[med-svn] [Git][med-team/htslib][master] 6 commits: fix-cram-external-header.patch: new patch
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Jun 11 19:34:40 BST 2023
Étienne Mollier pushed to branch master at Debian Med / htslib
Commits:
1cfe4203 by Étienne Mollier at 2023-06-11T18:58:14+02:00
fix-cram-external-header.patch: new patch
This fixes a typo causing failure to build from source.
- - - - -
ba6605ab by Étienne Mollier at 2023-06-11T19:25:29+02:00
d/changelog: TODO item resolved
- - - - -
020ac267 by Étienne Mollier at 2023-06-11T19:27:10+02:00
d/libhts3.symbols: update symbols table.
Upstream is now tracking symbols versionning. The diff is large with
numerous missing entries, but that is because of the "@Base" being
replaced by the the versioned "@HTSLIB_*" entries.
- - - - -
09537962 by Étienne Mollier at 2023-06-11T20:04:11+02:00
d/t/run-unit-test: copy htslib.map.
This file is needed for one of the linking tests done during the
autopkgtest run, otherwise it fails.
- - - - -
bba69f75 by Étienne Mollier at 2023-06-11T20:05:33+02:00
fix-whatis-entry.patch: new patch
This change fixes a bad whatis(1) entry caught by lintian.
- - - - -
5dc37525 by Étienne Mollier at 2023-06-11T20:21:56+02:00
ready to upload to experimental
- - - - -
6 changed files:
- debian/changelog
- debian/libhts3.symbols
- + debian/patches/fix-cram-external-header.patch
- + debian/patches/fix-whatis-entry.patch
- debian/patches/series
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,4 @@
-htslib (1.17+ds-0+exp1) UNRELEASED; urgency=medium
-
- TODO: upgrade of htslib to version 1.17 looks to require htscodecs upgrade
- first, otherwise we get the following build error:
- cram/cram_external.c:46:10: fatal error: htscodecs/rANS_static4x16.h.h: No such file or directory
+htslib (1.17+ds-0+exp1) experimental; urgency=medium
* New upstream version
* Standards-Version: 4.6.2 (routine-update)
@@ -14,8 +10,19 @@ htslib (1.17+ds-0+exp1) UNRELEASED; urgency=medium
- cram_to_bam_export.patch: unfuzz
- fix_sequence_of_linked_libs.patch: unfuzz
- trim-file-prefix.patch: refresh
-
- -- Étienne Mollier <emollier at debian.org> Sun, 11 Jun 2023 15:36:02 +0200
+ * fix-cram-external-header.patch: new patch.
+ This fixes a FTBFS caused by a typo in the source code.
+ * d/libhts3.symbols: update symbols table.
+ Upstream is now tracking symbols versioning. The change is large with
+ numerous missing entries, but that is because of the "@Base" being
+ replaced by the versioned "@HTSLIB_*" entries.
+ * d/t/run-unit-test: copy htslib.map.
+ This file is needed for one of the linking tests done during the
+ autopkgtest run, otherwise it fails.
+ * fix-whatis-entry.patch: new patch.
+ This change fixes a bad whatis(1) entry caught by lintian.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 11 Jun 2023 20:10:19 +0200
htslib (1.16+ds-3) unstable; urgency=medium
=====================================
debian/libhts3.symbols
=====================================
@@ -1,162 +1,183 @@
libhts.so.3 libhts3 #MINVER#
* Build-Depends-Package: libhts-dev
- bam_aux2A at Base 1.10
- bam_aux2Z at Base 1.10
- bam_aux2f at Base 1.10
- bam_aux2i at Base 1.10
- bam_auxB2f at Base 1.10
- bam_auxB2i at Base 1.10
- bam_auxB_len at Base 1.10
- bam_aux_append at Base 1.10
- bam_aux_del at Base 1.10
- bam_aux_get at Base 1.10
- bam_aux_update_array at Base 1.10
- bam_aux_update_float at Base 1.10
- bam_aux_update_int at Base 1.10
- bam_aux_update_str at Base 1.10
- bam_cigar2qlen at Base 1.10
- bam_cigar2rlen at Base 1.10
- bam_cigar_table at Base 1.10
- bam_copy1 at Base 1.10
- bam_destroy1 at Base 1.10
- bam_dup1 at Base 1.10
- bam_endpos at Base 1.10
- bam_flag2str at Base 1.10
- bam_hdr_read at Base 1.10
- bam_hdr_write at Base 1.10
+ HTSLIB_1.0 at HTSLIB_1.0 1.17
+ HTSLIB_1.10 at HTSLIB_1.10 1.17
+ HTSLIB_1.11 at HTSLIB_1.11 1.17
+ HTSLIB_1.12 at HTSLIB_1.12 1.17
+ HTSLIB_1.13 at HTSLIB_1.13 1.17
+ HTSLIB_1.14 at HTSLIB_1.14 1.17
+ HTSLIB_1.15 at HTSLIB_1.15 1.17
+ HTSLIB_1.16 at HTSLIB_1.16 1.17
+ HTSLIB_1.17 at HTSLIB_1.17 1.17
+ HTSLIB_1.1 at HTSLIB_1.1 1.17
+ HTSLIB_1.2.1 at HTSLIB_1.2.1 1.17
+ HTSLIB_1.3 at HTSLIB_1.3 1.17
+ HTSLIB_1.4 at HTSLIB_1.4 1.17
+ HTSLIB_1.5 at HTSLIB_1.5 1.17
+ HTSLIB_1.6 at HTSLIB_1.6 1.17
+ HTSLIB_1.7 at HTSLIB_1.7 1.17
+ HTSLIB_1.9 at HTSLIB_1.9 1.17
+ bam_aux2A at HTSLIB_1.0 1.17
+ bam_aux2Z at HTSLIB_1.0 1.17
+ bam_aux2f at HTSLIB_1.0 1.17
+ bam_aux2i at HTSLIB_1.0 1.17
+ bam_auxB2f at HTSLIB_1.4 1.17
+ bam_auxB2i at HTSLIB_1.4 1.17
+ bam_auxB_len at HTSLIB_1.4 1.17
+ bam_aux_append at HTSLIB_1.0 1.17
+ bam_aux_del at HTSLIB_1.0 1.17
+ bam_aux_first at HTSLIB_1.17 1.17
+ bam_aux_get at HTSLIB_1.0 1.17
+ bam_aux_next at HTSLIB_1.17 1.17
+ bam_aux_remove at HTSLIB_1.17 1.17
+ bam_aux_update_array at HTSLIB_1.9 1.17
+ bam_aux_update_float at HTSLIB_1.9 1.17
+ bam_aux_update_int at HTSLIB_1.9 1.17
+ bam_aux_update_str at HTSLIB_1.4 1.17
+ bam_cigar2qlen at HTSLIB_1.0 1.17
+ bam_cigar2rlen at HTSLIB_1.0 1.17
+ bam_cigar_table at HTSLIB_1.10 1.17
+ bam_copy1 at HTSLIB_1.0 1.17
+ bam_destroy1 at HTSLIB_1.0 1.17
+ bam_dup1 at HTSLIB_1.0 1.17
+ bam_endpos at HTSLIB_1.0 1.17
+ bam_flag2str at HTSLIB_1.0 1.17
+ bam_hdr_read at HTSLIB_1.0 1.17
+ bam_hdr_write at HTSLIB_1.0 1.17
bam_index_build at Base 1.16
- bam_init1 at Base 1.10
- bam_mods_at_next_pos at Base 1.16
- bam_mods_at_qpos at Base 1.16
- bam_mods_query_type at Base 1.16
- bam_mods_recorded at Base 1.16
- bam_mplp64_auto at Base 1.10
- bam_mplp_auto at Base 1.10
- bam_mplp_constructor at Base 1.10
- bam_mplp_destroy at Base 1.10
- bam_mplp_destructor at Base 1.10
- bam_mplp_init at Base 1.10
- bam_mplp_init_overlaps at Base 1.10
- bam_mplp_reset at Base 1.10
- bam_mplp_set_maxcnt at Base 1.10
- bam_next_basemod at Base 1.16
- bam_parse_basemod at Base 1.16
- bam_parse_cigar at Base 1.13
- bam_plp64_auto at Base 1.10
- bam_plp64_next at Base 1.10
- bam_plp_auto at Base 1.10
- bam_plp_constructor at Base 1.10
- bam_plp_destroy at Base 1.10
- bam_plp_destructor at Base 1.10
- bam_plp_init at Base 1.10
+ bam_init1 at HTSLIB_1.0 1.17
+ bam_mods_at_next_pos at HTSLIB_1.14 1.17
+ bam_mods_at_qpos at HTSLIB_1.14 1.17
+ bam_mods_query_type at HTSLIB_1.16 1.17
+ bam_mods_recorded at HTSLIB_1.16 1.17
+ bam_mplp64_auto at HTSLIB_1.10 1.17
+ bam_mplp_auto at HTSLIB_1.0 1.17
+ bam_mplp_constructor at HTSLIB_1.4 1.17
+ bam_mplp_destroy at HTSLIB_1.0 1.17
+ bam_mplp_destructor at HTSLIB_1.4 1.17
+ bam_mplp_init at HTSLIB_1.0 1.17
+ bam_mplp_init_overlaps at HTSLIB_1.0 1.17
+ bam_mplp_reset at HTSLIB_1.4 1.17
+ bam_mplp_set_maxcnt at HTSLIB_1.0 1.17
+ bam_next_basemod at HTSLIB_1.14 1.17
