Hi Graham, I migrated htslib 1.19 to unstable in the past weekend (and in turn it migrated to testing this morning). The experimental distribution being now available, I am preparing an upload with your changes for the migration to the 64-bit time_t. You will find the new debdiff in attachment; normally there should be no surprises here, but just in case.
In hope this helps, -- .''`. Étienne Mollier <emoll...@debian.org> : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- on air: Crippled Black Phoenix - Bonefire
diff -Nru htslib-1.19+ds/debian/changelog htslib-1.19+ds/debian/changelog --- htslib-1.19+ds/debian/changelog 2024-02-17 11:42:52.000000000 +0100 +++ htslib-1.19+ds/debian/changelog 2024-02-20 19:55:09.000000000 +0100 @@ -1,3 +1,13 @@ +htslib (1.19+ds-1+exp1) experimental; urgency=medium + + * Rename libraries for 64-bit time_t transition. + This change was initially proposed as NMU, but it didn't make it to + experimental due to a conflicting version already present at the time + of the upload. See also #1062344. + Thanks to Graham Inggs for the initial version and work on 64-bit time_t + + -- Étienne Mollier <emoll...@debian.org> Tue, 20 Feb 2024 19:55:09 +0100 + htslib (1.19+ds-1) unstable; urgency=medium * Migrate htslib 1.19 from experimental to unstable. diff -Nru htslib-1.19+ds/debian/control htslib-1.19+ds/debian/control --- htslib-1.19+ds/debian/control 2023-12-15 17:43:46.000000000 +0100 +++ htslib-1.19+ds/debian/control 2024-02-20 19:55:09.000000000 +0100 @@ -21,18 +21,20 @@ Homepage: https://github.com/samtools/htslib Rules-Requires-Root: no -Package: libhts3 +Package: libhts3t64 +Provides: ${t64:Provides} Architecture: any Multi-Arch: same Section: libs Depends: ${misc:Depends}, ${shlibs:Depends} Pre-Depends: ${misc:Pre-Depends} -Breaks: libtabixpp (<< 1.0.0-5~), +Breaks: libhts3 (<< ${source:Version}), + libtabixpp (<< 1.0.0-5~), libhts-dev (<< 1.13~), samtools (<< 1.17~), ivar (<< 1.3.1~) -Replaces: libhts-dev (<< 1.13~) +Replaces: libhts3, libhts-dev (<< 1.13~) Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call @@ -48,7 +50,7 @@ Architecture: any Multi-Arch: same Section: libdevel -Depends: libhts3 (= ${binary:Version}), +Depends: libhts3t64 (= ${binary:Version}), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, diff -Nru htslib-1.19+ds/debian/libhts3.install htslib-1.19+ds/debian/libhts3.install --- htslib-1.19+ds/debian/libhts3.install 2022-10-19 16:55:31.000000000 +0200 +++ htslib-1.19+ds/debian/libhts3.install 1970-01-01 01:00:00.000000000 +0100 @@ -1,3 +0,0 @@ -usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH} -usr/lib/${DEB_HOST_MULTIARCH}/htslib usr/lib/${DEB_HOST_MULTIARCH} -usr/share/man/man5/* usr/share/man/man5 diff -Nru htslib-1.19+ds/debian/libhts3.manpages htslib-1.19+ds/debian/libhts3.manpages --- htslib-1.19+ds/debian/libhts3.manpages 2022-07-03 09:14:15.000000000 +0200 +++ htslib-1.19+ds/debian/libhts3.manpages 1970-01-01 01:00:00.000000000 +0100 @@ -1 +0,0 @@ -htslib-s3-plugin.7 diff -Nru htslib-1.19+ds/debian/libhts3.symbols htslib-1.19+ds/debian/libhts3.symbols --- htslib-1.19+ds/debian/libhts3.symbols 