src/htslib/./htslib/hts_endian.h linenumber=5119 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=5120 get_int_aux_val /src/htslib/sam.c linenumber=5121 hts_log /src/htslib/hts.c linenumber=1524 hts_log /src/htslib/hts.c linenumber=1553 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1554 hts_expr_val_free /src/htslib/./htslib/hts_expr.h linenumber=1559 sam_write1 /src/htslib/sam.c linenumber=107 bam_write_idx1 /src/htslib/sam.c linenumber=4552 bam_write1 /src/htslib/sam.c linenumber=948 __errno_location linenumber=880 hts_log /src/htslib/hts.c linenumber=887 bgzf_flush_try /src/htslib/bgzf.c linenumber=899 lazy_flush /src/htslib/bgzf.c linenumber=2019 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=901 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=903 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=903 bgzf_write /src/htslib/bgzf.c linenumber=198 swap_data /src/htslib/sam.c linenumber=904 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=906 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=908 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=909 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=911 bam_cigar2rlen /src/htslib/sam.c linenumber=915 hts_log /src/htslib/hts.c linenumber=919 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=928 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=929 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=930 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=931 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=932 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=933 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=934 bgzf_write_small /src/htslib/./htslib/bgzf.h linenumber=935 swap_data /src/htslib/sam.c linenumber=937 bgzf_flush_try /src/htslib/bgzf.c linenumber=951 hts_idx_amend_last /src/htslib/hts.c linenumber=954 bam_write1 /src/htslib/sam.c linenumber=956 bam_endpos /src/htslib/sam.c linenumber=960 bgzf_idx_push /src/htslib/bgzf.c linenumber=960 hts_idx_push /src/htslib/hts.c linenumber=195 hts_idx_check_range /src/htslib/hts.c linenumber=2570 hts_idx_maxpos /src/htslib/hts.c linenumber=2548 hts_bin_maxpos /src/htslib/./htslib/hts.h linenumber=2543 hts_log /src/htslib/hts.c linenumber=2553 idx_format_name /src/htslib/hts.c linenumber=2558 hts_log /src/htslib/hts.c linenumber=2558 __errno_location linenumber=2562 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2577 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2581 hts_log /src/htslib/hts.c linenumber=2594 hts_log /src/htslib/hts.c linenumber=2599 hts_log /src/htslib/hts.c linenumber=2605 hts_log /src/htslib/hts.c linenumber=2610 kh_init_bin /src/htslib/hts.c linenumber=2615 calloc linenumber=2249 insert_to_l /src/htslib/hts.c linenumber=2620 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2365 hts_reg2bin /src/htslib/./htslib/hts.h linenumber=2624 insert_to_b /src/htslib/hts.c linenumber=2627 kh_put_bin /src/htslib/hts.c linenumber=2332 kh_resize_bin /src/htslib/hts.c linenumber=2249 __errno_location linenumber=2249 realloc linenumber=2249 calloc linenumber=2337 kh_del_bin /src/htslib/hts.c linenumber=2339 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2344 insert_to_b /src/htslib/hts.c linenumber=2632 insert_to_b /src/htslib/hts.c linenumber=2634 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=961 sam_hdr_tid2len /src/htslib/header.c linenumber=961 kh_get_s2i /src/htslib/hts.c linenumber=2443 hts_log /src/htslib/hts.c linenumber=961 cram_put_bam_seq /src/htslib/cram/cram_encode.c linenumber=4555 cram_new_container /src/htslib/cram/cram_io.c linenumber=3960 pthread_mutex_lock linenumber=3966 pthread_mutex_unlock linenumber=3969 hts_log /src/htslib/hts.c linenumber=3994 pthread_mutex_lock linenumber=3997 hts_log /src/htslib/hts.c linenumber=4000 pthread_mutex_unlock linenumber=4002 cram_next_container /src/htslib/cram/cram_encode.c linenumber=4011 cram_update_curr_slice /src/htslib/cram/cram_encode.c linenumber=3219 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=4257 calloc linenumber=4261 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4269 hts_malloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4271 cram_new_block /src/htslib/cram/cram_io.c linenumber=4274 cram_new_block /src/htslib/cram/cram_io.c linenumber=4275 cram_new_block /src/htslib/cram/cram_io.c linenumber=4276 cram_new_block /src/htslib/cram/cram_io.c linenumber=4277 cram_new_block /src/htslib/cram/cram_io.c linenumber=4278 cram_new_block /src/htslib/cram/cram_io.c linenumber=4279 string_pool_create /src/htslib/cram/string_alloc.c linenumber=4290 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4291 kh_init_m_s2i /src/htslib/cram/../header.h linenumber=4292 cram_free_slice /src/htslib/cram/cram_io.c linenumber=4302 pthread_mutex_lock linenumber=4043 hts_log /src/htslib/hts.c linenumber=4045 pthread_mutex_unlock linenumber=4056 pthread_mutex_lock linenumber=4059 calloc linenumber=4060 pthread_mutex_unlock linenumber=4061 pthread_mutex_lock linenumber=4075 calloc linenumber=4076 pthread_mutex_unlock linenumber=4077 pthread_mutex_lock linenumber=4081 pthread_mutex_unlock linenumber=4084 pthread_mutex_lock linenumber=4094 hts_realloc_p /src/htslib/cram/../htslib/hts_alloc.h linenumber=4099 pthread_mutex_unlock linenumber=4102 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4108 calloc linenumber=4116 pthread_mutex_unlock linenumber=4119 bam_set_mempolicy /src/htslib/cram/../htslib/sam.h linenumber=4124 pthread_mutex_unlock linenumber=4126 bam_copy1 /src/htslib/sam.c linenumber=4133 bam_cigar2qlen /src/htslib/sam.c linenumber=4143 hts_log /src/htslib/hts.c linenumber=4145 pthread_create linenumber=4578 sam_dispatcher_write /src/htslib/sam.c linenumber=4578 hts_tpool_next_result_wait /src/htslib/thread_pool.c linenumber=3497 hts_tpool_result_data /src/htslib/thread_pool.c linenumber=3498 sam_state_err /src/htslib/sam.c linenumber=3500 bgzf_flush_try /src/htslib/bgzf.c linenumber=3515 bgzf_write /src/htslib/bgzf.c linenumber=3517 hwrite /src/htslib/./htslib/hfile.h linenumber=3520 bam_endpos /src/htslib/sam.c linenumber=3527 bgzf_idx_push /src/htslib/bgzf.c linenumber=3526 __errno_location linenumber=3530 sam_state_err /src/htslib/sam.c linenumber=3530 sam_hdr_tid2name /src/htslib/header.c linenumber=3531 sam_hdr_tid2len /src/htslib/header.c linenumber=3531 hts_log /src/htslib/hts.c linenumber=3531 bam_endpos /src/htslib/sam.c linenumber=3536 hts_idx_push /src/htslib/hts.c linenumber=3536 __errno_location linenumber=3538 sam_state_err /src/htslib/sam.c linenumber=3538 sam_hdr_tid2name /src/htslib/header.c linenumber=3539 sam_hdr_tid2len /src/htslib/header.c linenumber=3539 hts_log /src/htslib/hts.c linenumber=3539 __assert_fail linenumber=3546 pthread_mutex_lock linenumber=3549 pthread_mutex_unlock linenumber=3553 bgzf_write /src/htslib/bgzf.c linenumber=3600 bgzf_flush_try /src/htslib/bgzf.c linenumber=3608 bgzf_write /src/htslib/bgzf.c linenumber=3613 hwrite /src/htslib/./htslib/hfile.h linenumber=3620 hts_tpool_delete_result /src/htslib/thread_pool.c linenumber=3625 pthread_mutex_lock linenumber=3628 pthread_mutex_unlock linenumber=3631 sam_state_err /src/htslib/sam.c linenumber=3634 hts_tpool_process_shutdown /src/htslib/thread_pool.c linenumber=3635 __errno_location linenumber=3639 sam_state_err /src/htslib/sam.c linenumber=3639 hts_log /src/htslib/hts.c linenumber=4585 pthread_mutex_lock linenumber=4592 pthread_mutex_unlock linenumber=4599 pthread_mutex_unlock linenumber=4601 calloc linenumber=4602 calloc linenumber=4603 bam_copy1 /src/htslib/sam.c linenumber=4616 pthread_mutex_lock linenumber=4623 pthread_mutex_unlock linenumber=4625 hts_tpool_dispatch3 /src/htslib/thread_pool.c linenumber=4628 sam_format_worker /src/htslib/sam.c linenumber=4628 cleanup_sp_bams /src/htslib/sam.c linenumber=4628 cleanup_sp_lines /src/htslib/sam.c linenumber=4628 pthread_mutex_unlock linenumber=4631 pthread_mutex_unlock linenumber=4634 sam_format1 /src/htslib/sam.c linenumber=4643 sam_format1_append /src/htslib/sam.c linenumber=4400 kputc /src/htslib/./htslib/kstring.h linenumber=4644 bgzf_flush_try /src/htslib/bgzf.c linenumber=4646 bgzf_write /src/htslib/bgzf.c linenumber=4648 hwrite /src/htslib/./htslib/hfile.h linenumber=4650 bam_endpos /src/htslib/sam.c linenumber=4655 bgzf_idx_push /src/htslib/bgzf.c linenumber=4655 sam_hdr_tid2name /src/htslib/header.c linenumber=4657 sam_hdr_tid2len /src/htslib/header.c linenumber=4657 hts_log /src/htslib/hts.c linenumber=4657 bam_endpos /src/htslib/sam.c linenumber=4662 hts_idx_push /src/htslib/hts.c linenumber=4662 sam_hdr_tid2name /src/htslib/header.c linenumber=4664 sam_hdr_tid2len /src/htslib/header.c linenumber=4664 hts_log /src/htslib/hts.c linenumber=4664 fastq_state_init /src/htslib/sam.c linenumber=4679 fastq_format1 /src/htslib/sam.c linenumber=4684 kputc /src/htslib/./htslib/kstring.h linenumber=4413 kputs /src/htslib/./htslib/kstring.h linenumber=4413 bam_aux_get /src/htslib/sam.c linenumber=4435 kputc /src/htslib/./htslib/kstring.h linenumber=4437 isalpha_c /src/htslib/./textutils_internal.h linenumber=4440 toupper_c /src/htslib/./textutils_internal.h linenumber=4440 kputc /src/htslib/./htslib/kstring.h linenumber=4440 kputs /src/htslib/./htslib/kstring.h linenumber=4445 kputs /src/htslib/./htslib/kstring.h linenumber=4453 kputs /src/htslib/./htslib/kstring.h linenumber=4456 bam_aux_get /src/htslib/sam.c linenumber=4466 ksprintf /src/htslib/kstring.c linenumber=4467 isupper_c /src/htslib/./textutils_internal.h linenumber=4471 __ctype_b_loc linenumber=177 islower_c /src/htslib/./textutils_internal.h linenumber=4471 __ctype_b_loc linenumber=173 hts_log /src/htslib/hts.c linenumber=4472 strlen linenumber=4473 strlen linenumber=4481 isalpha_c /src/htslib/./textutils_internal.h linenumber=4484 islower_c /src/htslib/./textutils_internal.h linenumber=4486 toupper_c /src/htslib/./textutils_internal.h linenumber=4487 kh_get_tag /src/htslib/sam.c linenumber=4498 kputc_ /src/htslib/./htslib/kstring.h linenumber=4499 sam_format_aux1 /src/htslib/./htslib/sam.h linenumber=4500 skip_aux /src/htslib/sam.c linenumber=4503 kputsn /src/htslib/./htslib/kstring.h linenumber=4506 ks_resize /src/htslib/./htslib/kstring.h linenumber=4509 kputc_ /src/htslib/./htslib/kstring.h linenumber=4510 kputc_ /src/htslib/./htslib/kstring.h linenumber=4516 kputc_ /src/htslib/./htslib/kstring.h linenumber=4519 kputsn /src/htslib/./htslib/kstring.h linenumber=4524 kputc_ /src/htslib/./htslib/kstring.h linenumber=4528 kputc_ /src/htslib/./htslib/kstring.h linenumber=4531 kputc_ /src/htslib/./htslib/kstring.h linenumber=4534 kputc /src/htslib/./htslib/kstring.h linenumber=4537 bgzf_flush_try /src/htslib/bgzf.c linenumber=4687 bgzf_write /src/htslib/bgzf.c linenumber=4689 hwrite /src/htslib/./htslib/hfile.h linenumber=4692 __errno_location linenumber=4699 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=1778 bcf_hdr_init /src/htslib/vcf.c linenumber=2678 calloc linenumber=1704 kh_init_vdict /src/htslib/vcf.c linenumber=1707 calloc linenumber=75 kh_resize_vdict /src/htslib/vcf.c linenumber=1710 __errno_location linenumber=75 realloc linenumber=75 __ac_FNV1a_hash_string /src/htslib/./htslib/khash.h linenumber=75 calloc linenumber=1713 kh_init_hdict /src/htslib/vcf.c linenumber=1715 strchr linenumber=1723 bcf_hdr_append /src/htslib/vcf.c linenumber=1725 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1557 calloc linenumber=672 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=674 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=684 isalpha_c /src/htslib/./textutils_internal.h linenumber=701 isalnum_c /src/htslib/./textutils_internal.h linenumber=704 bcf_hrec_add_key /src/htslib/vcf.c linenumber=714 __assert_fail linenumber=445 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=446 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=449 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=453 is_escaped /src/htslib/vcf.c linenumber=734 bcf_hrec_set_val /src/htslib/vcf.c linenumber=756 __errno_location linenumber=472 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=475 __errno_location linenumber=485 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=488 isspace_c /src/htslib/./textutils_internal.h linenumber=773 hts_strprint /src/htslib/textutils.c linenumber=776 hts_log /src/htslib/hts.c linenumber=776 bcf_hrec_destroy /src/htslib/vcf.c linenumber=786 hts_strprint /src/htslib/textutils.c linenumber=793 hts_log /src/htslib/hts.c linenumber=793 bcf_hrec_destroy /src/htslib/vcf.c linenumber=797 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1559 get_hdr_aux /src/htslib/vcf.c linenumber=1190 bcf_hrec_check /src/htslib/vcf.c linenumber=1195 bcf_hrec_set_type /src/htslib/vcf.c linenumber=600 strcmp linenumber=530 strcmp linenumber=531 strcmp linenumber=532 strcmp linenumber=533 bcf_hrec_find_key /src/htslib/vcf.c linenumber=604 strcasecmp linenumber=524 bcf_hrec_find_key /src/htslib/vcf.c linenumber=614 strcmp linenumber=617 bcf_hrec_find_key /src/htslib/vcf.c linenumber=625 hts_log /src/htslib/hts.c linenumber=636 hts_log /src/htslib/hts.c linenumber=640 hts_log /src/htslib/hts.c linenumber=644 bcf_hdr_register_hrec /src/htslib/vcf.c linenumber=1197 bcf_hrec_set_type /src/htslib/vcf.c linenumber=1060 bcf_hdr_register_hrec_ctg /src/htslib/vcf.c linenumber=1064 bcf_hrec_find_key /src/htslib/vcf.c linenumber=844 bcf_hrec_find_key /src/htslib/vcf.c linenumber=847 strtoll linenumber=852 hts_log /src/htslib/hts.c linenumber=854 strdup linenumber=863 kh_get_vdict /src/htslib/vcf.c linenumber=868 strcmp linenumber=75 kh_put_vdict /src/htslib/vcf.c linenumber=875 kh_resize_vdict /src/htslib/vcf.c linenumber=75 bcf_hrec_find_key /src/htslib/vcf.c linenumber=879 strtol linenumber=883 kh_del_vdict /src/htslib/vcf.c linenumber=887 hts_log /src/htslib/hts.c linenumber=890 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=899 hts_log /src/htslib/hts.c linenumber=811 __errno_location linenumber=813 hts_resize_array_ /src/htslib/hts.c linenumber=823 hts_log /src/htslib/hts.c linenumber=5124 __errno_location linenumber=5125 realloc