+ bam_parse_basemod at HTSLIB_1.14 1.17
+ bam_parse_cigar at HTSLIB_1.12 1.17
+ bam_plp64_auto at HTSLIB_1.10 1.17
+ bam_plp64_next at HTSLIB_1.10 1.17
+ bam_plp_auto at HTSLIB_1.0 1.17
+ bam_plp_constructor at HTSLIB_1.4 1.17
+ bam_plp_destroy at HTSLIB_1.0 1.17
+ bam_plp_destructor at HTSLIB_1.4 1.17
+ bam_plp_init at HTSLIB_1.0 1.17
bam_plp_init_overlaps at Base 1.16
- bam_plp_insertion at Base 1.10
- bam_plp_insertion_mod at Base 1.16
- bam_plp_next at Base 1.10
- bam_plp_push at Base 1.10
- bam_plp_reset at Base 1.10
- bam_plp_set_maxcnt at Base 1.10
- bam_read1 at Base 1.10
- bam_set1 at Base 1.13
- bam_set_qname at Base 1.10
- bam_str2flag at Base 1.10
- bam_write1 at Base 1.10
- bcf_add_filter at Base 1.10
- bcf_add_id at Base 1.10
- bcf_calc_ac at Base 1.10
- bcf_clear at Base 1.10
- bcf_copy at Base 1.10
- bcf_destroy at Base 1.10
- bcf_dup at Base 1.10
- bcf_empty at Base 1.10
- bcf_enc_vchar at Base 1.10
- bcf_enc_vfloat at Base 1.10
- bcf_enc_vint at Base 1.10
- bcf_float_missing at Base 1.10
- bcf_float_vector_end at Base 1.10
- bcf_fmt_array at Base 1.10
- bcf_fmt_sized_array at Base 1.10
- bcf_get_fmt at Base 1.10
- bcf_get_fmt_id at Base 1.10
- bcf_get_format_string at Base 1.10
- bcf_get_format_values at Base 1.10
- bcf_get_info at Base 1.10
- bcf_get_info_id at Base 1.10
- bcf_get_info_values at Base 1.10
- bcf_get_variant_type at Base 1.10
- bcf_get_variant_types at Base 1.10
- bcf_gt_type at Base 1.10
- bcf_has_filter at Base 1.10
- bcf_has_variant_type at Base 1.16
- bcf_has_variant_types at Base 1.16
- bcf_hdr_add_hrec at Base 1.10
- bcf_hdr_add_sample at Base 1.10
- bcf_hdr_append at Base 1.10
+ bam_plp_insertion at HTSLIB_1.10 1.17
+ bam_plp_insertion_mod at HTSLIB_1.14 1.17
+ bam_plp_next at HTSLIB_1.0 1.17
+ bam_plp_push at HTSLIB_1.0 1.17
+ bam_plp_reset at HTSLIB_1.0 1.17
+ bam_plp_set_maxcnt at HTSLIB_1.0 1.17
+ bam_read1 at HTSLIB_1.0 1.17
+ bam_set1 at HTSLIB_1.12 1.17
+ bam_set_qname at HTSLIB_1.10 1.17
+ bam_str2flag at HTSLIB_1.0 1.17
+ bam_write1 at HTSLIB_1.0 1.17
+ bcf_add_filter at HTSLIB_1.0 1.17
+ bcf_add_id at HTSLIB_1.3 1.17
+ bcf_calc_ac at HTSLIB_1.0 1.17
+ bcf_clear at HTSLIB_1.0 1.17
+ bcf_copy at HTSLIB_1.2.1 1.17
+ bcf_destroy at HTSLIB_1.0 1.17
+ bcf_dup at HTSLIB_1.0 1.17
+ bcf_empty at HTSLIB_1.3 1.17
+ bcf_enc_vchar at HTSLIB_1.0 1.17
+ bcf_enc_vfloat at HTSLIB_1.0 1.17
+ bcf_enc_vint at HTSLIB_1.0 1.17
+ bcf_float_missing at HTSLIB_1.0 1.17
+ bcf_float_vector_end at HTSLIB_1.0 1.17
+ bcf_fmt_array at HTSLIB_1.0 1.17
+ bcf_fmt_sized_array at HTSLIB_1.0 1.17
+ bcf_get_fmt at HTSLIB_1.0 1.17
+ bcf_get_fmt_id at HTSLIB_1.1 1.17
+ bcf_get_format_string at HTSLIB_1.0 1.17
+ bcf_get_format_values at HTSLIB_1.0 1.17
+ bcf_get_info at HTSLIB_1.0 1.17
+ bcf_get_info_id at HTSLIB_1.1 1.17
+ bcf_get_info_values at HTSLIB_1.0 1.17
+ bcf_get_variant_type at HTSLIB_1.0 1.17
+ bcf_get_variant_types at HTSLIB_1.0 1.17
+ bcf_gt_type at HTSLIB_1.0 1.17
+ bcf_has_filter at HTSLIB_1.0 1.17
+ bcf_has_variant_type at HTSLIB_1.16 1.17
+ bcf_has_variant_types at HTSLIB_1.16 1.17
+ bcf_hdr_add_hrec at HTSLIB_1.0 1.17
+ bcf_hdr_add_sample at HTSLIB_1.0 1.17
+ bcf_hdr_append at HTSLIB_1.0 1.17
bcf_hdr_check_sanity at Base 1.16
- bcf_hdr_combine at Base 1.10
- bcf_hdr_destroy at Base 1.10
- bcf_hdr_dup at Base 1.10
- bcf_hdr_fmt_text at Base 1.10
- bcf_hdr_format at Base 1.10
- bcf_hdr_get_hrec at Base 1.10
- bcf_hdr_get_version at Base 1.10
- bcf_hdr_id2int at Base 1.10
- bcf_hdr_init at Base 1.10
- bcf_hdr_merge at Base 1.10
- bcf_hdr_parse at Base 1.10
- bcf_hdr_parse_line at Base 1.10
+ bcf_hdr_combine at HTSLIB_1.0 1.17
+ bcf_hdr_destroy at HTSLIB_1.0 1.17
+ bcf_hdr_dup at HTSLIB_1.0 1.17
+ bcf_hdr_fmt_text at HTSLIB_1.0 1.17
+ bcf_hdr_format at HTSLIB_1.4 1.17
+ bcf_hdr_get_hrec at HTSLIB_1.0 1.17
+ bcf_hdr_get_version at HTSLIB_1.0 1.17
+ bcf_hdr_id2int at HTSLIB_1.0 1.17
+ bcf_hdr_init at HTSLIB_1.0 1.17
+ bcf_hdr_merge at HTSLIB_1.3 1.17
+ bcf_hdr_parse at HTSLIB_1.0 1.17
+ bcf_hdr_parse_line at HTSLIB_1.0 1.17
bcf_hdr_parse_sample_line at Base 1.16
- bcf_hdr_printf at Base 1.10
- bcf_hdr_read at Base 1.10
- bcf_hdr_remove at Base 1.10
- bcf_hdr_seqnames at Base 1.10
- bcf_hdr_set at Base 1.10
- bcf_hdr_set_samples at Base 1.10
- bcf_hdr_set_version at Base 1.10
- bcf_hdr_subset at Base 1.10
- bcf_hdr_sync at Base 1.10
- bcf_hdr_write at Base 1.10
+ bcf_hdr_printf at HTSLIB_1.0 1.17
+ bcf_hdr_read at HTSLIB_1.0 1.17
+ bcf_hdr_remove at HTSLIB_1.0 1.17
+ bcf_hdr_seqnames at HTSLIB_1.0 1.17
+ bcf_hdr_set at HTSLIB_1.0 1.17
+ bcf_hdr_set_samples at HTSLIB_1.0 1.17
+ bcf_hdr_set_version at HTSLIB_1.0 1.17
+ bcf_hdr_subset at HTSLIB_1.0 1.17
+ bcf_hdr_sync at HTSLIB_1.0 1.17
+ bcf_hdr_update_hrec at Base 1.17
+ bcf_hdr_write at HTSLIB_1.0 1.17
bcf_header_debug at Base 1.16
- bcf_hrec_add_key at Base 1.10
+ bcf_hrec_add_key at HTSLIB_1.0 1.17
bcf_hrec_debug at Base 1.16
- bcf_hrec_destroy at Base 1.10
- bcf_hrec_dup at Base 1.10
- bcf_hrec_find_key at Base 1.10
- bcf_hrec_format at Base 1.10
- bcf_hrec_set_val at Base 1.10
- bcf_idx_init at Base 1.10
- bcf_idx_save at Base 1.10
+ bcf_hrec_destroy at HTSLIB_1.0 1.17
+ bcf_hrec_dup at HTSLIB_1.0 1.17
+ bcf_hrec_find_key at HTSLIB_1.0 1.17
+ bcf_hrec_format at HTSLIB_1.0 1.17
+ bcf_hrec_set_val at HTSLIB_1.0 1.17
+ bcf_idx_init at HTSLIB_1.10 1.17
+ bcf_idx_save at HTSLIB_1.10 1.17
bcf_index at Base 1.16
- bcf_index_build2 at Base 1.10
- bcf_index_build3 at Base 1.10
- bcf_index_build at Base 1.10
- bcf_index_load2 at Base 1.10
- bcf_index_load3 at Base 1.10
- bcf_init at Base 1.10
- bcf_is_snp at Base 1.10
- bcf_read at Base 1.10
- bcf_readrec at Base 1.10
- bcf_remove_allele_set at Base 1.10
- bcf_remove_alleles at Base 1.10
- bcf_remove_filter at Base 1.10
- bcf_sr_add_reader at Base 1.10
- bcf_sr_destroy at Base 1.10
- bcf_sr_destroy_threads at Base 1.10
- bcf_sr_init at Base 1.10
- bcf_sr_next_line at Base 1.10
- bcf_sr_regions_destroy at Base 1.10
- bcf_sr_regions_flush at Base 1.10
- bcf_sr_regions_init at Base 1.10
- bcf_sr_regions_next at Base 1.10
- bcf_sr_regions_overlap at Base 1.10
- bcf_sr_regions_seek at Base 1.10
- bcf_sr_remove_reader at Base 1.10
- bcf_sr_seek at Base 1.10
- bcf_sr_set_opt at Base 1.10
- bcf_sr_set_regions at Base 1.10
- bcf_sr_set_samples at Base 1.10
- bcf_sr_set_targets at Base 1.10
- bcf_sr_set_threads at Base 1.10
+ bcf_index_build2 at HTSLIB_1.3 1.17
+ bcf_index_build3 at HTSLIB_1.4 1.17
+ bcf_index_build at HTSLIB_1.0 1.17
+ bcf_index_load2 at HTSLIB_1.3 1.17
+ bcf_index_load3 at HTSLIB_1.10 1.17
+ bcf_init at HTSLIB_1.0 1.17
+ bcf_is_snp at HTSLIB_1.0 1.17
+ bcf_read at HTSLIB_1.0 1.17
+ bcf_readrec at HTSLIB_1.0 1.17
