[med-svn] [Git][med-team/htslib][master] 6 commits: Add FIXME
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Sep 30 10:28:03 BST 2022
Andreas Tille pushed to branch master at Debian Med / htslib
Commits:
5f71a206 by Andreas Tille at 2022-09-30T10:29:18+02:00
Add FIXME
- - - - -
0db89314 by Andreas Tille at 2022-09-30T11:09:53+02:00
Additional symbols
- - - - -
bbebde54 by Andreas Tille at 2022-09-30T11:16:38+02:00
Fix lintian-overrides
- - - - -
2905146f by Andreas Tille at 2022-09-30T11:21:18+02:00
Fix build options to make sure symbols will remain in library
- - - - -
3509b32f by Andreas Tille at 2022-09-30T11:22:36+02:00
For some reason we have now even more symbols inside the library - may be this is connected to the -ffat-lto-objects just added in previous commit?
- - - - -
7d376003 by Andreas Tille at 2022-09-30T11:26:55+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/htslib-test.lintian-overrides
- debian/libhts3.symbols
- debian/patches/fix_sequence_of_linked_libs.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,11 @@
-htslib (1.16+ds-1) UNRELEASED; urgency=medium
+htslib (1.16+ds-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
+ * Fix lintian-overrides
+ * Fix build options to make sure symbols will remain in library
- -- Andreas Tille <tille at debian.org> Thu, 29 Sep 2022 13:39:16 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 30 Sep 2022 11:23:39 +0200
htslib (1.14+ds-1~exp1) experimental; urgency=medium
=====================================
debian/htslib-test.lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# As needed for testing
-compressed-duplicate usr/share/htslib-test/test/bgziptest.txt.gz
+htslib-test: compressed-duplicate [usr/share/htslib-test/test/bgziptest.txt.gz]
=====================================
debian/libhts3.symbols
=====================================
@@ -24,7 +24,12 @@ libhts.so.3 libhts3 #MINVER#
bam_flag2str at Base 1.10
bam_hdr_read at Base 1.10
bam_hdr_write at Base 1.10
+ 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
@@ -34,6 +39,8 @@ libhts.so.3 libhts3 #MINVER#
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
@@ -42,7 +49,9 @@ libhts.so.3 libhts3 #MINVER#
bam_plp_destroy at Base 1.10
bam_plp_destructor at Base 1.10
bam_plp_init at Base 1.10
+ 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
@@ -78,9 +87,12 @@ libhts.so.3 libhts3 #MINVER#
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
+ 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
@@ -93,6 +105,7 @@ libhts.so.3 libhts3 #MINVER#
bcf_hdr_merge at Base 1.10
bcf_hdr_parse at Base 1.10
bcf_hdr_parse_line at Base 1.10
+ 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
@@ -103,7 +116,9 @@ libhts.so.3 libhts3 #MINVER#
bcf_hdr_subset at Base 1.10
bcf_hdr_sync at Base 1.10
bcf_hdr_write at Base 1.10
+ bcf_header_debug at Base 1.16
bcf_hrec_add_key at Base 1.10
+ 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
@@ -111,6 +126,7 @@ libhts.so.3 libhts3 #MINVER#
bcf_hrec_set_val at Base 1.10
bcf_idx_init at Base 1.10
bcf_idx_save at Base 1.10
+ 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
@@ -141,6 +157,13 @@ libhts.so.3 libhts3 #MINVER#
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_sr_sort_add_active at Base 1.16
+ bcf_sr_sort_destroy at Base 1.16
+ bcf_sr_sort_init at Base 1.16
+ bcf_sr_sort_next at Base 1.16
+ 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
@@ -160,6 +183,7 @@ libhts.so.3 libhts3 #MINVER#
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
@@ -171,14 +195,20 @@ libhts.so.3 libhts3 #MINVER#
bgzf_flush_try at Base 1.10
bgzf_getc at Base 1.10
bgzf_getline at Base 1.10
+ bgzf_hfile at Base 1.16
bgzf_hopen at Base 1.10
+ 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_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_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
@@ -191,25 +221,68 @@ libhts.so.3 libhts3 #MINVER#
bgzf_useek at Base 1.10
bgzf_utell at Base 1.10
bgzf_write at Base 1.10
+ 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_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_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_size at Base 1.16