linenumber=5129 __errno_location linenumber=5131 __errno_location linenumber=5132 strerror linenumber=5132 hts_log /src/htslib/hts.c linenumber=5132 __errno_location linenumber=5133 abort linenumber=5142 abort linenumber=5153 kh_del_vdict /src/htslib/vcf.c linenumber=901 hrec_add_idx /src/htslib/vcf.c linenumber=907 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=499 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=503 strdup linenumber=507 kputw /src/htslib/./htslib/kstring.h linenumber=511 bcf_hdr_register_hrec_info /src/htslib/vcf.c linenumber=1069 strcmp linenumber=928 strcmp linenumber=929 strtol linenumber=932 hts_log /src/htslib/hts.c linenumber=935 strcmp linenumber=939 strcmp linenumber=941 strcmp linenumber=942 strcmp linenumber=943 strcmp linenumber=944 strcmp linenumber=945 hts_log /src/htslib/hts.c linenumber=948 strcmp linenumber=952 strcmp linenumber=955 strcmp linenumber=956 strcmp linenumber=957 strcmp linenumber=958 strcmp linenumber=959 strcmp linenumber=960 strcmp linenumber=961 strcmp linenumber=962 strcmp linenumber=963 __isoc99_sscanf linenumber=966 hts_log /src/htslib/hts.c linenumber=974 hts_log /src/htslib/hts.c linenumber=979 hts_log /src/htslib/hts.c linenumber=985 strdup linenumber=996 kh_get_vdict /src/htslib/vcf.c linenumber=1000 strcmp linenumber=1004 hrec_add_idx /src/htslib/vcf.c linenumber=1015 hrec_add_idx /src/htslib/vcf.c linenumber=1028 kh_put_vdict /src/htslib/vcf.c linenumber=1034 bcf_hdr_set_idx /src/htslib/vcf.c linenumber=1043 kh_del_vdict /src/htslib/vcf.c linenumber=1044 hrec_add_idx /src/htslib/vcf.c linenumber=1049 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1204 ksprintf /src/htslib/kstring.c linenumber=1208 kh_get_hdict /src/htslib/vcf.c linenumber=1213 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1217 bcf_get_version /src/htslib/vcf.c linenumber=1222 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=1661 ksprintf /src/htslib/kstring.c linenumber=1283 get_hdr_aux /src/htslib/vcf.c linenumber=1284 kh_get_hdict /src/htslib/vcf.c linenumber=1285 strcmp linenumber=1293 strcmp linenumber=1303 ksprintf /src/htslib/kstring.c linenumber=1306 get_hdr_aux /src/htslib/vcf.c linenumber=1307 kh_get_hdict /src/htslib/vcf.c linenumber=1308 strcmp linenumber=1316 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1317 strcmp linenumber=1318 kh_get_vdict /src/htslib/vcf.c linenumber=1323 hts_log /src/htslib/hts.c linenumber=1664 strstr linenumber=168 strchr linenumber=172 strtol linenumber=175 __errno_location linenumber=176 __errno_location linenumber=177 strtol linenumber=181 __errno_location linenumber=182 hts_log /src/htslib/hts.c linenumber=190 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1227 ksprintf /src/htslib/kstring.c linenumber=1229 kh_get_hdict /src/htslib/vcf.c linenumber=1234 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1238 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=1246 bcf_hdr_unregister_hrec /src/htslib/vcf.c linenumber=1249 bcf_hrec_find_key /src/htslib/vcf.c linenumber=1085 kh_get_vdict /src/htslib/vcf.c linenumber=1091 kh_put_hdict /src/htslib/vcf.c linenumber=1256 kh_resize_hdict /src/htslib/vcf.c linenumber=80 bcf_hdr_append /src/htslib/vcf.c linenumber=1727 kh_destroy_vdict /src/htslib/vcf.c linenumber=1734 hts_log /src/htslib/hts.c linenumber=2680 hts_getline /src/htslib/hts.c linenumber=2684 hts_log /src/htslib/hts.c linenumber=2688 hopen /src/htslib/hfile.c linenumber=2693 hts_log /src/htslib/hts.c linenumber=2695 khgetline /src/htslib/hfile.c linenumber=2698 strchr linenumber=2699 kputs /src/htslib/./htslib/kstring.h linenumber=2701 kputsn /src/htslib/./htslib/kstring.h linenumber=2702 kputs /src/htslib/./htslib/kstring.h linenumber=2703 atol linenumber=2704 kputl /src/htslib/./htslib/kstring.h linenumber=2704 kputll /src/htslib/./htslib/kstring.h linenumber=446 kputsn /src/htslib/./htslib/kstring.h linenumber=2705 hclose /src/htslib/hfile.c linenumber=2708 hts_log /src/htslib/hts.c linenumber=2709 kputsn /src/htslib/./htslib/kstring.h linenumber=2714 kputc /src/htslib/./htslib/kstring.h linenumber=2715 hts_log /src/htslib/hts.c linenumber=2721 bcf_hdr_parse /src/htslib/vcf.c linenumber=2724 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1479 strcasecmp linenumber=1480 hts_log /src/htslib/hts.c linenumber=1481 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1482 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1483 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1488 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1489 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1490 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=1496 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=1497 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1498 __assert_fail linenumber=1503 strerror linenumber=1506 hts_log /src/htslib/hts.c linenumber=1506 strncmp linenumber=1521 strchr linenumber=1522 hts_strprint /src/htslib/textutils.c linenumber=1525 hts_log /src/htslib/hts.c linenumber=1525 hts_log /src/htslib/hts.c linenumber=1542 bcf_hdr_parse_sample_line /src/htslib/vcf.c linenumber=1546 strlen linenumber=290 strncmp linenumber=290 hts_log /src/htslib/hts.c linenumber=292 strlen linenumber=296 strncmp linenumber=298 hts_log /src/htslib/hts.c linenumber=300 bcf_hdr_add_sample_len /src/htslib/vcf.c linenumber=310 isspace_c /src/htslib/./textutils_internal.h linenumber=236 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=252 kh_put_vdict /src/htslib/vcf.c linenumber=259 hts_log /src/htslib/hts.c linenumber=268 bcf_hdr_sync /src/htslib/vcf.c linenumber=1548 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=328 get_hdr_aux /src/htslib/vcf.c linenumber=342 bcf_hdr_check_sanity /src/htslib/vcf.c linenumber=1550 bcf_get_version /src/htslib/vcf.c linenumber=1334 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1413 kh_get_vdict /src/htslib/vcf.c linenumber=4712 atoi linenumber=1419 hts_log /src/htslib/hts.c linenumber=1424 hts_log /src/htslib/hts.c linenumber=1429 bcf_hdr_id2int /src/htslib/vcf.c linenumber=1440 atoi linenumber=1455 hts_log /src/htslib/hts.c linenumber=1460 hts_log /src/htslib/hts.c linenumber=1465 tbx_index_load3 /src/htslib/tbx.c linenumber=2727 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=5002 strstr linenumber=4935 strdup linenumber=4940 __errno_location linenumber=4942 strerror linenumber=4942 hts_log /src/htslib/hts.c linenumber=4942 hts_idx_load3 /src/htslib/hts.c linenumber=4947 hisremote /src/htslib/hfile.c linenumber=5006 stat linenumber=5008 hts_log /src/htslib/hts.c linenumber=5011 idx_test_and_fetch /src/htslib/hts.c linenumber=5016 hisremote /src/htslib/hfile.c linenumber=4640 strncmp linenumber=4645 strcspn linenumber=4645 kputsn /src/htslib/./htslib/kstring.h linenumber=4652 access linenumber=4653 hopen /src/htslib/hfile.c linenumber=4662 hts_log /src/htslib/hts.c linenumber=4663 hts_detect_format2 /src/htslib/hts.c linenumber=4667 hts_log /src/htslib/hts.c linenumber=4668 hts_log /src/htslib/hts.c linenumber=4673 hts_open_tmpfile /src/htslib/hts.c linenumber=4678 hts_log /src/htslib/hts.c linenumber=4679 hts_log /src/htslib/hts.c linenumber=4682 calloc linenumber=4683 __errno_location linenumber=4685 strerror linenumber=4685 hts_log /src/htslib/hts.c linenumber=4685 hread /src/htslib/./htslib/hfile.h linenumber=4688 hwrite /src/htslib/./htslib/hfile.h linenumber=4689 __errno_location linenumber=4690 strerror linenumber=4690 hts_log /src/htslib/hts.c linenumber=4690 hts_log /src/htslib/hts.c linenumber=4698 hclose /src/htslib/hfile.c linenumber=4701 __errno_location linenumber=4702 strerror linenumber=4702 hts_log /src/htslib/hts.c linenumber=4702 rename linenumber=4707 __errno_location linenumber=4708 strerror linenumber=4708 hts_log /src/htslib/hts.c linenumber=4708 ks_clear /src/htslib/./htslib/kstring.h linenumber=4711 hclose /src/htslib/hfile.c linenumber=4720 hts_log /src/htslib/hts.c linenumber=4721 hopen /src/htslib/hfile.c linenumber=4729 hclose_abruptly /src/htslib/hfile.c linenumber=4730 strlen linenumber=4732 __errno_location linenumber=4737 hclose_abruptly /src/htslib/hfile.c linenumber=4738 hclose_abruptly /src/htslib/hfile.c linenumber=4739 unlink linenumber=4740 __errno_location linenumber=4743 strdup linenumber=5018 idx_read /src/htslib/hts.c linenumber=5026 bgzf_open /src/htslib/bgzf.c linenumber=3004 ed_is_big /src/htslib/./htslib/hts.h linenumber=3006 bgzf_read /src/htslib/bgzf.c linenumber=3007 memcmp linenumber=3009 bgzf_read /src/htslib/bgzf.c linenumber=3011 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3012 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3015 bgzf_read /src/htslib/bgzf.c linenumber=3016 bgzf_read /src/htslib/bgzf.c linenumber=3020 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3021 hts_idx_init /src/htslib/hts.c linenumber=3023 calloc linenumber=2416 calloc linenumber=2428 calloc linenumber=2430 idx_read_core /src/htslib/hts.c linenumber=3027 ed_is_big /src/htslib/./htslib/hts.h linenumber=2936 kh_init_bin /src/htslib/hts.c linenumber=2944 bgzf_read /src/htslib/bgzf.c linenumber=2945 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2946 bgzf_read /src/htslib/bgzf.c linenumber=2950 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2951 kh_put_bin /src/htslib/hts.c linenumber=2952 bgzf_read /src/htslib/bgzf.c linenumber=2957 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2958 bgzf_read /src/htslib/bgzf.c linenumber=2960 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2961 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2965 bgzf_read /src/htslib/bgzf.c linenumber=2967 swap_bins /src/htslib/hts.c linenumber=2968 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2751 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2752 bgzf_read /src/htslib/bgzf.c linenumber=2973 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=2974 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=2979 bgzf_read /src/htslib/bgzf.c linenumber=2981 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2982 update_loff /src/htslib/hts.c linenumber=2986 hts_bin_bot /src/htslib/./htslib/hts.h linenumber=2456 hts_bin_level /src/htslib/./htslib/hts.h linenumber=1570 bgzf_read /src/htslib/bgzf.c linenumber=2989 ed_swap_8p /src/htslib/./htslib/hts.h linenumber=2990 memcmp linenumber=3029 bgzf_read /src/htslib/bgzf.c linenumber=3033 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3034 hts_idx_init /src/htslib/hts.c linenumber=3036 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=3037 hts_malloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=3040 bgzf_read /src/htslib/bgzf.c linenumber=3045 idx_read_core /src/htslib/hts.c linenumber=3048 memcmp linenumber=3050 bgzf_read /src/htslib/bgzf.c linenumber=3052 ed_swap_4p /src/htslib/./htslib/hts.h linenumber=3053 hts_idx_init /src/htslib/hts.c linenumber=3055 idx_read_core /src/htslib/hts.c linenumber=3056 __errno_location linenumber=3058 bgzf_close /src/htslib/bgzf.c linenumber=3060 bgzf_close /src/htslib/bgzf.c linenumber=3064 hts_idx_destroy /src/htslib/hts.c linenumber=3065 __errno_location linenumber=5028 strerror linenumber=5028 hts_log /src/htslib/hts.c linenumber=5028 hts_idx_check_local /src/htslib/hts.c linenumber=4952 hisremote /src/htslib/hfile.c linenumber=4778 strlen linenumber=4779 strncmp linenumber=4786 strncmp linenumber=4787 hts_log /src/htslib/hts.c linenumber=4797 strlen linenumber=4798 calloc linenumber=4799 strcpy linenumber=4805 stat linenumber=4806 strcpy linenumber=4812 stat linenumber=4813 strcpy linenumber=4822 stat linenumber=4823 strcpy linenumber=4829 stat linenumber=4830 strcpy linenumber=4838 stat linenumber=4839 strcpy linenumber=4845 stat linenumber=4846 strcpy linenumber=4854 stat linenumber=4855 strcpy linenumber=4861 stat linenumber=4862 strcpy linenumber=4871 strcmp linenumber=4873 strcmp linenumber=4874 strcpy linenumber=4875 stat linenumber=4876 strcpy linenumber=4881 stat linenumber=4883 hisremote /src/htslib/hfile.c linenumber=4952 idx_filename /src/htslib/hts.c linenumber=4954 haddextension /src/htslib/hfile.c linenumber=4900 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=4904 haddextension /src/htslib/hfile.c linenumber=4906 idx_test_and_fetch /src/htslib/hts.c linenumber=4910 idx_filename /src/htslib/hts.c linenumber=4957 idx_filename /src/htslib/hts.c linenumber=4958 idx_filename /src/htslib/hts.c linenumber=4963 idx_filename /src/htslib/hts.c linenumber=4966 idx_filename /src/htslib/hts.c linenumber=4967 hts_log /src/htslib/hts.c linenumber=4975 hts_idx_load3 /src/htslib/hts.c linenumber=4980 idx_read /src/htslib/hts.c linenumber=4982 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=2731 calloc linenumber=661 calloc linenumber=664 __assert_fail linenumber=674 __assert_fail linenumber=679 bcf_hdr_get_hrec /src/htslib/vcf.c linenumber=2735 add_missing_contig_hrec /src/htslib/vcf.c linenumber=2737 calloc linenumber=2649 strdup linenumber=2653 bcf_hrec_add_key /src/htslib/vcf.c linenumber=2656 strlen linenumber=2657 bcf_hrec_set_val /src/htslib/vcf.c linenumber=2657 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=2659 __errno_location linenumber=2664 __errno_location linenumber=2665 strerror linenumber=2665 hts_log /src/htslib/hts.c linenumber=2665 bcf_hrec_destroy /src/htslib/vcf.c linenumber=2666 __errno_location linenumber=2667 bcf_hdr_sync /src/htslib/vcf.c linenumber=2741 tbx_destroy /src/htslib/tbx.c linenumber=2744 tbx_destroy /src/htslib/tbx.c linenumber=2750 bcf_hdr_destroy /src/htslib/vcf.c linenumber=2753 get_hdr_aux /src/htslib/vcf.c linenumber=1744 kh_destroy_hdict /src/htslib/vcf.c linenumber=1759 kh_destroy_vdict /src/htslib/vcf.c linenumber=1762 bcf_hrec_destroy /src/htslib/vcf.c linenumber=1766 hts_log /src/htslib/hts.c linenumber=1780 __assert_fail linenumber=1784 bcf_hdr_init /src/htslib/vcf.c linenumber=1789 bgzf_read /src/htslib/bgzf.c linenumber=1794 hts_log /src/htslib/hts.c linenumber=1796 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1797 strncmp linenumber=1800 strncmp linenumber=1802 hts_log /src/htslib/hts.c linenumber=1803 hts_log /src/htslib/hts.c