+ bcf_remove_allele_set at HTSLIB_1.3 1.17
+ bcf_remove_alleles at HTSLIB_1.0 1.17
+ bcf_remove_filter at HTSLIB_1.0 1.17
+ bcf_sr_add_reader at HTSLIB_1.0 1.17
+ bcf_sr_destroy at HTSLIB_1.0 1.17
+ bcf_sr_destroy_threads at HTSLIB_1.4 1.17
+ bcf_sr_init at HTSLIB_1.0 1.17
+ bcf_sr_next_line at HTSLIB_1.0 1.17
+ bcf_sr_regions_destroy at HTSLIB_1.0 1.17
+ bcf_sr_regions_flush at HTSLIB_1.0 1.17
+ bcf_sr_regions_init at HTSLIB_1.0 1.17
+ bcf_sr_regions_next at HTSLIB_1.0 1.17
+ bcf_sr_regions_overlap at HTSLIB_1.0 1.17
+ bcf_sr_regions_seek at HTSLIB_1.0 1.17
+ bcf_sr_remove_reader at HTSLIB_1.0 1.17
+ bcf_sr_seek at HTSLIB_1.0 1.17
+ bcf_sr_set_opt at HTSLIB_1.4 1.17
+ bcf_sr_set_regions at HTSLIB_1.0 1.17
+ bcf_sr_set_samples at HTSLIB_1.0 1.17
+ bcf_sr_set_targets at HTSLIB_1.0 1.17
+ bcf_sr_set_threads at HTSLIB_1.4 1.17
bcf_sr_sort_add_active at Base 1.16
bcf_sr_sort_destroy at Base 1.16
bcf_sr_sort_init at Base 1.16
@@ -164,99 +185,103 @@ libhts.so.3 libhts3 #MINVER#
bcf_sr_sort_remove_reader at Base 1.16
bcf_sr_sort_reset at Base 1.16
bcf_sr_sort_set_active at Base 1.16
- bcf_sr_strerror at Base 1.10
- bcf_subset at Base 1.10
- bcf_subset_format at Base 1.10
- bcf_sweep_bwd at Base 1.10
- bcf_sweep_destroy at Base 1.10
- bcf_sweep_fwd at Base 1.10
- bcf_sweep_hdr at Base 1.10
- bcf_sweep_init at Base 1.10
- bcf_translate at Base 1.10
- bcf_trim_alleles at Base 1.10
- bcf_type_shift at Base 1.10
- bcf_unpack at Base 1.10
- bcf_update_alleles at Base 1.10
- bcf_update_alleles_str at Base 1.10
- bcf_update_filter at Base 1.10
- bcf_update_format at Base 1.10
- bcf_update_format_string at Base 1.10
- bcf_update_id at Base 1.10
- bcf_update_info at Base 1.10
- bcf_variant_length at Base 1.16
- bcf_write at Base 1.10
- bgzf_block_write at Base 1.10
- bgzf_check_EOF at Base 1.10
- bgzf_close at Base 1.10
- bgzf_compress at Base 1.10
- bgzf_compression at Base 1.10
- bgzf_dopen at Base 1.10
- bgzf_flush at Base 1.10
- bgzf_flush_try at Base 1.10
- bgzf_getc at Base 1.10
- bgzf_getline at Base 1.10
+ bcf_sr_strerror at HTSLIB_1.2.1 1.17
+ bcf_strerror at HTSLIB_1.17 1.17
+ bcf_subset at HTSLIB_1.0 1.17
+ bcf_subset_format at HTSLIB_1.0 1.17
+ bcf_sweep_bwd at HTSLIB_1.0 1.17
+ bcf_sweep_destroy at HTSLIB_1.0 1.17
+ bcf_sweep_fwd at HTSLIB_1.0 1.17
+ bcf_sweep_hdr at HTSLIB_1.0 1.17
+ bcf_sweep_init at HTSLIB_1.0 1.17
+ bcf_translate at HTSLIB_1.0 1.17
+ bcf_trim_alleles at HTSLIB_1.0 1.17
+ bcf_type_shift at HTSLIB_1.0 1.17
+ bcf_unpack at HTSLIB_1.0 1.17
+ bcf_update_alleles at HTSLIB_1.0 1.17
+ bcf_update_alleles_str at HTSLIB_1.0 1.17
+ bcf_update_filter at HTSLIB_1.0 1.17
+ bcf_update_format at HTSLIB_1.0 1.17
+ bcf_update_format_string at HTSLIB_1.0 1.17
+ bcf_update_id at HTSLIB_1.0 1.17
+ bcf_update_info at HTSLIB_1.0 1.17
+ bcf_variant_length at HTSLIB_1.16 1.17
+ bcf_write at HTSLIB_1.0 1.17
+ bgzf_block_write at HTSLIB_1.4 1.17
+ bgzf_check_EOF at HTSLIB_1.0 1.17
+ bgzf_close at HTSLIB_1.0 1.17
+ bgzf_compress at HTSLIB_1.3 1.17
+ bgzf_compression at HTSLIB_1.4 1.17
+ bgzf_dopen at HTSLIB_1.0 1.17
+ bgzf_flush at HTSLIB_1.0 1.17
+ bgzf_flush_try at HTSLIB_1.0 1.17
+ bgzf_getc at HTSLIB_1.0 1.17
+ bgzf_getline at HTSLIB_1.0 1.17
bgzf_hfile at Base 1.16
- bgzf_hopen at Base 1.10
+ bgzf_hopen at HTSLIB_1.0 1.17
bgzf_idx_amend_last at Base 1.16
bgzf_idx_push at Base 1.16
bgzf_index_add_block at Base 1.16
- bgzf_index_build_init at Base 1.10
+ bgzf_index_build_init at HTSLIB_1.0 1.17
bgzf_index_destroy at Base 1.16
- bgzf_index_dump at Base 1.10
- bgzf_index_dump_hfile at Base 1.10
- bgzf_index_load at Base 1.10
- bgzf_index_load_hfile at Base 1.10
- bgzf_is_bgzf at Base 1.10
- bgzf_mt at Base 1.10
+ bgzf_index_dump at HTSLIB_1.0 1.17
+ bgzf_index_dump_hfile at HTSLIB_1.4 1.17
+ bgzf_index_load at HTSLIB_1.0 1.17
+ bgzf_index_load_hfile at HTSLIB_1.4 1.17
+ bgzf_is_bgzf at HTSLIB_1.0 1.17
+ bgzf_mt at HTSLIB_1.0 1.17
bgzf_mt_read_block at Base 1.16
- bgzf_open at Base 1.10
- bgzf_peek at Base 1.10
- bgzf_raw_read at Base 1.10
- bgzf_raw_write at Base 1.10
- bgzf_read at Base 1.10
- bgzf_read_block at Base 1.10
- bgzf_seek at Base 1.10
- bgzf_set_cache_size at Base 1.10
- bgzf_thread_pool at Base 1.10
- bgzf_useek at Base 1.10
- bgzf_utell at Base 1.10
- bgzf_write at Base 1.10
+ bgzf_open at HTSLIB_1.0 1.17
+ bgzf_peek at HTSLIB_1.10 1.17
+ bgzf_raw_read at HTSLIB_1.0 1.17
+ bgzf_raw_write at HTSLIB_1.0 1.17
+ bgzf_read at HTSLIB_1.0 1.17
+ bgzf_read_block at HTSLIB_1.0 1.17
+ bgzf_seek at HTSLIB_1.0 1.17
+ bgzf_set_cache_size at HTSLIB_1.0 1.17
+ bgzf_thread_pool at HTSLIB_1.4 1.17
+ bgzf_useek at HTSLIB_1.0 1.17
+ bgzf_utell at HTSLIB_1.0 1.17
+ bgzf_write at HTSLIB_1.0 1.17
close_plugin at Base 1.16
cram_beta_decode_char at Base 1.16
cram_beta_decode_free at Base 1.16
cram_beta_decode_init at Base 1.16
cram_beta_decode_int at Base 1.16
cram_beta_decode_long at Base 1.16
+ cram_beta_describe at Base 1.17
cram_beta_encode_char at Base 1.16
cram_beta_encode_free at Base 1.16
cram_beta_encode_init at Base 1.16
cram_beta_encode_int at Base 1.16
cram_beta_encode_long at Base 1.16
cram_beta_encode_store at Base 1.16
- cram_block_append at Base 1.10
+ cram_block_append at HTSLIB_1.3 1.17
cram_block_compression_hdr_decoder2encoder at Base 1.16
cram_block_compression_hdr_set_rg at Base 1.16
- cram_block_get_comp_size at Base 1.10
- cram_block_get_content_id at Base 1.10
- cram_block_get_content_type at Base 1.10
- cram_block_get_crc32 at Base 1.10
- cram_block_get_data at Base 1.10
- cram_block_get_offset at Base 1.10
+ cram_block_get_comp_size at HTSLIB_1.3 1.17
+ cram_block_get_content_id at HTSLIB_1.3 1.17
+ cram_block_get_content_type at HTSLIB_1.3 1.17
+ cram_block_get_crc32 at HTSLIB_1.3 1.17
+ cram_block_get_data at HTSLIB_1.3 1.17
+ cram_block_get_method at HTSLIB_1.17 1.17
+ cram_block_get_offset at HTSLIB_1.3 1.17
cram_block_get_size at Base 1.16
- cram_block_get_uncomp_size at Base 1.10
+ cram_block_get_uncomp_size at HTSLIB_1.3 1.17
cram_block_method2str at Base 1.16
- cram_block_set_comp_size at Base 1.10
- cram_block_set_content_id at Base 1.10
- cram_block_set_crc32 at Base 1.10
- cram_block_set_data at Base 1.10
- cram_block_set_offset at Base 1.10
+ cram_block_set_comp_size at HTSLIB_1.3 1.17
+ cram_block_set_content_id at HTSLIB_1.3 1.17
+ cram_block_set_crc32 at HTSLIB_1.3 1.17
+ cram_block_set_data at HTSLIB_1.3 1.17
+ cram_block_set_offset at HTSLIB_1.3 1.17
cram_block_set_size at Base 1.16
- cram_block_set_uncomp_size at Base 1.10
- cram_block_size at Base 1.10
- cram_block_update_size at Base 1.10
+ cram_block_set_uncomp_size at HTSLIB_1.3 1.17
+ cram_block_size at HTSLIB_1.3 1.17