cram_block_get_uncomp_size at Base 1.10
+ 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_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_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_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
+ cram_byte_array_len_encode_store at Base 1.16
+ 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_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_codec_decoder2encoder at Base 1.16
+ cram_codec_to_id at Base 1.16
+ cram_compress_block2 at Base 1.16
cram_compress_block at Base 1.10
+ 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_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
@@ -218,9 +291,40 @@ libhts.so.3 libhts3 #MINVER#
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_content_type2str at Base 1.16
cram_copy_slice at Base 1.10
+ cram_decode_TD at Base 1.16
+ cram_decode_compression_header at Base 1.16
+ 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_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_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_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_encode_char at Base 1.16
+ cram_external_encode_free at Base 1.16
+ cram_external_encode_init at Base 1.16
+ cram_external_encode_int at Base 1.16
+ cram_external_encode_long at Base 1.16
+ cram_external_encode_sint at Base 1.16
+ 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
@@ -228,25 +332,150 @@ libhts.so.3 libhts3 #MINVER#
cram_fd_set_header at Base 1.10
cram_fd_set_version at Base 1.10
cram_flush at Base 1.10
+ 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_file_def at Base 1.16
+ cram_free_slice at Base 1.16
+ cram_free_slice_header at Base 1.16
+ cram_gamma_decode at Base 1.16
+ cram_gamma_decode_free at Base 1.16
+ cram_gamma_decode_init at Base 1.16
+ cram_get_bam_seq at Base 1.16
+ cram_get_ref at Base 1.16
cram_get_refs at Base 1.10
+ cram_get_seq at Base 1.16
+ cram_huffman_decode_char0 at Base 1.16
+ cram_huffman_decode_char at Base 1.16
+ cram_huffman_decode_free at Base 1.16
+ cram_huffman_decode_init at Base 1.16
+ cram_huffman_decode_int0 at Base 1.16
+ cram_huffman_decode_int at Base 1.16
+ 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_encode_char0 at Base 1.16
+ cram_huffman_encode_char at Base 1.16
+ cram_huffman_encode_free at Base 1.16
+ cram_huffman_encode_init at Base 1.16
+ cram_huffman_encode_int0 at Base 1.16
+ cram_huffman_encode_int at Base 1.16
+ cram_huffman_encode_long0 at Base 1.16
+ cram_huffman_encode_long at Base 1.16
+ cram_huffman_encode_store at Base 1.16
+ cram_index_build at Base 1.16
+ cram_index_free at Base 1.16
+ cram_index_last at Base 1.16
+ cram_index_load at Base 1.16
+ cram_index_query at Base 1.16
+ 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_new_compression_header at Base 1.16
cram_new_container at Base 1.10
+ cram_new_metrics at Base 1.16
+ cram_new_slice at Base 1.16
cram_open at Base 1.10
+ 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_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_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_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_subexp_decode at Base 1.16
+ cram_subexp_decode_free at Base 1.16
+ cram_subexp_decode_init at Base 1.16
+ cram_to_bam at Base 1.16
cram_transcode_rg at Base 1.10
cram_uncompress_block at Base 1.10
+ cram_update_curr_slice at Base 1.16
+ cram_varint_decode_free at Base 1.16
+ cram_varint_decode_init at Base 1.16
+ cram_varint_decode_int at Base 1.16
+ cram_varint_decode_long at Base 1.16
+ 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_encode_free at Base 1.16
+ cram_varint_encode_init at Base 1.16
+ cram_varint_encode_int at Base 1.16
+ cram_varint_encode_long at Base 1.16
+ cram_varint_encode_sint at Base 1.16
+ cram_varint_encode_slong at Base 1.16
+ 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_eof_block at Base 1.16
+ cram_write_file_def at Base 1.16
+ cram_xdelta_decode_block at Base 1.16