linenumber=1805 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1806 bgzf_read /src/htslib/bgzf.c linenumber=1812 __errno_location linenumber=1814 __errno_location linenumber=1816 bgzf_read /src/htslib/bgzf.c linenumber=1820 bcf_hdr_parse /src/htslib/vcf.c linenumber=1822 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1825 get_hdr_aux /src/htslib/vcf.c linenumber=199 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1826 __assert_fail linenumber=53 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1826 bcf_hdr_decr_ref /src/htslib/vcf.c linenumber=216 get_hdr_aux /src/htslib/vcf.c linenumber=205 bcf_hdr_destroy /src/htslib/vcf.c linenumber=210 hts_log /src/htslib/hts.c linenumber=1830 bcf_hdr_destroy /src/htslib/vcf.c linenumber=1832 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=1839 bcf_hdr_sync /src/htslib/vcf.c linenumber=1843 vcf_hdr_write /src/htslib/vcf.c linenumber=1848 bcf_hdr_format /src/htslib/vcf.c linenumber=2891 _bcf_hrec_format /src/htslib/vcf.c linenumber=2821 ksprintf /src/htslib/kstring.c linenumber=2795 strcmp linenumber=2799 kputc /src/htslib/./htslib/kstring.h linenumber=2800 ksprintf /src/htslib/kstring.c linenumber=2801 ksprintf /src/htslib/kstring.c linenumber=2804 ksprintf /src/htslib/kstring.c linenumber=2807 ksprintf /src/htslib/kstring.c linenumber=2823 ksprintf /src/htslib/kstring.c linenumber=2826 ksprintf /src/htslib/kstring.c linenumber=2828 ksprintf /src/htslib/kstring.c linenumber=2830 bgzf_write /src/htslib/bgzf.c linenumber=2898 bgzf_flush /src/htslib/bgzf.c linenumber=2899 hwrite /src/htslib/./htslib/hfile.h linenumber=2901 bcf_hdr_format /src/htslib/vcf.c linenumber=1855 kputc /src/htslib/./htslib/kstring.h linenumber=1859 bgzf_write /src/htslib/bgzf.c linenumber=1862 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=1864 bgzf_write /src/htslib/bgzf.c linenumber=1865 bgzf_write /src/htslib/bgzf.c linenumber=1866 bgzf_flush /src/htslib/bgzf.c linenumber=1867 bcf_hdr_incr_ref /src/htslib/vcf.c linenumber=1869 bgzf_set_private_data /src/htslib/./bgzf_internal.h linenumber=1870 hdr_bgzf_private_data_cleanup /src/htslib/vcf.c linenumber=1870 bcf_init /src/htslib/vcf.c linenumber=155 calloc linenumber=1883 bcf_read /src/htslib/vcf.c linenumber=159 vcf_read /src/htslib/vcf.c linenumber=2335 hts_getline /src/htslib/hts.c linenumber=4260 vcf_parse /src/htslib/vcf.c linenumber=4262 ks_resize /src/htslib/./htslib/kstring.h linenumber=4095 bcf_clear /src/htslib/vcf.c linenumber=4108 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=1907 kstrtok /src/htslib/kstring.c linenumber=4113 kh_get_vdict /src/htslib/vcf.c linenumber=4118 hts_log /src/htslib/hts.c linenumber=4120 hts_log /src/htslib/hts.c linenumber=4122 fix_chromosome /src/htslib/vcf.c linenumber=4124 ksprintf /src/htslib/kstring.c linenumber=3830 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3832 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3834 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3835 bcf_hdr_sync /src/htslib/vcf.c linenumber=3836 kh_get_vdict /src/htslib/vcf.c linenumber=3837 hts_log /src/htslib/hts.c linenumber=4125 kstrtok /src/htslib/kstring.c linenumber=4133 hts_str2uint /src/htslib/./textutils_internal.h linenumber=4139 hts_log /src/htslib/hts.c linenumber=4141 hts_log /src/htslib/hts.c linenumber=4144 kstrtok /src/htslib/kstring.c linenumber=4153 memcmp linenumber=4157 bcf_enc_vchar /src/htslib/vcf.c linenumber=4157 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3049 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=3050 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=4158 kstrtok /src/htslib/kstring.c linenumber=4161 bcf_enc_vchar /src/htslib/vcf.c linenumber=4165 kstrtok /src/htslib/kstring.c linenumber=4169 memcmp linenumber=4173 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4177 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=4177 bcf_enc_vchar /src/htslib/vcf.c linenumber=4182 kstrtok /src/htslib/kstring.c linenumber=4191 memcmp linenumber=4195 atof linenumber=4195 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4196 kstrtok /src/htslib/kstring.c linenumber=4200 memcmp linenumber=4204 vcf_parse_filter /src/htslib/vcf.c linenumber=4205 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3854 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3856 hts_log /src/htslib/hts.c linenumber=3856 kstrtok /src/htslib/kstring.c linenumber=3863 kh_get_vdict /src/htslib/vcf.c linenumber=3865 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3870 hts_log /src/htslib/hts.c linenumber=3870 hts_log /src/htslib/hts.c linenumber=3873 ksprintf /src/htslib/kstring.c linenumber=3876 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3877 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3879 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3880 bcf_hdr_sync /src/htslib/vcf.c linenumber=3881 kh_get_vdict /src/htslib/vcf.c linenumber=3882 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3885 hts_log /src/htslib/hts.c linenumber=3885 bcf_enc_vint /src/htslib/vcf.c linenumber=3894 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2916 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=2918 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=2958 ks_resize /src/htslib/./htslib/kstring.h linenumber=2959 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2970 ks_resize /src/htslib/./htslib/kstring.h linenumber=2971 i16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2980 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2986 ks_resize /src/htslib/./htslib/kstring.h linenumber=2987 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2991 bcf_enc_vint /src/htslib/vcf.c linenumber=4208 kstrtok /src/htslib/kstring.c linenumber=4212 memcmp linenumber=4216 vcf_parse_info /src/htslib/vcf.c linenumber=4217 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3915 hts_log /src/htslib/hts.c linenumber=3915 kh_get_vdict /src/htslib/vcf.c linenumber=3929 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3932 hts_log /src/htslib/hts.c linenumber=3932 hts_log /src/htslib/hts.c linenumber=3935 ksprintf /src/htslib/kstring.c linenumber=3938 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3939 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3941 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3942 bcf_hdr_sync /src/htslib/vcf.c linenumber=3943 kh_get_vdict /src/htslib/vcf.c linenumber=3944 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3947 hts_log /src/htslib/hts.c linenumber=3947 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3954 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3956 bcf_enc_vchar /src/htslib/vcf.c linenumber=3958 hts_realloc_p /src/htslib/./htslib/hts_alloc.h linenumber=3966 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3968 hts_log /src/htslib/hts.c linenumber=3968 hts_str2int /src/htslib/./textutils_internal.h linenumber=4004 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4010 hts_log /src/htslib/hts.c linenumber=4010 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=4029 