2023-12-15 22:15:41.000000000 +0100 +++ htslib-1.19+ds/debian/libhts3.symbols 1970-01-01 01:00:00.000000000 +0100 @@ -1,929 +0,0 @@ -libhts.so.3 libhts3 #MINVER# -* Build-Depends-Package: libhts-dev - HTSLIB_1.0@HTSLIB_1.0 1.17 - HTSLIB_1.10@HTSLIB_1.10 1.17 - HTSLIB_1.11@HTSLIB_1.11 1.17 - HTSLIB_1.12@HTSLIB_1.12 1.17 - HTSLIB_1.13@HTSLIB_1.13 1.17 - HTSLIB_1.14@HTSLIB_1.14 1.17 - HTSLIB_1.15@HTSLIB_1.15 1.17 - HTSLIB_1.16@HTSLIB_1.16 1.17 - HTSLIB_1.17@HTSLIB_1.17 1.17 - HTSLIB_1.18@HTSLIB_1.18 1.18 - HTSLIB_1.1@HTSLIB_1.1 1.17 - HTSLIB_1.2.1@HTSLIB_1.2.1 1.17 - HTSLIB_1.3@HTSLIB_1.3 1.17 - HTSLIB_1.4@HTSLIB_1.4 1.17 - HTSLIB_1.5@HTSLIB_1.5 1.17 - HTSLIB_1.6@HTSLIB_1.6 1.17 - HTSLIB_1.7@HTSLIB_1.7 1.17 - 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cram_external_encode_init@Base 1.16 - cram_external_encode_int@Base 1.16 - cram_external_encode_long@Base 1.16 - cram_external_encode_sint@Base 1.16 - cram_external_encode_slong@Base 1.16 - cram_external_encode_store@Base 1.16 - cram_external_get_block@Base 1.16 - cram_fd_get_fp@HTSLIB_1.3 1.17 - cram_fd_get_header@HTSLIB_1.3 1.17 - cram_fd_get_version@HTSLIB_1.3 1.17 - cram_fd_set_fp@HTSLIB_1.3 1.17 - cram_fd_set_header@HTSLIB_1.3 1.17 - cram_fd_set_version@HTSLIB_1.3 1.17 - cram_flush@HTSLIB_1.0 1.17 - cram_flush_container@Base 1.16 - cram_flush_container_mt@Base 1.16 - cram_flush_thread@Base 1.16 - cram_free_block@HTSLIB_1.0 1.17 - cram_free_compression_header@HTSLIB_1.17 1.17 - cram_free_container@HTSLIB_1.0 1.17 - cram_free_file_def@Base 1.16 - cram_free_slice@Base 1.16 - cram_free_slice_header@HTSLIB_1.16 1.17 - cram_gamma_decode@Base 1.16 - cram_gamma_decode_free@Base 1.16 - cram_gamma_decode_init@Base 1.16 - cram_gamma_describe@Base 1.17 - cram_get_bam_seq@Base 1.16 - cram_get_ref@Base 1.16 - cram_get_refs@HTSLIB_1.4 1.17 - cram_get_seq@Base 1.16 - cram_huffman_decode_char0@Base 1.16 - cram_huffman_decode_char@Base 1.16 - cram_huffman_decode_free@Base 1.16 - cram_huffman_decode_init@Base 1.16 - cram_huffman_decode_int0@Base 1.16 - cram_huffman_decode_int@Base 1.16 - cram_huffman_decode_long0@Base 1.16 - cram_huffman_decode_long@Base 1.16 - cram_huffman_decode_null@Base 1.16 - cram_huffman_describe@Base 1.17 - cram_huffman_encode_char0@Base 1.16 - cram_huffman_encode_char@Base 1.16 - cram_huffman_encode_free@Base 1.16 - cram_huffman_encode_init@Base 1.16 - cram_huffman_encode_int0@Base 1.16 - cram_huffman_encode_int@Base 1.16 - cram_huffman_encode_long0@Base 1.16 - cram_huffman_encode_long@Base 1.16 - cram_huffman_encode_store@Base 1.16 - cram_index_build@Base 1.16 - cram_index_free@Base 1.16 - cram_index_last@Base 1.16 - cram_index_load@Base 1.16 - cram_index_query@Base 1.16 - cram_index_query_last@Base 1.16 - cram_index_slice@Base 1.16 - cram_load_reference@Base 1.16 - cram_major_vers@HTSLIB_1.3 1.17 - cram_minor_vers@HTSLIB_1.3 1.17 - cram_new_block@HTSLIB_1.0 1.17 - cram_new_compression_header@Base 1.16 - cram_new_container@HTSLIB_1.0 1.17 - cram_new_metrics@Base 1.16 - cram_new_slice@Base 1.16 - cram_open@HTSLIB_1.0 1.17 - cram_put_bam_seq@Base 1.16 - cram_read_SAM_hdr@Base 1.16 - cram_read_block@HTSLIB_1.0 