+ cram_block_update_size at HTSLIB_1.3 1.17
cram_byte_array_len_decode at Base 1.16
cram_byte_array_len_decode_free at Base 1.16
cram_byte_array_len_decode_init at Base 1.16
+ cram_byte_array_len_describe at Base 1.17
cram_byte_array_len_encode at Base 1.16
cram_byte_array_len_encode_free at Base 1.16
cram_byte_array_len_encode_init at Base 1.16
@@ -264,58 +289,69 @@ libhts.so.3 libhts3 #MINVER#
cram_byte_array_stop_decode_block at Base 1.16
cram_byte_array_stop_decode_free at Base 1.16
cram_byte_array_stop_decode_init at Base 1.16
+ cram_byte_array_stop_describe at Base 1.17
cram_byte_array_stop_encode at Base 1.16
cram_byte_array_stop_encode_free at Base 1.16
cram_byte_array_stop_encode_init at Base 1.16
cram_byte_array_stop_encode_store at Base 1.16
- cram_check_EOF at Base 1.10
- cram_close at Base 1.10
+ cram_check_EOF at HTSLIB_1.4 1.17
+ cram_cid2ds_free at HTSLIB_1.17 1.17
+ cram_cid2ds_query at HTSLIB_1.17 1.17
+ cram_close at HTSLIB_1.0 1.17
cram_codec_decoder2encoder at Base 1.16
+ cram_codec_describe at HTSLIB_1.17 1.17
+ cram_codec_get_content_ids at HTSLIB_1.17 1.17
cram_codec_to_id at Base 1.16
cram_compress_block2 at Base 1.16
- cram_compress_block at Base 1.10
+ cram_compress_block at HTSLIB_1.0 1.17
cram_const_decode_byte at Base 1.16
cram_const_decode_free at Base 1.16
cram_const_decode_init at Base 1.16
cram_const_decode_int at Base 1.16
cram_const_decode_long at Base 1.16
cram_const_decode_size at Base 1.16
+ cram_const_describe at Base 1.17
cram_const_encode at Base 1.16
cram_const_encode_init at Base 1.16
cram_const_encode_store at Base 1.16
- cram_container_get_landmarks at Base 1.10
- cram_container_get_length at Base 1.10
- cram_container_get_num_blocks at Base 1.10
- cram_container_is_empty at Base 1.10
- cram_container_set_landmarks at Base 1.10
- cram_container_set_length at Base 1.10
- cram_container_set_num_blocks at Base 1.10
- cram_container_size at Base 1.10
+ cram_container_get_landmarks at HTSLIB_1.3 1.17
+ cram_container_get_length at HTSLIB_1.3 1.17
+ cram_container_get_num_bases at HTSLIB_1.17 1.17
+ cram_container_get_num_blocks at HTSLIB_1.3 1.17
+ cram_container_get_num_records at HTSLIB_1.17 1.17
+ cram_container_is_empty at HTSLIB_1.3 1.17
+ cram_container_set_landmarks at HTSLIB_1.3 1.17
+ cram_container_set_length at HTSLIB_1.3 1.17
+ cram_container_set_num_blocks at HTSLIB_1.3 1.17
+ cram_container_size at HTSLIB_1.3 1.17
cram_content_type2str at Base 1.16
- cram_copy_slice at Base 1.10
+ cram_copy_slice at HTSLIB_1.3 1.17
cram_decode_TD at Base 1.16
- cram_decode_compression_header at Base 1.16
+ cram_decode_compression_header at HTSLIB_1.17 1.17
cram_decode_estimate_sizes at Base 1.16
cram_decode_slice at Base 1.16
- cram_decode_slice_header at Base 1.16
+ cram_decode_slice_header at HTSLIB_1.16 1.17
cram_decode_slice_mt at Base 1.16
cram_decode_slice_thread at Base 1.16
cram_decoder_init at Base 1.16
cram_dependent_data_series at Base 1.16
- cram_dopen at Base 1.10
+ cram_describe_encodings at HTSLIB_1.17 1.17
+ cram_dopen at HTSLIB_1.0 1.17
cram_drain_rqueue at Base 1.16
cram_encode_compression_header at Base 1.16
cram_encode_container at Base 1.16
cram_encode_slice_header at Base 1.16
cram_encoder_init at Base 1.16
cram_encoding2str at Base 1.16
- cram_eof at Base 1.10
+ cram_eof at HTSLIB_1.0 1.17
+ cram_expand_method at HTSLIB_1.17 1.17
cram_external_decode_char at Base 1.16
cram_external_decode_free at Base 1.16
cram_external_decode_init at Base 1.16
cram_external_decode_int at Base 1.16
cram_external_decode_long at Base 1.16
cram_external_decode_size at Base 1.16
+ cram_external_describe at Base 1.17
cram_external_encode_char at Base 1.16
cram_external_encode_free at Base 1.16
cram_external_encode_init at Base 1.16
@@ -325,28 +361,29 @@ libhts.so.3 libhts3 #MINVER#
cram_external_encode_slong at Base 1.16
cram_external_encode_store at Base 1.16
cram_external_get_block at Base 1.16
- cram_fd_get_fp at Base 1.10
- cram_fd_get_header at Base 1.10
- cram_fd_get_version at Base 1.10
- cram_fd_set_fp at Base 1.10
- cram_fd_set_header at Base 1.10
- cram_fd_set_version at Base 1.10
- cram_flush at Base 1.10
+ cram_fd_get_fp at HTSLIB_1.3 1.17
+ cram_fd_get_header at HTSLIB_1.3 1.17
+ cram_fd_get_version at HTSLIB_1.3 1.17
+ cram_fd_set_fp at HTSLIB_1.3 1.17
+ cram_fd_set_header at HTSLIB_1.3 1.17
+ cram_fd_set_version at HTSLIB_1.3 1.17
+ cram_flush at HTSLIB_1.0 1.17
cram_flush_container at Base 1.16
cram_flush_container_mt at Base 1.16
cram_flush_thread at Base 1.16
- cram_free_block at Base 1.10
- cram_free_compression_header at Base 1.16
- cram_free_container at Base 1.10
+ cram_free_block at HTSLIB_1.0 1.17
+ cram_free_compression_header at HTSLIB_1.17 1.17
+ cram_free_container at HTSLIB_1.0 1.17
cram_free_file_def at Base 1.16
cram_free_slice at Base 1.16
- cram_free_slice_header at Base 1.16
+ cram_free_slice_header at HTSLIB_1.16 1.17
cram_gamma_decode at Base 1.16
cram_gamma_decode_free at Base 1.16
cram_gamma_decode_init at Base 1.16
+ cram_gamma_describe at Base 1.17
cram_get_bam_seq at Base 1.16
cram_get_ref at Base 1.16
- cram_get_refs at Base 1.10
+ cram_get_refs at HTSLIB_1.4 1.17
cram_get_seq at Base 1.16
cram_huffman_decode_char0 at Base 1.16
cram_huffman_decode_char at Base 1.16
@@ -357,6 +394,7 @@ libhts.so.3 libhts3 #MINVER#
cram_huffman_decode_long0 at Base 1.16
cram_huffman_decode_long at Base 1.16
cram_huffman_decode_null at Base 1.16
+ cram_huffman_describe at Base 1.17
cram_huffman_encode_char0 at Base 1.16
cram_huffman_encode_char at Base 1.16
cram_huffman_encode_free at Base 1.16
@@ -374,44 +412,46 @@ libhts.so.3 libhts3 #MINVER#
cram_index_query_last at Base 1.16
cram_index_slice at Base 1.16
cram_load_reference at Base 1.16
- cram_major_vers at Base 1.10
- cram_minor_vers at Base 1.10
- cram_new_block at Base 1.10
+ cram_major_vers at HTSLIB_1.3 1.17
+ cram_minor_vers at HTSLIB_1.3 1.17
+ cram_new_block at HTSLIB_1.0 1.17
cram_new_compression_header at Base 1.16
- cram_new_container at Base 1.10
+ cram_new_container at HTSLIB_1.0 1.17
cram_new_metrics at Base 1.16
cram_new_slice at Base 1.16
- cram_open at Base 1.10
+ cram_open at HTSLIB_1.0 1.17
cram_put_bam_seq at Base 1.16
cram_read_SAM_hdr at Base 1.16
- cram_read_block at Base 1.10
- cram_read_container at Base 1.10
+ cram_read_block at HTSLIB_1.0 1.17
+ cram_read_container at HTSLIB_1.0 1.17
cram_read_file_def at Base 1.16
cram_read_slice at Base 1.16
cram_ref_decr at Base 1.16
cram_ref_incr at Base 1.16
cram_ref_load at Base 1.16
- cram_seek at Base 1.10
+ cram_seek at HTSLIB_1.0 1.17
cram_seek_to_refpos at Base 1.16
cram_set_header2 at Base 1.16
- cram_set_header at Base 1.10