+ cram_xdelta_decode_char at Base 1.16
+ cram_xdelta_decode_free at Base 1.16
+ cram_xdelta_decode_init at Base 1.16
+ cram_xdelta_decode_int at Base 1.16
+ cram_xdelta_decode_long at Base 1.16
+ cram_xdelta_decode_size at Base 1.16
+ cram_xdelta_encode_char at Base 1.16
+ cram_xdelta_encode_flush at Base 1.16
+ cram_xdelta_encode_free at Base 1.16
+ cram_xdelta_encode_init at Base 1.16
+ cram_xdelta_encode_int at Base 1.16
+ cram_xdelta_encode_long at Base 1.16
+ cram_xdelta_encode_store at Base 1.16
+ cram_xdelta_get_block at Base 1.16
+ cram_xpack_decode_char at Base 1.16
+ cram_xpack_decode_free at Base 1.16
+ cram_xpack_decode_init at Base 1.16
+ cram_xpack_decode_int at Base 1.16
+ cram_xpack_decode_long at Base 1.16
+ cram_xpack_decode_size at Base 1.16
+ cram_xpack_encode_char at Base 1.16
+ cram_xpack_encode_flush at Base 1.16
+ cram_xpack_encode_free at Base 1.16
+ cram_xpack_encode_init at Base 1.16
+ cram_xpack_encode_int at Base 1.16
+ cram_xpack_encode_long at Base 1.16
+ cram_xpack_encode_store at Base 1.16
+ cram_xpack_get_block at Base 1.16
+ cram_xrle_decode_char at Base 1.16
+ cram_xrle_decode_free at Base 1.16
+ cram_xrle_decode_init at Base 1.16
+ cram_xrle_decode_int at Base 1.16
+ cram_xrle_decode_long at Base 1.16
+ cram_xrle_decode_size at Base 1.16
+ cram_xrle_encode_char at Base 1.16
+ cram_xrle_encode_flush at Base 1.16
+ cram_xrle_encode_free at Base 1.16
+ cram_xrle_encode_init at Base 1.16
+ cram_xrle_encode_int at Base 1.16
+ 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
@@ -273,6 +502,11 @@ libhts.so.3 libhts3 #MINVER#
faidx_iseq at Base 1.10
faidx_nseq at Base 1.10
faidx_seq_len at Base 1.10
+ 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
@@ -283,35 +517,48 @@ libhts.so.3 libhts3 #MINVER#
hfile_destroy at Base 1.10
hfile_has_plugin at Base 1.13
hfile_init at Base 1.10
+ 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_plugin_init_crypt4gh_needed at Base 1.16
+ hfile_plugin_init_mem at Base 1.16
hfile_set_blksize at Base 1.10
+ 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
+ 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
+ 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_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
@@ -320,16 +567,21 @@ libhts.so.3 libhts3 #MINVER#
hts_get_log_level at Base 1.10
hts_getline at Base 1.10
hts_hopen at Base 1.10
+ 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_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_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
@@ -342,6 +594,7 @@ libhts.so.3 libhts3 #MINVER#
hts_itr_multi_cram at Base 1.10
hts_itr_multi_next at Base 1.10
hts_itr_next at Base 1.10
+ 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
@@ -364,6 +617,7 @@ libhts.so.3 libhts3 #MINVER#
hts_md5_update at Base 1.10
hts_open at Base 1.10
hts_open_format at Base 1.10
+ 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
@@ -373,6 +627,9 @@ libhts.so.3 libhts3 #MINVER#
hts_parse_reg64 at Base 1.10
hts_parse_reg at Base 1.10
hts_parse_region at Base 1.10
+ 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
@@ -387,6 +644,7 @@ libhts.so.3 libhts3 #MINVER#
hts_set_thread_pool at Base 1.10
hts_set_threads at Base 1.10
hts_srand48 at Base 1.10
+ 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
@@ -414,10 +672,18 @@ libhts.so.3 libhts3 #MINVER#
hts_tpool_result_data at Base 1.10
hts_tpool_size at Base 1.10
hts_tpool_wake_dispatch at Base 1.10
+ 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
+ int32_get_blk at Base 1.16
int32_put_blk at Base 1.10
+ 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
@@ -425,6 +691,13 @@ libhts.so.3 libhts3 #MINVER#
kf_lgamma at Base 1.10
kgetline2 at Base 1.10
kgetline at Base 1.10
+ kh_clear_s2i at Base 1.16
+ kh_del_s2i at Base 1.16
+ kh_destroy_s2i at Base 1.16
+ kh_get_s2i at Base 1.16
+ 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
@@ -439,7 +712,46 @@ libhts.so.3 libhts3 #MINVER#
kstrtok at Base 1.10
kt_fisher_exact at Base 1.10
kvsprintf at Base 1.10
+ load_plugin at Base 1.16
+ ltf8_bytes at Base 1.16