bcf_enc_vint /src/htslib/vcf.c linenumber=4032 memcmp linenumber=4035 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4041 hts_log /src/htslib/hts.c linenumber=4041 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=4051 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=4053 bcf_enc_vfloat /src/htslib/vcf.c linenumber=4056 __assert_fail linenumber=3041 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3042 serialize_float_array /src/htslib/vcf.c linenumber=3043 ks_resize /src/htslib/./htslib/kstring.h linenumber=3027 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=3031 kstrtok /src/htslib/kstring.c linenumber=4224 vcf_parse_format /src/htslib/vcf.c linenumber=4228 vcf_parse_format_empty1 /src/htslib/vcf.c linenumber=3776 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3219 hts_log /src/htslib/hts.c linenumber=3219 vcf_parse_format_dict2 /src/htslib/vcf.c linenumber=3780 kstrtok /src/htslib/kstring.c linenumber=3242 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3245 hts_log /src/htslib/hts.c linenumber=3245 kh_get_vdict /src/htslib/vcf.c linenumber=3251 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3255 hts_log /src/htslib/hts.c linenumber=3255 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3259 hts_log /src/htslib/hts.c linenumber=3259 hts_log /src/htslib/hts.c linenumber=3261 ksprintf /src/htslib/kstring.c linenumber=3264 bcf_hdr_parse_line /src/htslib/vcf.c linenumber=3265 bcf_hdr_add_hrec /src/htslib/vcf.c linenumber=3267 bcf_hrec_destroy /src/htslib/vcf.c linenumber=3268 bcf_hdr_sync /src/htslib/vcf.c linenumber=3269 kh_get_vdict /src/htslib/vcf.c linenumber=3271 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3274 hts_log /src/htslib/hts.c linenumber=3274 vcf_parse_format_max3 /src/htslib/vcf.c linenumber=3801 hts_log /src/htslib/hts.c linenumber=3355 vcf_parse_format_alloc4 /src/htslib/vcf.c linenumber=3805 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3391 hts_log /src/htslib/hts.c linenumber=3391 align_mem /src/htslib/vcf.c linenumber=3396 kputsn /src/htslib/./htslib/kstring.h linenumber=3206 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3397 hts_log /src/htslib/hts.c linenumber=3397 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3407 hts_log /src/htslib/hts.c linenumber=3407 ks_resize /src/htslib/./htslib/kstring.h linenumber=3416 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3417 hts_log /src/htslib/hts.c linenumber=3417 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3442 hts_log /src/htslib/hts.c linenumber=3442 vcf_parse_format_fill5 /src/htslib/vcf.c linenumber=3809 bcf_get_version /src/htslib/vcf.c linenumber=3464 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3487 hts_log /src/htslib/hts.c linenumber=3487 hts_str2uint /src/htslib/./textutils_internal.h linenumber=3535 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3560 hts_log /src/htslib/hts.c linenumber=3560 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3564 hts_log /src/htslib/hts.c linenumber=3564 hts_str2int /src/htslib/./textutils_internal.h linenumber=3590 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3595 hts_log /src/htslib/hts.c linenumber=3595 isdigit_c /src/htslib/./textutils_internal.h linenumber=3616 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3617 hts_str2dbl /src/htslib/./textutils_internal.h linenumber=3621 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=3624 hts_log /src/htslib/hts.c linenumber=3624 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3634 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3636 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3638 hts_log /src/htslib/hts.c linenumber=3638 hts_strprint /src/htslib/textutils.c linenumber=3651 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3651 hts_log /src/htslib/hts.c linenumber=3651 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3686 bcf_float_set /src/htslib/./htslib/vcf.h linenumber=3687 vcf_parse_format_gt6 /src/htslib/vcf.c linenumber=3813 bcf_enc_int1 /src/htslib/./htslib/vcf.h linenumber=3709 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3711 kputsn /src/htslib/./htslib/kstring.h linenumber=3712 bcf_enc_vint /src/htslib/vcf.c linenumber=3714 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=3716 serialize_float_array /src/htslib/vcf.c linenumber=3717 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3720 hts_log /src/htslib/hts.c linenumber=3720 vcf_parse_format_check7 /src/htslib/vcf.c linenumber=3817 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3746 hts_log /src/htslib/hts.c linenumber=3746 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=3753 hts_log /src/htslib/hts.c linenumber=3753 get_rlen /src/htslib/vcf.c linenumber=4234 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6547 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6558 strlen linenumber=186 memcmp linenumber=191 memcmp linenumber=192 memcmp linenumber=193 memcmp linenumber=194 strcmp linenumber=6562 strcmp linenumber=6563 strlen linenumber=6568 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6571 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=6576 svlen_on_ref_for_vcf_alt /src/htslib/./hts_internal.h linenumber=6580 strncmp linenumber=6584 strncmp linenumber=6585 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6596 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6601 bcf_get_info /src/htslib/vcf.c linenumber=6606 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6154 bcf_get_info_id /src/htslib/vcf.c linenumber=6156 bcf_unpack /src/htslib/vcf.c linenumber=6173 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4336 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=3161 bcf_fmt_array /src/htslib/vcf.c linenumber=3162 kputc_ /src/htslib/./htslib/kstring.h linenumber=3118 memchr linenumber=3127 kputsn /src/htslib/./htslib/kstring.h linenumber=3128 kputc /src/htslib/./htslib/kstring.h linenumber=3131 le_to_i8 /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_i16 /src/htslib/./htslib/hts_endian.h linenumber=3148 kputc_ /src/htslib/./htslib/kstring.h linenumber=3148 kputc /src/htslib/./htslib/kstring.h linenumber=3148 kputw /src/htslib/./htslib/kstring.h linenumber=3148 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3149 kputc_ /src/htslib/./htslib/kstring.h linenumber=3149 kputc /src/htslib/./htslib/kstring.h linenumber=3149 kputw /src/htslib/./htslib/kstring.h linenumber=3149 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3150 kputc_ /src/htslib/./htslib/kstring.h linenumber=3150 kputc /src/htslib/./htslib/kstring.h linenumber=3150 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3150 kputd /src/htslib/kstring.c linenumber=3150 hts_log /src/htslib/hts.c linenumber=3151 exit linenumber=3151 hts_realloc_or_die /src/htslib/hts.c linenumber=4342 bcf_fmt_sized_array /src/htslib/vcf.c linenumber=4348 kputc_ /src/htslib/./htslib/kstring.h linenumber=4349 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4364 hts_realloc_or_die /src/htslib/hts.c linenumber=4365 