- cram_set_option at Base 1.10
- cram_set_voption at Base 1.10
- cram_slice_hdr_get_coords at Base 1.16
- cram_slice_hdr_get_embed_ref_id at Base 1.16
- cram_slice_hdr_get_num_blocks at Base 1.16
+ cram_set_header at HTSLIB_1.0 1.17
+ cram_set_option at HTSLIB_1.0 1.17
+ cram_set_voption at HTSLIB_1.0 1.17
+ cram_slice_hdr_get_coords at HTSLIB_1.16 1.17
+ cram_slice_hdr_get_embed_ref_id at HTSLIB_1.16 1.17
+ cram_slice_hdr_get_num_blocks at HTSLIB_1.16 1.17
cram_stats_add at Base 1.16
cram_stats_create at Base 1.16
cram_stats_del at Base 1.16
cram_stats_encoding at Base 1.16
cram_stats_free at Base 1.16
- cram_store_container at Base 1.10
+ cram_store_container at HTSLIB_1.3 1.17
cram_subexp_decode at Base 1.16
cram_subexp_decode_free at Base 1.16
cram_subexp_decode_init at Base 1.16
+ cram_subexp_describe at Base 1.17
cram_to_bam at Base 1.16
- cram_transcode_rg at Base 1.10
- cram_uncompress_block at Base 1.10
+ cram_transcode_rg at HTSLIB_1.3 1.17
+ cram_uncompress_block at HTSLIB_1.0 1.17
+ cram_update_cid2ds_map at HTSLIB_1.17 1.17
cram_update_curr_slice at Base 1.16
cram_varint_decode_free at Base 1.16
cram_varint_decode_init at Base 1.16
@@ -420,6 +460,7 @@ libhts.so.3 libhts3 #MINVER#
cram_varint_decode_sint at Base 1.16
cram_varint_decode_size at Base 1.16
cram_varint_decode_slong at Base 1.16
+ cram_varint_describe at Base 1.17
cram_varint_encode_free at Base 1.16
cram_varint_encode_init at Base 1.16
cram_varint_encode_int at Base 1.16
@@ -429,8 +470,8 @@ libhts.so.3 libhts3 #MINVER#
cram_varint_encode_store at Base 1.16
cram_varint_get_block at Base 1.16
cram_write_SAM_hdr at Base 1.16
- cram_write_block at Base 1.10
- cram_write_container at Base 1.10
+ cram_write_block at HTSLIB_1.0 1.17
+ cram_write_container at HTSLIB_1.0 1.17
cram_write_eof_block at Base 1.16
cram_write_file_def at Base 1.16
cram_xdelta_decode_block at Base 1.16
@@ -476,221 +517,224 @@ libhts.so.3 libhts3 #MINVER#
cram_xrle_encode_long at Base 1.16
cram_xrle_encode_store at Base 1.16
cram_xrle_get_block at Base 1.16
- errmod_cal at Base 1.10
- errmod_destroy at Base 1.10
- errmod_init at Base 1.10
- fai_build3 at Base 1.10
- fai_build at Base 1.10
- fai_destroy at Base 1.10
- fai_fetch64 at Base 1.10
- fai_fetch at Base 1.10
- fai_fetchqual64 at Base 1.10
- fai_fetchqual at Base 1.10
- fai_load3 at Base 1.10
- fai_load3_format at Base 1.10
- fai_load at Base 1.10
- fai_load_format at Base 1.10
- fai_parse_region at Base 1.10
- fai_path at Base 1.11
- fai_set_cache_size at Base 1.10
- faidx_fetch_nseq at Base 1.10
- faidx_fetch_qual64 at Base 1.10
- faidx_fetch_qual at Base 1.10
- faidx_fetch_seq64 at Base 1.10
- faidx_fetch_seq at Base 1.10
- faidx_has_seq at Base 1.10
- faidx_iseq at Base 1.10
- faidx_nseq at Base 1.10
- faidx_seq_len at Base 1.10
+ errmod_cal at HTSLIB_1.4 1.17
+ errmod_destroy at HTSLIB_1.4 1.17
+ errmod_init at HTSLIB_1.4 1.17
+ fai_adjust_region at HTSLIB_1.17 1.17
+ fai_build3 at HTSLIB_1.4 1.17
+ fai_build at HTSLIB_1.0 1.17
+ fai_destroy at HTSLIB_1.0 1.17
+ fai_fetch64 at HTSLIB_1.10 1.17
+ fai_fetch at HTSLIB_1.0 1.17
+ fai_fetchqual64 at HTSLIB_1.10 1.17
+ fai_fetchqual at HTSLIB_1.9 1.17
+ fai_line_length at HTSLIB_1.17 1.17
+ fai_load3 at HTSLIB_1.4 1.17
+ fai_load3_format at HTSLIB_1.9 1.17
+ fai_load at HTSLIB_1.0 1.17
+ fai_load_format at HTSLIB_1.9 1.17
+ fai_parse_region at HTSLIB_1.10 1.17
+ fai_path at HTSLIB_1.11 1.17
+ fai_set_cache_size at HTSLIB_1.10 1.17
+ faidx_fetch_nseq at HTSLIB_1.0 1.17
+ faidx_fetch_qual64 at HTSLIB_1.10 1.17
+ faidx_fetch_qual at HTSLIB_1.9 1.17
+ faidx_fetch_seq64 at HTSLIB_1.10 1.17
+ faidx_fetch_seq at HTSLIB_1.0 1.17
+ faidx_has_seq at HTSLIB_1.0 1.17
+ faidx_iseq at HTSLIB_1.1 1.17
+ faidx_nseq at HTSLIB_1.1 1.17
+ faidx_seq_len64 at HTSLIB_1.17 1.17
+ faidx_seq_len at HTSLIB_1.1 1.17
fastq_format1 at Base 1.16
fastq_state_destroy at Base 1.16
fastq_state_set at Base 1.16
find_file_url at Base 1.16
find_path at Base 1.16
- haddextension at Base 1.10
- hclose at Base 1.10
- hclose_abruptly at Base 1.10
- hdopen at Base 1.10
- hfile_add_scheme_handler at Base 1.10
- hfile_always_local at Base 1.10
- hfile_always_remote at Base 1.10
- hfile_destroy at Base 1.10
- hfile_has_plugin at Base 1.13
- hfile_init at Base 1.10
+ haddextension at HTSLIB_1.10 1.17
+ hclose at HTSLIB_1.0 1.17
+ hclose_abruptly at HTSLIB_1.0 1.17
+ hdopen at HTSLIB_1.0 1.17
+ hfile_add_scheme_handler at HTSLIB_1.3 1.17
+ hfile_always_local at HTSLIB_1.3 1.17
+ hfile_always_remote at HTSLIB_1.3 1.17
+ hfile_destroy at HTSLIB_1.0 1.17
+ hfile_has_plugin at HTSLIB_1.12 1.17
+ hfile_init at HTSLIB_1.0 1.17
hfile_init_fixed at Base 1.16
- hfile_list_plugins at Base 1.13
- hfile_list_schemes at Base 1.13
- hfile_mem_get_buffer at Base 1.10
- hfile_mem_steal_buffer at Base 1.10
- hfile_oflags at Base 1.10
+ hfile_list_plugins at HTSLIB_1.12 1.17
+ hfile_list_schemes at HTSLIB_1.12 1.17
+ hfile_mem_get_buffer at HTSLIB_1.7 1.17
+ hfile_mem_steal_buffer at HTSLIB_1.7 1.17
+ hfile_oflags at HTSLIB_1.0 1.17
hfile_plugin_init_crypt4gh_needed at Base 1.16
hfile_plugin_init_mem at Base 1.16
- hfile_set_blksize at Base 1.10
+ hfile_set_blksize at HTSLIB_1.5 1.17
hfile_shutdown at Base 1.16
- hflush at Base 1.10
- hgetc2 at Base 1.10
- hgetdelim at Base 1.10
- hgets at Base 1.10
- hisremote at Base 1.10
- hopen at Base 1.10
+ hflush at HTSLIB_1.0 1.17
+ hgetc2 at HTSLIB_1.0 1.17
+ hgetdelim at HTSLIB_1.4 1.17
+ hgets at HTSLIB_1.4 1.17
+ hisremote at HTSLIB_1.2.1 1.17
+ hopen at HTSLIB_1.0 1.17
hopen_htsget_redirect at Base 1.16
- hpeek at Base 1.10
- hputc2 at Base 1.10
- hputs2 at Base 1.10
- hread2 at Base 1.10
- hrec_add_idx at Base 1.10
- hseek at Base 1.10
+ hpeek at HTSLIB_1.0 1.17
+ hputc2 at HTSLIB_1.0 1.17
+ hputs2 at HTSLIB_1.0 1.17
+ hread2 at HTSLIB_1.0 1.17
+ hrec_add_idx at HTSLIB_1.0 1.17
+ hseek at HTSLIB_1.0 1.17
hts_base64_decoded_length at Base 1.16
- hts_base_mod_state_alloc at Base 1.16
- hts_base_mod_state_free at Base 1.16
- hts_check_EOF at Base 1.10
- hts_close at Base 1.10
+ hts_base_mod_state_alloc at HTSLIB_1.14 1.17
+ hts_base_mod_state_free at HTSLIB_1.14 1.17
+ hts_check_EOF at HTSLIB_1.4 1.17
+ hts_close at HTSLIB_1.0 1.17
hts_decode_base64 at Base 1.16
hts_decode_percent at Base 1.16
- hts_detect_format2 at Base 1.16
- hts_detect_format at Base 1.10
- hts_drand48 at Base 1.10
- hts_erand48 at Base 1.10
- hts_feature_string at Base 1.13
- hts_features at Base 1.13
- hts_file_type at Base 1.10
- hts_filter_eval2 at Base 1.16
- hts_filter_eval at Base 1.13
- hts_filter_free at Base 1.13
- hts_filter_init at Base 1.13
- hts_flush at Base 1.16
- hts_format_description at Base 1.10