+ ltf8_decode at Base 1.16
+ ltf8_decode_crc at Base 1.16
+ ltf8_put_blk at Base 1.16
+ mfascii at Base 1.16
+ mfclose at Base 1.16
+ mfcreate at Base 1.16
+ mfcreate_from at Base 1.16
+ mfdestroy at Base 1.16
+ mfdetach at Base 1.16
+ mfeof at Base 1.16
+ mfflush at Base 1.16
+ mfgetc at Base 1.16
+ mfgets at Base 1.16
+ mfmmap at Base 1.16
+ mfopen at Base 1.16
+ mfread at Base 1.16
+ mfrecreate at Base 1.16
+ mfreopen at Base 1.16
+ mfseek at Base 1.16
+ mfsteal at Base 1.16
+ mftell at Base 1.16
+ mftruncate at Base 1.16
+ mfwrite at Base 1.16
+ mrewind at Base 1.16
+ mstderr at Base 1.16
+ mstdin at Base 1.16
+ mstdout at Base 1.16
+ mungetc at Base 1.16
+ open_path_mfile at Base 1.16
+ plugin_func at Base 1.16
+ plugin_sym at Base 1.16
+ pool_alloc at Base 1.16
+ pool_create at Base 1.16
+ pool_destroy at Base 1.16
+ pool_free at Base 1.16
probaln_glocal at Base 1.10
+ 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
@@ -460,6 +772,7 @@ libhts.so.3 libhts3 #MINVER#
regitr_loop at Base 1.10
regitr_overlap at Base 1.10
regitr_reset at Base 1.10
+ 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
@@ -469,6 +782,8 @@ libhts.so.3 libhts3 #MINVER#
sam_hdr_count_lines at Base 1.10
sam_hdr_destroy at Base 1.10
sam_hdr_dup at Base 1.10
+ 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
@@ -483,6 +798,7 @@ libhts.so.3 libhts3 #MINVER#
sam_hdr_parse at Base 1.10
sam_hdr_pg_id at Base 1.10
sam_hdr_read at Base 1.10
+ 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
@@ -492,7 +808,17 @@ libhts.so.3 libhts3 #MINVER#
sam_hdr_tid2len at Base 1.10
sam_hdr_tid2name at Base 1.10
sam_hdr_update_line at Base 1.10
+ sam_hdr_update_target_arrays at Base 1.16
sam_hdr_write at Base 1.10
+ 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
+ sam_hrecs_free at Base 1.16
+ sam_hrecs_group_order at Base 1.16
+ sam_hrecs_new at Base 1.16
+ 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
@@ -513,10 +839,19 @@ libhts.so.3 libhts3 #MINVER#
sam_passes_filter at Base 1.13
sam_prob_realn at Base 1.10
sam_read1 at Base 1.10
+ 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
+ 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
@@ -532,8 +867,10 @@ libhts.so.3 libhts3 #MINVER#
tbx_index_load3 at Base 1.10
tbx_index_load at Base 1.10
tbx_name2id at Base 1.10
+ tbx_parse1 at Base 1.16
tbx_readrec at Base 1.10
tbx_seqnames at Base 1.10
+ 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
@@ -542,3 +879,4 @@ libhts.so.3 libhts3 #MINVER#
vcf_read at Base 1.10
vcf_write at Base 1.10
vcf_write_line at Base 1.10
+ zlib_mem_inflate at Base 1.16
=====================================
debian/patches/fix_sequence_of_linked_libs.patch
=====================================
@@ -2,6 +2,8 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 29 Sep 2022 13:39:16 +0200
Origin: https://lists.debian.org/debian-med/2022/09/msg00053.html
Description: Make sure all symbols of libhts will be really found
+FIXME: It would be more elegant to specify libhts.a at the *correct* position rather than force it twice.
+ Even better would be dynamic linking since we are creating libhts.so as well
--- a/Makefile
+++ b/Makefile
=====================================
debian/rules
=====================================
@@ -8,8 +8,8 @@ include /usr/share/dpkg/default.mk
ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
DEB_CFLAGS_MAINT_APPEND=-msse -mfpmath=sse
endif
-DEB_CFLAGS_MAINT_APPEND+=-flto -fvisibility=hidden
-DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto -fvisibility=hidden
+DEB_CFLAGS_MAINT_APPEND+=-ffat-lto-objects
+DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto -fvisibility=hidden -ffat-lto-objects
export DEB_CFLAGS_MAINT_APPEND
export DEB_LDFLAGS_MAINT_APPEND
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/c49ca309c0c5ac9ce92b3e0a959d692bb92a0132...7d3760033521913bfc0dda157688672f61804d9b
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/c49ca309c0c5ac9ce92b3e0a959d692bb92a0132...7d3760033521913bfc0dda157688672f61804d9b
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