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=4367 hts_realloc_or_die /src/htslib/hts.c linenumber=4374 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=4377 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4283 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4284 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=4296 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=4300 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=4304 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=4308 hts_realloc_or_die /src/htslib/hts.c linenumber=4382 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=4385 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4268 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4269 bcf_get_info /src/htslib/vcf.c linenumber=6607 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6610 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6612 bcf_unpack_info_core1 /src/htslib/vcf.c linenumber=6618 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6625 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6634 bcf_get_fmt /src/htslib/vcf.c linenumber=6641 bcf_hdr_id2int /src/htslib/vcf.c linenumber=6147 bcf_get_fmt_id /src/htslib/vcf.c linenumber=6149 bcf_unpack /src/htslib/vcf.c linenumber=6162 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=6644 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=6646 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=6651 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6681 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6685 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6689 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6693 le_to_i8 /src/htslib/./htslib/hts_endian.h linenumber=6725 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=6729 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6733 le_to_i64 /src/htslib/./htslib/hts_endian.h linenumber=6737 bgzf_get_private_data /src/htslib/./bgzf_internal.h linenumber=2337 __assert_fail linenumber=68 bcf_read1_core /src/htslib/vcf.c linenumber=2338 bgzf_read /src/htslib/bgzf.c linenumber=1944 bcf_clear /src/htslib/vcf.c linenumber=1948 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1949 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1952 ks_resize /src/htslib/./htslib/kstring.h linenumber=1957 ks_resize /src/htslib/./htslib/kstring.h linenumber=1958 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1959 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1960 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1962 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=1963 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1964 le_to_u16 /src/htslib/./htslib/hts_endian.h linenumber=1965 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=1966 bgzf_read /src/htslib/bgzf.c linenumber=1973 bgzf_read /src/htslib/bgzf.c linenumber=1974 bcf_record_check /src/htslib/vcf.c linenumber=2339 bcf_get_version /src/htslib/vcf.c linenumber=2127 bcf_hdr_id2int /src/htslib/vcf.c linenumber=2128 hts_log /src/htslib/hts.c linenumber=2135 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2142 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2025 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=1995 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=1998 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2144 get_type_name /src/htslib/vcf.c linenumber=2144 hts_log /src/htslib/hts.c linenumber=2144 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2153 hts_log /src/htslib/hts.c linenumber=2153 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2160 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2163 get_type_name /src/htslib/vcf.c linenumber=2163 hts_log /src/htslib/hts.c linenumber=2163 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2173 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2177 get_type_name /src/htslib/vcf.c linenumber=2177 hts_log /src/htslib/hts.c linenumber=2177 bcf_dec_int1 /src/htslib/./htslib/vcf.h linenumber=2184 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2189 hts_log /src/htslib/hts.c linenumber=2189 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2201 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2205 hts_log /src/htslib/hts.c linenumber=2205 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2208 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2212 get_type_name /src/htslib/vcf.c linenumber=2212 hts_log /src/htslib/hts.c linenumber=2212 bcf_dec_typed_int1_safe /src/htslib/vcf.c linenumber=2226 bcf_record_check_err /src/htslib/vcf.c linenumber=2230 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2099 hts_log /src/htslib/hts.c linenumber=2099 bcf_dec_size_safe /src/htslib/vcf.c linenumber=2233 bcf_record_check_err /src/htslib/vcf.c linenumber=2236 updatephasing /src/htslib/vcf.c linenumber=2251 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2264 hts_log /src/htslib/hts.c linenumber=2264 get_rlen /src/htslib/vcf.c linenumber=2270 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2279 hts_log /src/htslib/hts.c linenumber=2279 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2283 hts_log /src/htslib/hts.c linenumber=2283 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2287 hts_log /src/htslib/hts.c linenumber=2287 bcf_subset_format /src/htslib/vcf.c linenumber=2341 hts_realloc_or_die /src/htslib/hts.c linenumber=2304 bcf_unpack_fmt_core1 /src/htslib/vcf.c linenumber=2309 bcf_write /src/htslib/vcf.c linenumber=160 bcf_hdr_sync /src/htslib/vcf.c linenumber=2590 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2594 vcf_write /src/htslib/vcf.c linenumber=2600 vcf_format /src/htslib/vcf.c linenumber=4678 bcf_seqname /src/htslib/./htslib/vcf.h linenumber=4395 hts_log /src/htslib/hts.c linenumber=4397 __errno_location linenumber=4399 bcf_unpack /src/htslib/vcf.c linenumber=4403 get_hdr_aux /src/htslib/vcf.c linenumber=4414 calloc linenumber=4416 kputs /src/htslib/./htslib/kstring.h linenumber=4421 kputc_ /src/htslib/./htslib/kstring.h linenumber=4422 kputll /src/htslib/./htslib/kstring.h linenumber=4422 kputc_ /src/htslib/./htslib/kstring.h linenumber=4423 kputs /src/htslib/./htslib/kstring.h linenumber=4423 kputc_ /src/htslib/./htslib/kstring.h linenumber=4424 kputs /src/htslib/./htslib/kstring.h linenumber=4425 kputc_ /src/htslib/./htslib/kstring.h linenumber=4426 kputc_ /src/htslib/./htslib/kstring.h linenumber=4427 kputc_ /src/htslib/./htslib/kstring.h linenumber=4430 kputs /src/htslib/./htslib/kstring.h linenumber=4431 kputc_ /src/htslib/./htslib/kstring.h linenumber=4433 kputc_ /src/htslib/./htslib/kstring.h linenumber=4434 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4435 kputc_ /src/htslib/./htslib/kstring.h linenumber=4435 kputd /src/htslib/kstring.c linenumber=4436 kputc_ /src/htslib/./htslib/kstring.h linenumber=4437 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4443 hts_log /src/htslib/hts.c linenumber=4443 __errno_location linenumber=4445 kputc_ /src/htslib/./htslib/kstring.h linenumber=4448 strlen linenumber=4450 