- hts_format_file_extension at Base 1.10
- hts_free at Base 1.10
- hts_get_bgzfp at Base 1.10
- hts_get_format at Base 1.10
- hts_get_log_level at Base 1.10
- hts_getline at Base 1.10
- hts_hopen at Base 1.10
+ hts_detect_format2 at HTSLIB_1.15 1.17
+ hts_detect_format at HTSLIB_1.2.1 1.17
+ hts_drand48 at HTSLIB_1.6 1.17
+ hts_erand48 at HTSLIB_1.6 1.17
+ hts_feature_string at HTSLIB_1.12 1.17
+ hts_features at HTSLIB_1.12 1.17
+ hts_file_type at HTSLIB_1.0 1.17
+ hts_filter_eval2 at HTSLIB_1.16 1.17
+ hts_filter_eval at HTSLIB_1.12 1.17
+ hts_filter_free at HTSLIB_1.12 1.17
+ hts_filter_init at HTSLIB_1.12 1.17
+ hts_flush at HTSLIB_1.14 1.17
+ hts_format_description at HTSLIB_1.2.1 1.17
+ hts_format_file_extension at HTSLIB_1.3 1.17
+ hts_free at HTSLIB_1.10 1.17
+ hts_get_bgzfp at HTSLIB_1.0 1.17
+ hts_get_format at HTSLIB_1.2.1 1.17
+ hts_get_log_level at HTSLIB_1.5 1.17
+ hts_getline at HTSLIB_1.0 1.17
+ hts_hopen at HTSLIB_1.2.1 1.17
hts_idx_amend_last at Base 1.16
hts_idx_check_local at Base 1.16
hts_idx_check_range at Base 1.16
- hts_idx_destroy at Base 1.10
- hts_idx_finish at Base 1.10
- hts_idx_fmt at Base 1.10
- hts_idx_get_meta at Base 1.10
- hts_idx_get_n_no_coor at Base 1.10
- hts_idx_get_stat at Base 1.10
+ hts_idx_destroy at HTSLIB_1.0 1.17
+ hts_idx_finish at HTSLIB_1.0 1.17
+ hts_idx_fmt at HTSLIB_1.10 1.17
+ hts_idx_get_meta at HTSLIB_1.0 1.17
+ hts_idx_get_n_no_coor at HTSLIB_1.0 1.17
+ hts_idx_get_stat at HTSLIB_1.0 1.17
hts_idx_getfn at Base 1.16
- hts_idx_init at Base 1.10
- hts_idx_load2 at Base 1.10
- hts_idx_load3 at Base 1.10
- hts_idx_load at Base 1.10
+ hts_idx_init at HTSLIB_1.0 1.17
+ hts_idx_load2 at HTSLIB_1.3 1.17
+ hts_idx_load3 at HTSLIB_1.10 1.17
+ hts_idx_load at HTSLIB_1.0 1.17
hts_idx_locatefn at Base 1.16
- hts_idx_nseq at Base 1.13
- hts_idx_push at Base 1.10
- hts_idx_save at Base 1.10
- hts_idx_save_as at Base 1.10
- hts_idx_seqnames at Base 1.10
- hts_idx_set_meta at Base 1.10
- hts_idx_tbi_name at Base 1.10
- hts_itr_destroy at Base 1.10
- hts_itr_multi_bam at Base 1.10
- hts_itr_multi_cram at Base 1.10
- hts_itr_multi_next at Base 1.10
- hts_itr_next at Base 1.10
+ hts_idx_nseq at HTSLIB_1.13 1.17
+ hts_idx_push at HTSLIB_1.0 1.17
+ hts_idx_save at HTSLIB_1.0 1.17
+ hts_idx_save_as at HTSLIB_1.3 1.17
+ hts_idx_seqnames at HTSLIB_1.0 1.17
+ hts_idx_set_meta at HTSLIB_1.0 1.17
+ hts_idx_tbi_name at HTSLIB_1.10 1.17
+ hts_itr_destroy at HTSLIB_1.0 1.17
+ hts_itr_multi_bam at HTSLIB_1.7 1.17
+ hts_itr_multi_cram at HTSLIB_1.7 1.17
+ hts_itr_multi_next at HTSLIB_1.7 1.17
+ hts_itr_next at HTSLIB_1.0 1.17
hts_itr_off at Base 1.16
- hts_itr_query at Base 1.10
- hts_itr_querys at Base 1.10
- hts_itr_regions at Base 1.10
- hts_json_alloc_token at Base 1.10
- hts_json_fnext at Base 1.10
- hts_json_free_token at Base 1.10
- hts_json_fskip_value at Base 1.10
- hts_json_snext at Base 1.10
- hts_json_sskip_value at Base 1.10
- hts_json_token_str at Base 1.10
- hts_json_token_type at Base 1.10
- hts_lib_shutdown at Base 1.11
- hts_log at Base 1.10
- hts_lrand48 at Base 1.10
- hts_md5_destroy at Base 1.10
- hts_md5_final at Base 1.10
- hts_md5_hex at Base 1.10
- hts_md5_init at Base 1.10
- hts_md5_reset at Base 1.10
- hts_md5_update at Base 1.10
- hts_open at Base 1.10
- hts_open_format at Base 1.10
+ hts_itr_query at HTSLIB_1.0 1.17
+ hts_itr_querys at HTSLIB_1.0 1.17
+ hts_itr_regions at HTSLIB_1.7 1.17
+ hts_json_alloc_token at HTSLIB_1.7 1.17
+ hts_json_fnext at HTSLIB_1.4 1.17
+ hts_json_free_token at HTSLIB_1.7 1.17
+ hts_json_fskip_value at HTSLIB_1.4 1.17
+ hts_json_snext at HTSLIB_1.4 1.17
+ hts_json_sskip_value at HTSLIB_1.4 1.17
+ hts_json_token_str at HTSLIB_1.7 1.17
+ hts_json_token_type at HTSLIB_1.7 1.17
+ hts_lib_shutdown at HTSLIB_1.11 1.17
+ hts_log at HTSLIB_1.5 1.17
+ hts_lrand48 at HTSLIB_1.6 1.17
+ hts_md5_destroy at HTSLIB_1.3 1.17
+ hts_md5_final at HTSLIB_1.3 1.17
+ hts_md5_hex at HTSLIB_1.3 1.17
+ hts_md5_init at HTSLIB_1.3 1.17
+ hts_md5_reset at HTSLIB_1.3 1.17
+ hts_md5_update at HTSLIB_1.3 1.17
+ hts_open at HTSLIB_1.0 1.17
+ hts_open_format at HTSLIB_1.3 1.17
hts_open_tmpfile at Base 1.16
- hts_opt_add at Base 1.10
- hts_opt_apply at Base 1.10
- hts_opt_free at Base 1.10
- hts_parse_decimal at Base 1.10
- hts_parse_format at Base 1.10
- hts_parse_opt_list at Base 1.10
- hts_parse_reg64 at Base 1.10
- hts_parse_reg at Base 1.10
- hts_parse_region at Base 1.10
+ hts_opt_add at HTSLIB_1.3 1.17
+ hts_opt_apply at HTSLIB_1.3 1.17
+ hts_opt_free at HTSLIB_1.3 1.17
+ hts_parse_decimal at HTSLIB_1.3 1.17
+ hts_parse_format at HTSLIB_1.3 1.17
+ hts_parse_opt_list at HTSLIB_1.3 1.17
+ hts_parse_reg64 at HTSLIB_1.10 1.17
+ hts_parse_reg at HTSLIB_1.0 1.17
+ hts_parse_region at HTSLIB_1.10 1.17
hts_path_itr_next at Base 1.16
hts_path_itr_setup at Base 1.16
hts_plugin_path at Base 1.16
- hts_readlines at Base 1.10
- hts_readlist at Base 1.10
- hts_realloc_or_die at Base 1.10
- hts_reglist_create at Base 1.10
- hts_reglist_free at Base 1.10
- hts_resize_array_ at Base 1.10
- hts_set_cache_size at Base 1.10
- hts_set_fai_filename at Base 1.10
- hts_set_filter_expression at Base 1.13
- hts_set_log_level at Base 1.10
- hts_set_opt at Base 1.10
- hts_set_thread_pool at Base 1.10
- hts_set_threads at Base 1.10
- hts_srand48 at Base 1.10
+ hts_readlines at HTSLIB_1.0 1.17
+ hts_readlist at HTSLIB_1.0 1.17
+ hts_realloc_or_die at HTSLIB_1.4 1.17
+ hts_reglist_create at HTSLIB_1.10 1.17
+ hts_reglist_free at HTSLIB_1.7 1.17
+ hts_resize_array_ at HTSLIB_1.10 1.17
+ hts_set_cache_size at HTSLIB_1.4 1.17
+ hts_set_fai_filename at HTSLIB_1.0 1.17
+ hts_set_filter_expression at HTSLIB_1.12 1.17
+ hts_set_log_level at HTSLIB_1.5 1.17
+ hts_set_opt at HTSLIB_1.2.1 1.17
+ hts_set_thread_pool at HTSLIB_1.4 1.17
+ hts_set_threads at HTSLIB_1.0 1.17
+ hts_srand48 at HTSLIB_1.6 1.17
hts_strprint at Base 1.16
- hts_test_feature at Base 1.13
- hts_tpool_delete_result at Base 1.10
- hts_tpool_destroy at Base 1.10
- hts_tpool_dispatch2 at Base 1.10
- hts_tpool_dispatch3 at Base 1.10
- hts_tpool_dispatch at Base 1.10
- hts_tpool_init at Base 1.10
- hts_tpool_kill at Base 1.10
- hts_tpool_next_result at Base 1.10
- hts_tpool_next_result_wait at Base 1.10
- hts_tpool_process_attach at Base 1.10
- hts_tpool_process_destroy at Base 1.10
- hts_tpool_process_detach at Base 1.10
- hts_tpool_process_empty at Base 1.10
- hts_tpool_process_flush at Base 1.10
- hts_tpool_process_init at Base 1.10
- hts_tpool_process_is_shutdown at Base 1.11
- hts_tpool_process_len at Base 1.10
- hts_tpool_process_qsize at Base 1.10
- hts_tpool_process_ref_decr at Base 1.10
- hts_tpool_process_ref_incr at Base 1.10