1.17 - cram_read_container@HTSLIB_1.0 1.17 - cram_read_file_def@Base 1.16 - cram_read_slice@Base 1.16 - cram_ref_decr@Base 1.16 - cram_ref_incr@Base 1.16 - cram_ref_load@Base 1.16 - cram_seek@HTSLIB_1.0 1.17 - cram_seek_to_refpos@Base 1.16 - cram_set_header2@Base 1.16 - cram_set_header@HTSLIB_1.0 1.17 - cram_set_option@HTSLIB_1.0 1.17 - cram_set_voption@HTSLIB_1.0 1.17 - cram_slice_hdr_get_coords@HTSLIB_1.16 1.17 - cram_slice_hdr_get_embed_ref_id@HTSLIB_1.16 1.17 - cram_slice_hdr_get_num_blocks@HTSLIB_1.16 1.17 - cram_stats_add@Base 1.16 - cram_stats_create@Base 1.16 - cram_stats_del@Base 1.16 - cram_stats_encoding@Base 1.16 - cram_stats_free@Base 1.16 - cram_store_container@HTSLIB_1.3 1.17 - cram_subexp_decode@Base 1.16 - cram_subexp_decode_free@Base 1.16 - cram_subexp_decode_init@Base 1.16 - cram_subexp_describe@Base 1.17 - cram_to_bam@Base 1.16 - cram_transcode_rg@HTSLIB_1.3 1.17 - cram_uncompress_block@HTSLIB_1.0 1.17 - cram_update_cid2ds_map@HTSLIB_1.17 1.17 - cram_update_curr_slice@Base 1.16 - cram_varint_decode_free@Base 1.16 - cram_varint_decode_init@Base 1.16 - cram_varint_decode_int@Base 1.16 - cram_varint_decode_long@Base 1.16 - cram_varint_decode_sint@Base 1.16 - cram_varint_decode_size@Base 1.16 - cram_varint_decode_slong@Base 1.16 - cram_varint_describe@Base 1.17 - cram_varint_encode_free@Base 1.16 - cram_varint_encode_init@Base 1.16 - cram_varint_encode_int@Base 1.16 - cram_varint_encode_long@Base 1.16 - cram_varint_encode_sint@Base 1.16 - cram_varint_encode_slong@Base 1.16 - cram_varint_encode_store@Base 1.16 - cram_varint_get_block@Base 1.16 - cram_write_SAM_hdr@Base 1.16 - cram_write_block@HTSLIB_1.0 1.17 - cram_write_container@HTSLIB_1.0 1.17 - cram_write_eof_block@Base 1.16 - cram_write_file_def@Base 1.16 - cram_xdelta_decode_block@Base 1.16 - cram_xdelta_decode_char@Base 1.16 - cram_xdelta_decode_free@Base 1.16 - cram_xdelta_decode_init@Base 1.16 - cram_xdelta_decode_int@Base 1.16 - cram_xdelta_decode_long@Base 1.16 - cram_xdelta_decode_size@Base 1.16 - cram_xdelta_encode_char@Base 1.16 - cram_xdelta_encode_flush@Base 1.16 - cram_xdelta_encode_free@Base 1.16 - cram_xdelta_encode_init@Base 1.16 - cram_xdelta_encode_int@Base 1.16 - cram_xdelta_encode_long@Base 1.16 - cram_xdelta_encode_store@Base 1.16 - cram_xdelta_get_block@Base 1.16 - cram_xpack_decode_char@Base 1.16 - cram_xpack_decode_free@Base 1.16 - cram_xpack_decode_init@Base 1.16 - cram_xpack_decode_int@Base 1.16 - cram_xpack_decode_long@Base 1.16 - cram_xpack_decode_size@Base 1.16 - cram_xpack_encode_char@Base 1.16 - cram_xpack_encode_flush@Base 1.16 - cram_xpack_encode_free@Base 1.16 - cram_xpack_encode_init@Base 1.16 - cram_xpack_encode_int@Base 1.16 - cram_xpack_encode_long@Base 1.16 - cram_xpack_encode_store@Base 1.16 - cram_xpack_get_block@Base 1.16 - cram_xrle_decode_char@Base 1.16 - cram_xrle_decode_free@Base 1.16 - cram_xrle_decode_init@Base 1.16 - cram_xrle_decode_int@Base 1.16 - cram_xrle_decode_long@Base 1.16 - cram_xrle_decode_size@Base 1.16 - cram_xrle_encode_char@Base 1.16 - cram_xrle_encode_flush@Base 1.16 - cram_xrle_encode_free@Base 1.16 - cram_xrle_encode_init@Base 1.16 - cram_xrle_encode_int@Base 1.16 - cram_xrle_encode_long@Base 1.16 - cram_xrle_encode_store@Base 1.16 - cram_xrle_get_block@Base 1.16 - errmod_cal@HTSLIB_1.4 1.17 - errmod_destroy@HTSLIB_1.4 1.17 - errmod_init@HTSLIB_1.4 1.17 - fai_adjust_region@HTSLIB_1.17 1.17 - fai_build3@HTSLIB_1.4 1.17 - fai_build@HTSLIB_1.0 1.17 - fai_destroy@HTSLIB_1.0 1.17 - fai_fetch64@HTSLIB_1.10 1.17 - fai_fetch@HTSLIB_1.0 1.17 - fai_fetchqual64@HTSLIB_1.10 1.17 - fai_fetchqual@HTSLIB_1.9 1.17 - fai_line_length@HTSLIB_1.17 1.17 - fai_load3@HTSLIB_1.4 1.17 - fai_load3_format@HTSLIB_1.9 1.17 - fai_load@HTSLIB_1.0 1.17 - fai_load_format@HTSLIB_1.9 1.17 - fai_parse_region@HTSLIB_1.10 1.17 - fai_path@HTSLIB_1.11 1.17 - fai_set_cache_size@HTSLIB_1.10 1.17 - fai_thread_pool@HTSLIB_1.18 1.18 - faidx_fetch_nseq@HTSLIB_1.0 1.17 - faidx_fetch_qual64@HTSLIB_1.10 1.17 - faidx_fetch_qual@HTSLIB_1.9 1.17 - faidx_fetch_seq64@HTSLIB_1.10 1.17 - faidx_fetch_seq@HTSLIB_1.0 1.17 - faidx_has_seq@HTSLIB_1.0 1.17 - faidx_iseq@HTSLIB_1.1 1.17 - faidx_nseq@HTSLIB_1.1 1.17 - faidx_seq_len64@HTSLIB_1.17 1.17 - faidx_seq_len@HTSLIB_1.1 1.17 - fastq_format1@Base 1.16 - fastq_state_destroy@Base 1.16 - fastq_state_set@Base 1.16 - find_file_url@Base 1.16 - find_path@Base 1.16 - haddextension@HTSLIB_1.10 1.17 - hclose@HTSLIB_1.0 1.17 - hclose_abruptly@HTSLIB_1.0 1.17 - hdopen@HTSLIB_1.0 1.17 - hfile_add_scheme_handler@HTSLIB_1.3 1.17 - hfile_always_local@HTSLIB_1.3 1.17 - hfile_always_remote@HTSLIB_1.3 1.17 - hfile_destroy@HTSLIB_1.0 1.17 - hfile_has_plugin@HTSLIB_1.12 1.17 - hfile_init@HTSLIB_1.0 1.17 - hfile_init_fixed@Base 1.16 - hfile_list_plugins@HTSLIB_1.12 1.17 - hfile_list_schemes@HTSLIB_1.12 1.17 - hfile_mem_get_buffer@HTSLIB_1.7 1.17 - hfile_mem_steal_buffer@HTSLIB_1.7 1.17 - hfile_oflags@HTSLIB_1.0 1.17 - hfile_plugin_init_crypt4gh_needed@Base 1.16 - hfile_plugin_init_mem@Base 1.16 - hfile_set_blksize@HTSLIB_1.5 1.17 - hfile_shutdown@Base 1.16 - hflush@HTSLIB_1.0 1.17 - hgetc2@HTSLIB_1.0 1.17 - hgetdelim@HTSLIB_1.4 1.17 - hgets@HTSLIB_1.4 1.17 - hisremote@HTSLIB_1.2.1 1.17 - hopen@HTSLIB_1.0 1.17 - hopen_htsget_redirect@Base 1.16 - hpeek@HTSLIB_1.0 1.17 - hputc2@HTSLIB_1.0 1.17 - hputs2@HTSLIB_1.0 1.17 - hread2@HTSLIB_1.0 1.17 - hrec_add_idx@HTSLIB_1.0 1.17 - hseek@HTSLIB_1.0 1.17 - hts_base64_decoded_length@Base 1.16 - hts_base_mod_state_alloc@HTSLIB_1.14 1.17 - hts_base_mod_state_free@HTSLIB_1.14 1.17 - hts_check_EOF@HTSLIB_1.4 1.17 - hts_close@HTSLIB_1.0 1.17 - hts_decode_base64@Base 1.16 - hts_decode_percent@Base 1.16 - hts_detect_format2@HTSLIB_1.15 1.17 - hts_detect_format@HTSLIB_1.2.1 1.17 - hts_drand48@HTSLIB_1.6 1.17 - hts_erand48@HTSLIB_1.6 1.17 - hts_feature_string@HTSLIB_1.12 1.17 - hts_features@HTSLIB_1.12 1.17 - hts_file_type@HTSLIB_1.0 1.17 - hts_filter_eval2@HTSLIB_1.16 1.17 - hts_filter_eval@HTSLIB_1.12 1.17 - hts_filter_free@HTSLIB_1.12 1.17 - hts_filter_init@HTSLIB_1.12 1.17 - hts_flush@HTSLIB_1.14 1.17 - hts_format_description@HTSLIB_1.2.1 1.17 - hts_format_file_extension@HTSLIB_1.3 1.17 - hts_free@HTSLIB_1.10 1.17 - hts_get_bgzfp@HTSLIB_1.0 1.17 - hts_get_format@HTSLIB_1.2.1 1.17 - hts_get_log_level@HTSLIB_1.5 