kputsn /src/htslib/./htslib/kstring.h linenumber=4451 kputc_ /src/htslib/./htslib/kstring.h linenumber=4453 kputc_ /src/htslib/./htslib/kstring.h linenumber=4455 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4475 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4476 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4492 hts_log /src/htslib/hts.c linenumber=4492 __errno_location linenumber=4497 strlen linenumber=4503 ks_resize /src/htslib/./htslib/kstring.h linenumber=4505 bcf_fmt_array /src/htslib/vcf.c linenumber=4522 bcf_float_is_missing /src/htslib/./htslib/vcf.h linenumber=4527 kputd /src/htslib/kstring.c linenumber=4530 kputc_ /src/htslib/./htslib/kstring.h linenumber=4532 kputc_ /src/htslib/./htslib/kstring.h linenumber=4541 kputw /src/htslib/./htslib/kstring.h linenumber=4543 kputc_ /src/htslib/./htslib/kstring.h linenumber=4546 kputll /src/htslib/./htslib/kstring.h linenumber=4548 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4550 hts_log /src/htslib/hts.c linenumber=4550 __errno_location linenumber=4551 kputc_ /src/htslib/./htslib/kstring.h linenumber=4556 kputc_ /src/htslib/./htslib/kstring.h linenumber=4557 hts_malloc_p /src/htslib/./htslib/hts_alloc.h linenumber=4576 bcf_dec_typed_int1 /src/htslib/./htslib/vcf.h linenumber=4586 bcf_dec_size /src/htslib/./htslib/vcf.h linenumber=4587 kputc_ /src/htslib/./htslib/kstring.h linenumber=4593 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4600 hts_log /src/htslib/hts.c linenumber=4600 __errno_location linenumber=4601 strlen linenumber=4608 kputsn /src/htslib/./htslib/kstring.h linenumber=4610 kputsn /src/htslib/./htslib/kstring.h linenumber=4614 kputc_ /src/htslib/./htslib/kstring.h linenumber=4618 kputc_ /src/htslib/./htslib/kstring.h linenumber=4623 bcf_format_gt_v2 /src/htslib/vcf.c linenumber=4626 le_to_i8 /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_i16 /src/htslib/./htslib/hts_endian.h linenumber=6487 kputc /src/htslib/./htslib/kstring.h linenumber=6487 kputw /src/htslib/./htslib/kstring.h linenumber=6487 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=6489 kputc /src/htslib/./htslib/kstring.h linenumber=6489 kputw /src/htslib/./htslib/kstring.h linenumber=6489 kputc /src/htslib/./htslib/kstring.h linenumber=6491 hts_log /src/htslib/hts.c linenumber=6492 get_hdr_aux /src/htslib/vcf.c linenumber=6496 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6506 ks_resize /src/htslib/./htslib/kstring.h linenumber=474 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6508 kinsert_char /src/htslib/./htslib/kstring.h linenumber=6515 hts_log /src/htslib/hts.c linenumber=4627 __errno_location linenumber=4628 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4636 kputc_ /src/htslib/./htslib/kstring.h linenumber=3068 kputc_ /src/htslib/./htslib/kstring.h linenumber=3074 kputw /src/htslib/./htslib/kstring.h linenumber=3075 le_to_i16 /src/htslib/./htslib/hts_endian.h linenumber=3079 kputc_ /src/htslib/./htslib/kstring.h linenumber=3082 kputw /src/htslib/./htslib/kstring.h linenumber=3083 le_to_i32 /src/htslib/./htslib/hts_endian.h linenumber=3088 kputc_ /src/htslib/./htslib/kstring.h linenumber=3091 kputw /src/htslib/./htslib/kstring.h linenumber=3092 le_to_u32 /src/htslib/./htslib/hts_endian.h linenumber=3097 kputc_ /src/htslib/./htslib/kstring.h linenumber=3100 le_to_float /src/htslib/./htslib/hts_endian.h linenumber=3101 kputd /src/htslib/kstring.c linenumber=3101 hts_log /src/htslib/hts.c linenumber=3106 bcf_fmt_array /src/htslib/vcf.c linenumber=4638 kputc_ /src/htslib/./htslib/kstring.h linenumber=4644 bcf_fmt_array1 /src/htslib/vcf.c linenumber=4646 bcf_fmt_array /src/htslib/vcf.c linenumber=4648 kputc_ /src/htslib/./htslib/kstring.h linenumber=4650 kputsn /src/htslib/./htslib/kstring.h linenumber=4657 kputc /src/htslib/./htslib/kstring.h linenumber=4659 bgzf_flush_try /src/htslib/bgzf.c linenumber=4681 hts_idx_amend_last /src/htslib/hts.c linenumber=4684 bgzf_write /src/htslib/bgzf.c linenumber=4685 hwrite /src/htslib/./htslib/hfile.h linenumber=4687 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=4692 hts_idx_tbi_name /src/htslib/hts.c linenumber=4692 strlen linenumber=2663 hts_realloc_ps /src/htslib/./htslib/hts_alloc.h linenumber=2664 strcpy linenumber=2670 le_to_u32 /src/htslib/./cram/../htslib/hts_endian.h linenumber=2674 u32_to_le /src/htslib/./cram/../htslib/hts_endian.h linenumber=2674 bgzf_idx_push /src/htslib/bgzf.c linenumber=4695 bcf_strerror /src/htslib/vcf.c linenumber=2609 add_desc_to_buffer /src/htslib/vcf.c linenumber=6433 strlen linenumber=6407 snprintf linenumber=6408 snprintf linenumber=6411 add_desc_to_buffer /src/htslib/vcf.c linenumber=6442 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2609 hts_log /src/htslib/hts.c linenumber=2609 bcf1_sync /src/htslib/vcf.c linenumber=2612 bcf1_sync_id /src/htslib/vcf.c linenumber=2419 strcmp linenumber=2358 strlen linenumber=2359 bcf_enc_vchar /src/htslib/vcf.c linenumber=2359 bcf_enc_size /src/htslib/./htslib/vcf.h linenumber=2361 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2422 strlen linenumber=2369 bcf_enc_vchar /src/htslib/vcf.c linenumber=2369 strlen linenumber=2372 bcf1_sync_filter /src/htslib/vcf.c linenumber=2425 bcf_enc_vint /src/htslib/vcf.c linenumber=2379 bcf_enc_vint /src/htslib/vcf.c linenumber=2381 bcf1_sync_info /src/htslib/vcf.c linenumber=2428 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2398 bcf_unpack /src/htslib/vcf.c linenumber=2435 bcf1_sync_id /src/htslib/vcf.c linenumber=2442 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2444 bcf1_sync_alleles /src/htslib/vcf.c linenumber=2450 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2453 strlen linenumber=2454 bcf1_sync_filter /src/htslib/vcf.c linenumber=2463 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2465 bcf_enc_vint /src/htslib/vcf.c linenumber=2467 bcf1_sync_info /src/htslib/vcf.c linenumber=2476 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2483 kputsn_ /src/htslib/./htslib/kstring.h linenumber=2520 bcf_seqname_safe /src/htslib/./htslib/vcf.h linenumber=2616 hts_log /src/htslib/hts.c linenumber=2616 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2622 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2623 i32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2624 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2625 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2626 float_to_le /src/htslib/./htslib/hts_endian.h linenumber=2627 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2628 u16_to_le /src/htslib/./htslib/hts_endian.h linenumber=2629 u32_to_le /src/htslib/./htslib/hts_endian.h linenumber=2630 bgzf_write /src/htslib/bgzf.c linenumber=2631 bgzf_write /src/htslib/bgzf.c linenumber=2632 bgzf_write /src/htslib/bgzf.c linenumber=2633 bgzf_idx_push /src/htslib/bgzf.c linenumber=2636 bcf_destroy /src/htslib/vcf.c linenumber=163 bcf_empty /src/htslib/vcf.c linenumber=1935 bcf_clear /src/htslib/vcf.c linenumber=1921 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 ====================================