- hts_tpool_process_reset at Base 1.10
- hts_tpool_process_shutdown at Base 1.10
- hts_tpool_process_sz at Base 1.10
- hts_tpool_result_data at Base 1.10
- hts_tpool_size at Base 1.10
- hts_tpool_wake_dispatch at Base 1.10
+ hts_test_feature at HTSLIB_1.12 1.17
+ hts_tpool_delete_result at HTSLIB_1.4 1.17
+ hts_tpool_destroy at HTSLIB_1.4 1.17
+ hts_tpool_dispatch2 at HTSLIB_1.4 1.17
+ hts_tpool_dispatch3 at HTSLIB_1.10 1.17
+ hts_tpool_dispatch at HTSLIB_1.4 1.17
+ hts_tpool_init at HTSLIB_1.4 1.17
+ hts_tpool_kill at HTSLIB_1.4 1.17
+ hts_tpool_next_result at HTSLIB_1.4 1.17
+ hts_tpool_next_result_wait at HTSLIB_1.4 1.17
+ hts_tpool_process_attach at HTSLIB_1.4 1.17
+ hts_tpool_process_destroy at HTSLIB_1.4 1.17
+ hts_tpool_process_detach at HTSLIB_1.4 1.17
+ hts_tpool_process_empty at HTSLIB_1.4 1.17
+ hts_tpool_process_flush at HTSLIB_1.4 1.17
+ hts_tpool_process_init at HTSLIB_1.4 1.17
+ hts_tpool_process_is_shutdown at HTSLIB_1.11 1.17
+ hts_tpool_process_len at HTSLIB_1.4 1.17
+ hts_tpool_process_qsize at HTSLIB_1.4 1.17
+ hts_tpool_process_ref_decr at HTSLIB_1.4 1.17
+ hts_tpool_process_ref_incr at HTSLIB_1.4 1.17
+ hts_tpool_process_reset at HTSLIB_1.4 1.17
+ hts_tpool_process_shutdown at HTSLIB_1.4 1.17
+ hts_tpool_process_sz at HTSLIB_1.4 1.17
+ hts_tpool_result_data at HTSLIB_1.4 1.17
+ hts_tpool_size at HTSLIB_1.4 1.17
+ hts_tpool_wake_dispatch at HTSLIB_1.4 1.17
hts_useek at Base 1.16
hts_utell at Base 1.16
- hts_verbose at Base 1.10
- hts_version at Base 1.10
- hwrite2 at Base 1.10
+ hts_verbose at HTSLIB_1.0 1.17
+ hts_version at HTSLIB_1.0 1.17
+ hwrite2 at HTSLIB_1.0 1.17
int32_get_blk at Base 1.16
- int32_put_blk at Base 1.10
+ int32_put_blk at HTSLIB_1.3 1.17
itf8_bytes at Base 1.16
itf8_decode at Base 1.16
itf8_decode_crc at Base 1.16
itf8_encode at Base 1.16
itf8_put_blk at Base 1.16
- kf_betai at Base 1.10
- kf_erfc at Base 1.10
- kf_gammap at Base 1.10
- kf_gammaq at Base 1.10
- kf_lgamma at Base 1.10
- kgetline2 at Base 1.10
- kgetline at Base 1.10
+ kf_betai at HTSLIB_1.0 1.17
+ kf_erfc at HTSLIB_1.0 1.17
+ kf_gammap at HTSLIB_1.0 1.17
+ kf_gammaq at HTSLIB_1.0 1.17
+ kf_lgamma at HTSLIB_1.0 1.17
+ kgetline2 at HTSLIB_1.10 1.17
+ kgetline at HTSLIB_1.3 1.17
kh_clear_s2i at Base 1.16
kh_del_s2i at Base 1.16
kh_destroy_s2i at Base 1.16
@@ -698,20 +742,20 @@ libhts.so.3 libhts3 #MINVER#
kh_init_s2i at Base 1.16
kh_put_s2i at Base 1.16
kh_resize_s2i at Base 1.16
- kmemmem at Base 1.10
- knet_close at Base 1.10
- knet_dopen at Base 1.10
- knet_open at Base 1.10
- knet_read at Base 1.10
- knet_seek at Base 1.10
- kputd at Base 1.10
- ksplit_core at Base 1.10
- ksprintf at Base 1.10
- kstrnstr at Base 1.10
- kstrstr at Base 1.10
- kstrtok at Base 1.10
- kt_fisher_exact at Base 1.10
- kvsprintf at Base 1.10
+ kmemmem at HTSLIB_1.0 1.17
+ knet_close at HTSLIB_1.0 1.17
+ knet_dopen at HTSLIB_1.0 1.17
+ knet_open at HTSLIB_1.0 1.17
+ knet_read at HTSLIB_1.0 1.17
+ knet_seek at HTSLIB_1.0 1.17
+ kputd at HTSLIB_1.4 1.17
+ ksplit_core at HTSLIB_1.0 1.17
+ ksprintf at HTSLIB_1.0 1.17
+ kstrnstr at HTSLIB_1.0 1.17
+ kstrstr at HTSLIB_1.0 1.17
+ kstrtok at HTSLIB_1.0 1.17
+ kt_fisher_exact at HTSLIB_1.0 1.17
+ kvsprintf at HTSLIB_1.0 1.17
load_plugin at Base 1.16
ltf8_bytes at Base 1.16
ltf8_decode at Base 1.16
@@ -749,67 +793,67 @@ libhts.so.3 libhts3 #MINVER#
pool_create at Base 1.16
pool_destroy at Base 1.16
pool_free at Base 1.16
- probaln_glocal at Base 1.10
+ probaln_glocal at HTSLIB_1.4 1.17
refs2id at Base 1.16
refs_free at Base 1.16
- regidx_destroy at Base 1.10
- regidx_init at Base 1.10
- regidx_init_string at Base 1.10
- regidx_insert at Base 1.10
- regidx_insert_list at Base 1.10
- regidx_nregs at Base 1.10
- regidx_overlap at Base 1.10
- regidx_parse_bed at Base 1.10
- regidx_parse_reg at Base 1.10
- regidx_parse_tab at Base 1.10
- regidx_parse_vcf at Base 1.10
- regidx_push at Base 1.10
- regidx_seq_names at Base 1.10
- regidx_seq_nregs at Base 1.10
- regitr_copy at Base 1.10
- regitr_destroy at Base 1.10
- regitr_init at Base 1.10
- regitr_loop at Base 1.10
- regitr_overlap at Base 1.10
- regitr_reset at Base 1.10
+ regidx_destroy at HTSLIB_1.2.1 1.17
+ regidx_init at HTSLIB_1.2.1 1.17
+ regidx_init_string at HTSLIB_1.10 1.17
+ regidx_insert at HTSLIB_1.2.1 1.17
+ regidx_insert_list at HTSLIB_1.10 1.17
+ regidx_nregs at HTSLIB_1.2.1 1.17
+ regidx_overlap at HTSLIB_1.2.1 1.17
+ regidx_parse_bed at HTSLIB_1.2.1 1.17
+ regidx_parse_reg at HTSLIB_1.10 1.17
+ regidx_parse_tab at HTSLIB_1.2.1 1.17
+ regidx_parse_vcf at HTSLIB_1.10 1.17
+ regidx_push at HTSLIB_1.10 1.17
+ regidx_seq_names at HTSLIB_1.2.1 1.17
+ regidx_seq_nregs at HTSLIB_1.2.1 1.17
+ regitr_copy at HTSLIB_1.10 1.17
+ regitr_destroy at HTSLIB_1.10 1.17
+ regitr_init at HTSLIB_1.10 1.17
+ regitr_loop at HTSLIB_1.10 1.17
+ regitr_overlap at HTSLIB_1.10 1.17
+ regitr_reset at HTSLIB_1.10 1.17
reset_metrics at Base 1.16
- sam_cap_mapq at Base 1.10
- sam_format1 at Base 1.10
- sam_hdr_add_line at Base 1.10
- sam_hdr_add_lines at Base 1.10
- sam_hdr_add_pg at Base 1.10
- sam_hdr_change_HD at Base 1.10
- sam_hdr_count_lines at Base 1.10
- sam_hdr_destroy at Base 1.10
- sam_hdr_dup at Base 1.10
+ sam_cap_mapq at HTSLIB_1.4 1.17
+ sam_format1 at HTSLIB_1.0 1.17
+ sam_hdr_add_line at HTSLIB_1.10 1.17
+ sam_hdr_add_lines at HTSLIB_1.0 1.17
+ sam_hdr_add_pg at HTSLIB_1.10 1.17
+ sam_hdr_change_HD at HTSLIB_1.7 1.17
+ sam_hdr_count_lines at HTSLIB_1.10 1.17
+ sam_hdr_destroy at HTSLIB_1.10 1.17
+ sam_hdr_dup at HTSLIB_1.0 1.17
sam_hdr_dup_sdict at Base 1.16
sam_hdr_fill_hrecs at Base 1.16
- sam_hdr_find_line_id at Base 1.10
- sam_hdr_find_line_pos at Base 1.10
- sam_hdr_find_tag_id at Base 1.10
- sam_hdr_find_tag_pos at Base 1.10
- sam_hdr_incr_ref at Base 1.10
- sam_hdr_init at Base 1.10
- sam_hdr_length at Base 1.10
- sam_hdr_line_index at Base 1.10
- sam_hdr_line_name at Base 1.10
- sam_hdr_name2tid at Base 1.10
- sam_hdr_nref at Base 1.10
- sam_hdr_parse at Base 1.10
- sam_hdr_pg_id at Base 1.10
- sam_hdr_read at Base 1.10
+ sam_hdr_find_line_id at HTSLIB_1.10 1.17
+ sam_hdr_find_line_pos at HTSLIB_1.10 1.17
+ sam_hdr_find_tag_id at HTSLIB_1.10 1.17
+ sam_hdr_find_tag_pos at HTSLIB_1.10 1.17
+ sam_hdr_incr_ref at HTSLIB_1.0 1.17
+ sam_hdr_init at HTSLIB_1.10 1.17
+ sam_hdr_length at HTSLIB_1.0 1.17
+ sam_hdr_line_index at HTSLIB_1.10 1.17
+ sam_hdr_line_name at HTSLIB_1.10 1.17
+ sam_hdr_name2tid at HTSLIB_1.10 1.17
+ sam_hdr_nref at HTSLIB_1.10 1.17
+ sam_hdr_parse at HTSLIB_1.0 1.17
+ sam_hdr_pg_id at HTSLIB_1.10 1.17
+ sam_hdr_read at HTSLIB_1.0 1.17
sam_hdr_rebuild at Base 1.16
- sam_hdr_remove_except at Base 1.10
- sam_hdr_remove_line_id at Base 1.10