1.17 - hts_getline@HTSLIB_1.0 1.17 - hts_hopen@HTSLIB_1.2.1 1.17 - hts_idx_amend_last@Base 1.16 - hts_idx_check_local@Base 1.16 - hts_idx_check_range@Base 1.16 - hts_idx_destroy@HTSLIB_1.0 1.17 - hts_idx_finish@HTSLIB_1.0 1.17 - hts_idx_fmt@HTSLIB_1.10 1.17 - hts_idx_get_meta@HTSLIB_1.0 1.17 - hts_idx_get_n_no_coor@HTSLIB_1.0 1.17 - hts_idx_get_stat@HTSLIB_1.0 1.17 - hts_idx_getfn@Base 1.16 - hts_idx_init@HTSLIB_1.0 1.17 - hts_idx_load2@HTSLIB_1.3 1.17 - hts_idx_load3@HTSLIB_1.10 1.17 - hts_idx_load@HTSLIB_1.0 1.17 - hts_idx_locatefn@Base 1.16 - hts_idx_nseq@HTSLIB_1.13 1.17 - hts_idx_push@HTSLIB_1.0 1.17 - hts_idx_save@HTSLIB_1.0 1.17 - hts_idx_save_as@HTSLIB_1.3 1.17 - hts_idx_seqnames@HTSLIB_1.0 1.17 - hts_idx_set_meta@HTSLIB_1.0 1.17 - hts_idx_tbi_name@HTSLIB_1.10 1.17 - hts_itr_destroy@HTSLIB_1.0 1.17 - hts_itr_multi_bam@HTSLIB_1.7 1.17 - hts_itr_multi_cram@HTSLIB_1.7 1.17 - hts_itr_multi_next@HTSLIB_1.7 1.17 - hts_itr_next@HTSLIB_1.0 1.17 - hts_itr_off@Base 1.16 - hts_itr_query@HTSLIB_1.0 1.17 - hts_itr_querys@HTSLIB_1.0 1.17 - hts_itr_regions@HTSLIB_1.7 1.17 - hts_json_alloc_token@HTSLIB_1.7 1.17 - hts_json_fnext@HTSLIB_1.4 1.17 - hts_json_free_token@HTSLIB_1.7 1.17 - hts_json_fskip_value@HTSLIB_1.4 1.17 - hts_json_snext@HTSLIB_1.4 1.17 - hts_json_sskip_value@HTSLIB_1.4 1.17 - hts_json_token_str@HTSLIB_1.7 1.17 - hts_json_token_type@HTSLIB_1.7 1.17 - hts_lib_shutdown@HTSLIB_1.11 1.17 - hts_log@HTSLIB_1.5 1.17 - hts_lrand48@HTSLIB_1.6 1.17 - hts_md5_destroy@HTSLIB_1.3 1.17 - hts_md5_final@HTSLIB_1.3 1.17 - hts_md5_hex@HTSLIB_1.3 1.17 - hts_md5_init@HTSLIB_1.3 1.17 - hts_md5_reset@HTSLIB_1.3 1.17 - hts_md5_update@HTSLIB_1.3 1.17 - hts_open@HTSLIB_1.0 1.17 - hts_open_format@HTSLIB_1.3 1.17 - hts_open_tmpfile@Base 1.16 - hts_opt_add@HTSLIB_1.3 1.17 - hts_opt_apply@HTSLIB_1.3 1.17 - hts_opt_free@HTSLIB_1.3 1.17 - hts_parse_decimal@HTSLIB_1.3 1.17 - hts_parse_format@HTSLIB_1.3 1.17 - hts_parse_opt_list@HTSLIB_1.3 1.17 - hts_parse_reg64@HTSLIB_1.10 1.17 - hts_parse_reg@HTSLIB_1.0 1.17 - hts_parse_region@HTSLIB_1.10 1.17 - hts_path_itr_next@Base 1.16 - hts_path_itr_setup@Base 1.16 - hts_plugin_path@Base 1.16 - hts_readlines@HTSLIB_1.0 1.17 - hts_readlist@HTSLIB_1.0 1.17 - hts_realloc_or_die@HTSLIB_1.4 1.17 - hts_reglist_create@HTSLIB_1.10 1.17 - hts_reglist_free@HTSLIB_1.7 1.17 - hts_resize_array_@HTSLIB_1.10 1.17 - hts_set_cache_size@HTSLIB_1.4 1.17 - hts_set_fai_filename@HTSLIB_1.0 1.17 - hts_set_filter_expression@HTSLIB_1.12 1.17 - hts_set_log_level@HTSLIB_1.5 1.17 - hts_set_opt@HTSLIB_1.2.1 1.17 - hts_set_thread_pool@HTSLIB_1.4 1.17 - hts_set_threads@HTSLIB_1.0 1.17 - hts_srand48@HTSLIB_1.6 1.17 - hts_strprint@Base 1.16 - hts_test_feature@HTSLIB_1.12 1.17 - hts_tpool_delete_result@HTSLIB_1.4 1.17 - hts_tpool_destroy@HTSLIB_1.4 1.17 - hts_tpool_dispatch2@HTSLIB_1.4 1.17 - hts_tpool_dispatch3@HTSLIB_1.10 1.17 - hts_tpool_dispatch@HTSLIB_1.4 1.17 - hts_tpool_init@HTSLIB_1.4 1.17 - hts_tpool_kill@HTSLIB_1.4 1.17 - hts_tpool_next_result@HTSLIB_1.4 1.17 - hts_tpool_next_result_wait@HTSLIB_1.4 1.17 - hts_tpool_process_attach@HTSLIB_1.4 1.17 - hts_tpool_process_destroy@HTSLIB_1.4 