- sam_hdr_remove_line_pos at Base 1.10
- sam_hdr_remove_lines at Base 1.10
- sam_hdr_remove_tag_id at Base 1.10
- sam_hdr_str at Base 1.10
- sam_hdr_tid2len at Base 1.10
- sam_hdr_tid2name at Base 1.10
- sam_hdr_update_line at Base 1.10
+ sam_hdr_remove_except at HTSLIB_1.10 1.17
+ sam_hdr_remove_line_id at HTSLIB_1.10 1.17
+ sam_hdr_remove_line_pos at HTSLIB_1.10 1.17
+ sam_hdr_remove_lines at HTSLIB_1.10 1.17
+ sam_hdr_remove_tag_id at HTSLIB_1.10 1.17
+ sam_hdr_str at HTSLIB_1.0 1.17
+ sam_hdr_tid2len at HTSLIB_1.10 1.17
+ sam_hdr_tid2name at HTSLIB_1.10 1.17
+ sam_hdr_update_line at HTSLIB_1.10 1.17
sam_hdr_update_target_arrays at Base 1.16
- sam_hdr_write at Base 1.10
+ sam_hdr_write at HTSLIB_1.0 1.17
sam_hrecs_find_key at Base 1.16
sam_hrecs_find_rg at Base 1.16
sam_hrecs_find_type_id at Base 1.16
@@ -819,64 +863,64 @@ libhts.so.3 libhts3 #MINVER#
sam_hrecs_rebuild_text at Base 1.16
sam_hrecs_remove_key at Base 1.16
sam_hrecs_sort_order at Base 1.16
- sam_idx_init at Base 1.10
- sam_idx_save at Base 1.10
- sam_index_build2 at Base 1.10
- sam_index_build3 at Base 1.10
- sam_index_build at Base 1.10
- sam_index_load2 at Base 1.10
- sam_index_load3 at Base 1.10
- sam_index_load at Base 1.10
- sam_itr_queryi at Base 1.10
- sam_itr_querys at Base 1.10
- sam_itr_regarray at Base 1.10
- sam_itr_regions at Base 1.10
- sam_open_mode at Base 1.10
- sam_open_mode_opts at Base 1.10
- sam_parse1 at Base 1.10
- sam_parse_cigar at Base 1.13
- sam_parse_region at Base 1.10
- sam_passes_filter at Base 1.13
- sam_prob_realn at Base 1.10
- sam_read1 at Base 1.10
+ sam_idx_init at HTSLIB_1.10 1.17
+ sam_idx_save at HTSLIB_1.10 1.17
+ sam_index_build2 at HTSLIB_1.3 1.17
+ sam_index_build3 at HTSLIB_1.4 1.17
+ sam_index_build at HTSLIB_1.3 1.17
+ sam_index_load2 at HTSLIB_1.3 1.17
+ sam_index_load3 at HTSLIB_1.10 1.17
+ sam_index_load at HTSLIB_1.0 1.17
+ sam_itr_queryi at HTSLIB_1.0 1.17
+ sam_itr_querys at HTSLIB_1.0 1.17
+ sam_itr_regarray at HTSLIB_1.10 1.17
+ sam_itr_regions at HTSLIB_1.7 1.17
+ sam_open_mode at HTSLIB_1.0 1.17
+ sam_open_mode_opts at HTSLIB_1.3 1.17
+ sam_parse1 at HTSLIB_1.0 1.17
+ sam_parse_cigar at HTSLIB_1.12 1.17
+ sam_parse_region at HTSLIB_1.10 1.17
+ sam_passes_filter at HTSLIB_1.12 1.17
+ sam_prob_realn at HTSLIB_1.4 1.17
+ sam_read1 at HTSLIB_1.0 1.17
sam_realloc_bam_data at Base 1.16
sam_set_thread_pool at Base 1.16
sam_set_threads at Base 1.16
sam_state_destroy at Base 1.16
- sam_write1 at Base 1.10
- seq_nt16_int at Base 1.10
- seq_nt16_str at Base 1.10
- seq_nt16_table at Base 1.10
+ sam_write1 at HTSLIB_1.0 1.17
+ seq_nt16_int at HTSLIB_1.2.1 1.17
+ seq_nt16_str at HTSLIB_1.0 1.17
+ seq_nt16_table at HTSLIB_1.0 1.17
string_alloc at Base 1.16
string_dup at Base 1.16
string_ndup at Base 1.16
string_pool_create at Base 1.16
string_pool_destroy at Base 1.16
- stringify_argv at Base 1.10
- tbx_conf_bed at Base 1.10
- tbx_conf_gff at Base 1.10
- tbx_conf_psltbl at Base 1.10
- tbx_conf_sam at Base 1.10
- tbx_conf_vcf at Base 1.10
- tbx_destroy at Base 1.10
- tbx_index at Base 1.10
- tbx_index_build2 at Base 1.10
- tbx_index_build3 at Base 1.10
- tbx_index_build at Base 1.10
- tbx_index_load2 at Base 1.10
- tbx_index_load3 at Base 1.10
- tbx_index_load at Base 1.10
- tbx_name2id at Base 1.10
+ stringify_argv at HTSLIB_1.0 1.17
+ tbx_conf_bed at HTSLIB_1.0 1.17
+ tbx_conf_gff at HTSLIB_1.0 1.17
+ tbx_conf_psltbl at HTSLIB_1.0 1.17
+ tbx_conf_sam at HTSLIB_1.0 1.17
+ tbx_conf_vcf at HTSLIB_1.0 1.17
+ tbx_destroy at HTSLIB_1.0 1.17
+ tbx_index at HTSLIB_1.0 1.17
+ tbx_index_build2 at HTSLIB_1.3 1.17
+ tbx_index_build3 at HTSLIB_1.4 1.17
+ tbx_index_build at HTSLIB_1.0 1.17
+ tbx_index_load2 at HTSLIB_1.3 1.17
+ tbx_index_load3 at HTSLIB_1.10 1.17
+ tbx_index_load at HTSLIB_1.0 1.17
+ tbx_name2id at HTSLIB_1.0 1.17
tbx_parse1 at Base 1.16
- tbx_readrec at Base 1.10
- tbx_seqnames at Base 1.10
+ tbx_readrec at HTSLIB_1.0 1.17
+ tbx_seqnames at HTSLIB_1.0 1.17
tokenise_search_path at Base 1.16
- vcf_format at Base 1.10
- vcf_hdr_read at Base 1.10
- vcf_hdr_write at Base 1.10
- vcf_open_mode at Base 1.11
- vcf_parse at Base 1.10
- vcf_read at Base 1.10
- vcf_write at Base 1.10
- vcf_write_line at Base 1.10
+ vcf_format at HTSLIB_1.0 1.17
+ vcf_hdr_read at HTSLIB_1.0 1.17
+ vcf_hdr_write at HTSLIB_1.0 1.17
+ vcf_open_mode at HTSLIB_1.11 1.17
+ vcf_parse at HTSLIB_1.0 1.17
+ vcf_read at HTSLIB_1.0 1.17
+ vcf_write at HTSLIB_1.0 1.17
+ vcf_write_line at HTSLIB_1.0 1.17
zlib_mem_inflate at Base 1.16
=====================================
debian/patches/fix-cram-external-header.patch
=====================================
@@ -0,0 +1,17 @@
+Description: fix cram htscodecs duplicate extension in header inclusion
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/samtools/htslib/pull/1633
+Last-Update: 2023-06-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- htslib.orig/cram/cram_external.c
++++ htslib/cram/cram_external.c
+@@ -43,7 +43,7 @@
+ #include <stdint.h>
+
+ #if defined(HAVE_EXTERNAL_LIBHTSCODECS)
+-#include <htscodecs/rANS_static4x16.h.h>
++#include <htscodecs/rANS_static4x16.h>
+ #else
+ #include "../htscodecs/htscodecs/rANS_static4x16.h"
+ #endif
=====================================
debian/patches/fix-whatis-entry.patch
=====================================
@@ -0,0 +1,16 @@
+Description: htslib-s3-plugin.7: fix whatis entry
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/samtools/htslib/pull/1634
+Last-Update: 2023-06-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- htslib.orig/htslib-s3-plugin.7
++++ htslib/htslib-s3-plugin.7
+@@ -1,6 +1,6 @@
+ .TH htslib-s3-plugin 7 "21 February 2023" "htslib-1.17" "Bioinformatics tools"
+ .SH NAME
+-s3 plugin \- htslib AWS S3 plugin
++htslib-s3-plugin \- htslib AWS S3 plugin
+ .\"
+ .\" Copyright (C) 2021-2022 Genome Research Ltd.
+ .\"
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,5 @@ fix_float_precision
cram_to_bam_export.patch
fix_sequence_of_linked_libs.patch
trim-file-prefix.patch
+fix-cram-external-header.patch
+fix-whatis-entry.patch
=====================================
debian/tests/run-unit-test
=====================================
@@ -11,6 +11,7 @@ fi
cp -aL /usr/share/${pkg}-test/* "$AUTOPKGTEST_TMP"
cp -aL htslib.pc.in "$AUTOPKGTEST_TMP"
+cp -aL htslib.map "$AUTOPKGTEST_TMP"
cd "$AUTOPKGTEST_TMP"
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/2bd712a9c86fa7f217a84d612a6365cacd87b028...5dc37525773cec05ad64534991dcd13567077b6e
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/2bd712a9c86fa7f217a84d612a6365cacd87b028...5dc37525773cec05ad64534991dcd13567077b6e
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