1.17 - hts_tpool_process_detach@HTSLIB_1.4 1.17 - hts_tpool_process_empty@HTSLIB_1.4 1.17 - hts_tpool_process_flush@HTSLIB_1.4 1.17 - hts_tpool_process_init@HTSLIB_1.4 1.17 - hts_tpool_process_is_shutdown@HTSLIB_1.11 1.17 - hts_tpool_process_len@HTSLIB_1.4 1.17 - hts_tpool_process_qsize@HTSLIB_1.4 1.17 - hts_tpool_process_ref_decr@HTSLIB_1.4 1.17 - hts_tpool_process_ref_incr@HTSLIB_1.4 1.17 - hts_tpool_process_reset@HTSLIB_1.4 1.17 - hts_tpool_process_shutdown@HTSLIB_1.4 1.17 - hts_tpool_process_sz@HTSLIB_1.4 1.17 - hts_tpool_result_data@HTSLIB_1.4 1.17 - hts_tpool_size@HTSLIB_1.4 1.17 - hts_tpool_wake_dispatch@HTSLIB_1.4 1.17 - hts_useek@Base 1.16 - hts_utell@Base 1.16 - hts_verbose@HTSLIB_1.0 1.17 - hts_version@HTSLIB_1.0 1.17 - hwrite2@HTSLIB_1.0 1.17 - int32_get_blk@Base 1.16 - int32_put_blk@HTSLIB_1.3 1.17 - itf8_bytes@Base 1.16 - itf8_decode@Base 1.16 - itf8_decode_crc@Base 1.16 - itf8_encode@Base 1.16 - itf8_put_blk@Base 1.16 - kf_betai@HTSLIB_1.0 1.17 - kf_erfc@HTSLIB_1.0 1.17 - kf_gammap@HTSLIB_1.0 1.17 - kf_gammaq@HTSLIB_1.0 1.17 - kf_lgamma@HTSLIB_1.0 1.17 - kgetline2@HTSLIB_1.10 1.17 - kgetline@HTSLIB_1.3 1.17 - kh_clear_s2i@Base 1.16 - kh_del_s2i@Base 1.16 - kh_destroy_s2i@Base 1.16 - kh_get_s2i@Base 1.16 - kh_init_s2i@Base 1.16 - kh_put_s2i@Base 1.16 - kh_resize_s2i@Base 1.16 - kmemmem@HTSLIB_1.0 1.17 - knet_close@HTSLIB_1.0 1.17 - knet_dopen@HTSLIB_1.0 1.17 - knet_open@HTSLIB_1.0 1.17 - knet_read@HTSLIB_1.0 1.17 - knet_seek@HTSLIB_1.0 1.17 - kputd@HTSLIB_1.4 1.17 - ksplit_core@HTSLIB_1.0 1.17 - ksprintf@HTSLIB_1.0 1.17 - kstrnstr@HTSLIB_1.0 1.17 - kstrstr@HTSLIB_1.0 1.17 - kstrtok@HTSLIB_1.0 1.17 - kt_fisher_exact@HTSLIB_1.0 1.17 - kvsprintf@HTSLIB_1.0 1.17 - load_plugin@Base 1.16 - ltf8_bytes@Base 1.16 - ltf8_decode@Base 1.16 - ltf8_decode_crc@Base 1.16 - ltf8_put_blk@Base 1.16 - mfascii@Base 1.16 - mfclose@Base 1.16 - mfcreate@Base 1.16 - mfcreate_from@Base 1.16 - mfdestroy@Base 1.16 - mfdetach@Base 1.16 - mfeof@Base 1.16 - mfflush@Base 1.16 - mfgetc@Base 1.16 - mfgets@Base 1.16 - mfmmap@Base 1.16 - mfopen@Base 1.16 - mfread@Base 1.16 - mfrecreate@Base 1.16 - mfreopen@Base 1.16 - mfseek@Base 1.16 - mfsteal@Base 1.16 - mftell@Base 1.16 - mftruncate@Base 1.16 - mfwrite@Base 1.16 - mrewind@Base 1.16 - mstderr@Base 1.16 - mstdin@Base 1.16 - mstdout@Base 1.16 - mungetc@Base 1.16 - open_path_mfile@Base 1.16 - plugin_func@Base 1.16 - plugin_sym@Base 1.16 - pool_alloc@Base 1.16 - pool_create@Base 1.16 - pool_destroy@Base 1.16 - pool_free@Base 1.16 - probaln_glocal@HTSLIB_1.4 1.17 - refs2id@Base 1.16 - refs_free@Base 1.16 - regidx_destroy@HTSLIB_1.2.1 1.17 - regidx_init@HTSLIB_1.2.1 1.17 - regidx_init_string@HTSLIB_1.10 1.17 - regidx_insert@HTSLIB_1.2.1 1.17 - regidx_insert_list@HTSLIB_1.10 1.17 - regidx_nregs@HTSLIB_1.2.1 1.17 - regidx_overlap@HTSLIB_1.2.1 1.17 - regidx_parse_bed@HTSLIB_1.2.1 1.17 - regidx_parse_reg@HTSLIB_1.10 1.17 - regidx_parse_tab@HTSLIB_1.2.1 1.17 - regidx_parse_vcf@HTSLIB_1.10 1.17 - regidx_push@HTSLIB_1.10 1.17 - regidx_seq_names@HTSLIB_1.2.1 1.17 - regidx_seq_nregs@HTSLIB_1.2.1 1.17 - regitr_copy@HTSLIB_1.10 1.17 - regitr_destroy@HTSLIB_1.10 1.17 - regitr_init@HTSLIB_1.10 1.17 - regitr_loop@HTSLIB_1.10 1.17 - regitr_overlap@HTSLIB_1.10 1.17 - regitr_reset@HTSLIB_1.10 1.17 - reset_metrics@Base 1.16 - sam_cap_mapq@HTSLIB_1.4 1.17 - sam_format1@HTSLIB_1.0 1.17 - sam_hdr_add_line@HTSLIB_1.10 1.17 - sam_hdr_add_lines@HTSLIB_1.0 1.17 - sam_hdr_add_pg@HTSLIB_1.10 1.17 - sam_hdr_change_HD@HTSLIB_1.7 1.17 - sam_hdr_count_lines@HTSLIB_1.10 1.17 - sam_hdr_destroy@HTSLIB_1.10 1.17 - sam_hdr_dup@HTSLIB_1.0 1.17 - sam_hdr_dup_sdict@Base 1.16 - sam_hdr_fill_hrecs@Base 1.16 - sam_hdr_find_line_id@HTSLIB_1.10 1.17 - sam_hdr_find_line_pos@HTSLIB_1.10 1.17 - sam_hdr_find_tag_id@HTSLIB_1.10 1.17 - sam_hdr_find_tag_pos@HTSLIB_1.10 1.17 - sam_hdr_incr_ref@HTSLIB_1.0 1.17 - sam_hdr_init@HTSLIB_1.10 1.17 - sam_hdr_length@HTSLIB_1.0 1.17 - sam_hdr_line_index@HTSLIB_1.10 1.17 - sam_hdr_line_name@HTSLIB_1.10 1.17 - sam_hdr_name2tid@HTSLIB_1.10 1.17 - sam_hdr_nref@HTSLIB_1.10 1.17 - sam_hdr_parse@HTSLIB_1.0 1.17 - sam_hdr_pg_id@HTSLIB_1.10 1.17 - sam_hdr_read@HTSLIB_1.0 1.17 - sam_hdr_rebuild@Base 1.16 - sam_hdr_remove_except@HTSLIB_1.10 1.17 - sam_hdr_remove_line_id@HTSLIB_1.10 1.17 - sam_hdr_remove_line_pos@HTSLIB_1.10 1.17 - sam_hdr_remove_lines@HTSLIB_1.10 1.17 - sam_hdr_remove_tag_id@HTSLIB_1.10 1.17 - sam_hdr_str@HTSLIB_1.0 1.17 - sam_hdr_tid2len@HTSLIB_1.10 1.17 - sam_hdr_tid2name@HTSLIB_1.10 1.17 - sam_hdr_update_line@HTSLIB_1.10 1.17 - sam_hdr_update_target_arrays@Base 1.16 - sam_hdr_write@HTSLIB_1.0 1.17 - sam_hrecs_find_key@Base 1.16 - sam_hrecs_find_rg@Base 1.16 - sam_hrecs_find_type_id@Base 1.16 - sam_hrecs_free@Base 1.16 - sam_hrecs_group_order@Base 1.16 - sam_hrecs_new@Base 1.16 - sam_hrecs_rebuild_text@Base 1.16 - sam_hrecs_remove_key@Base 1.16 - sam_hrecs_sort_order@Base 1.16 - sam_idx_init@HTSLIB_1.10 1.17 - sam_idx_save@HTSLIB_1.10 1.17 - sam_index_build2@HTSLIB_1.3 1.17 - sam_index_build3@HTSLIB_1.4 1.17 - sam_index_build@HTSLIB_1.3 1.17 - sam_index_load2@HTSLIB_1.3 1.17 - sam_index_load3@HTSLIB_1.10 1.17 - sam_index_load@HTSLIB_1.0 1.17 - sam_itr_queryi@HTSLIB_1.0 1.17 - sam_itr_querys@HTSLIB_1.0 1.17 - sam_itr_regarray@HTSLIB_1.10 1.17 - sam_itr_regions@HTSLIB_1.7 1.17 - sam_open_mode@HTSLIB_1.0 1.17 - sam_open_mode_opts@HTSLIB_1.3 1.17 - sam_parse1@HTSLIB_1.0 1.17 - sam_parse_cigar@HTSLIB_1.12 1.17 - sam_parse_region@HTSLIB_1.10 1.17 - sam_passes_filter@HTSLIB_1.12 1.17 - sam_prob_realn@HTSLIB_1.4 1.17 - sam_read1@HTSLIB_1.0 1.17 - sam_realloc_bam_data@Base 1.16 - sam_set_thread_pool@Base 1.16 - sam_set_threads@Base 1.16 - sam_state_destroy@Base 1.16 - sam_write1@HTSLIB_1.0 1.17 - seq_nt16_int@HTSLIB_1.2.1 1.17 - seq_nt16_str@HTSLIB_1.0 1.17 - seq_nt16_table@HTSLIB_1.0 1.17 - string_alloc@Base 1.16 - string_dup@Base 1.16 - string_ndup@Base 1.16 - string_pool_create@Base 1.16 - string_pool_destroy@Base 1.16 - stringify_argv@HTSLIB_1.0 1.17 - tbx_conf_bed@HTSLIB_1.0 1.17 - tbx_conf_gff@HTSLIB_1.0 1.17 - tbx_conf_psltbl@HTSLIB_1.0 1.17 - tbx_conf_sam@HTSLIB_1.0 1.17 - tbx_conf_vcf@HTSLIB_1.0 1.17 - tbx_destroy@HTSLIB_1.0 1.17 - tbx_index@HTSLIB_1.0 1.17 - tbx_index_build2@HTSLIB_1.3 1.17 - tbx_index_build3@HTSLIB_1.4 1.17 - tbx_index_build@HTSLIB_1.0 1.17 - tbx_index_load2@HTSLIB_1.3 1.17 - tbx_index_load3@HTSLIB_1.10 1.17 - tbx_index_load@HTSLIB_1.0 1.17 - tbx_name2id@HTSLIB_1.0 1.17 - tbx_parse1@Base 1.16 - tbx_readrec@HTSLIB_1.0 1.17 - tbx_seqnames@HTSLIB_1.0 1.17 - tokenise_search_path@Base 1.16 - vcf_format@HTSLIB_1.0 1.17 - vcf_hdr_read@HTSLIB_1.0 1.17 - vcf_hdr_write@HTSLIB_1.0 1.17 - vcf_open_mode@HTSLIB_1.11 1.17 - vcf_parse@HTSLIB_1.0 1.17 - vcf_read@HTSLIB_1.0 1.17 - vcf_write@HTSLIB_1.0 1.17 - vcf_write_line@HTSLIB_1.0 1.17 - zlib_mem_inflate@Base 1.16 diff -Nru htslib-1.19+ds/debian/libhts3t64.install htslib-1.19+ds/debian/libhts3t64.install --- htslib-1.19+ds/debian/libhts3t64.install 1970-01-01 01:00:00.000000000 +0100 +++ htslib-1.19+ds/debian/libhts3t64.install 2024-02-20 19:45:13.000000000 +0100 @@ -0,0 +1,3 @@ +usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH} +usr/lib/${DEB_HOST_MULTIARCH}/htslib usr/lib/${DEB_HOST_MULTIARCH} +usr/share/man/man5/* usr/share/man/man5 diff -Nru htslib-1.19+ds/debian/libhts3t64.lintian-overrides htslib-1.19+ds/debian/libhts3t64.lintian-overrides --- htslib-1.19+ds/debian/libhts3t64.lintian-overrides 1970-01-01 01:00:00.000000000 +0100 +++ htslib-1.19+ds/debian/libhts3t64.lintian-overrides 2024-02-20 19:55:09.000000000 +0100 @@ -0,0 +1 @@ +libhts3t64: package-name-doesnt-match-sonames libhts3 diff -Nru htslib-1.19+ds/debian/libhts3t64.manpages htslib-1.19+ds/debian/libhts3t64.manpages --- htslib-1.19+ds/debian/libhts3t64.manpages 1970-01-01 01:00:00.000000000 +0100 +++ htslib-1.19+ds/debian/libhts3t64.manpages 2024-02-20 19:48:27.000000000 +0100 @@ -0,0 +1 @@ +htslib-s3-plugin.7 diff -Nru htslib-1.19+ds/debian/libhts3t64.symbols htslib-1.19+ds/debian/libhts3t64.symbols --- htslib-1.19+ds/debian/libhts3t64.symbols 1970-01-01 01:00:00.000000000 +0100 +++ htslib-1.19+ds/debian/libhts3t64.symbols 2024-02-20 19:55:09.000000000 +0100 @@ -0,0 +1,929 @@ +libhts.so.3 libhts3t64 #MINVER# +* Build-Depends-Package: libhts-dev + HTSLIB_1.0@HTSLIB_1.0 1.17 + HTSLIB_1.10@HTSLIB_1.10 1.17 + HTSLIB_1.11@HTSLIB_1.11 1.17 + HTSLIB_1.12@HTSLIB_1.12 1.17 + HTSLIB_1.13@HTSLIB_1.13 1.17 + HTSLIB_1.14@HTSLIB_1.14 1.17 + HTSLIB_1.15@HTSLIB_1.15 1.17 + HTSLIB_1.16@HTSLIB_1.16 1.17 + HTSLIB_1.17@HTSLIB_1.17 1.17 + HTSLIB_1.18@HTSLIB_1.18 1.18 + HTSLIB_1.1@HTSLIB_1.1 1.17 + HTSLIB_1.2.1@HTSLIB_1.2.1 1.17 + HTSLIB_1.3@HTSLIB_1.3 1.17 + HTSLIB_1.4@HTSLIB_1.4 1.17 + HTSLIB_1.5@HTSLIB_1.5 1.17 + HTSLIB_1.6@HTSLIB_1.6 1.17 + HTSLIB_1.7@HTSLIB_1.7 1.17 + HTSLIB_1.9@HTSLIB_1.9 1.17 + bam_aux2A@HTSLIB_1.0 1.17 + bam_aux2Z@HTSLIB_1.0 1.17 + bam_aux2f@HTSLIB_1.0 1.17 + bam_aux2i@HTSLIB_1.0 1.17 + bam_auxB2f@HTSLIB_1.4 1.17 + bam_auxB2i@HTSLIB_1.4 1.17 + bam_auxB_len@HTSLIB_1.4 1.17 + bam_aux_append@HTSLIB_1.0 1.17 + bam_aux_del@HTSLIB_1.0 1.17 + bam_aux_first@HTSLIB_1.17 1.17 + bam_aux_get@HTSLIB_1.0 1.17 + bam_aux_next@HTSLIB_1.17 1.17 + bam_aux_remove@HTSLIB_1.17 1.17 + bam_aux_update_array@HTSLIB_1.9 1.17 + bam_aux_update_float@HTSLIB_1.9 1.17 + bam_aux_update_int@HTSLIB_1.9 1.17 + bam_aux_update_str@HTSLIB_1.4 1.17 + bam_cigar2qlen@HTSLIB_1.0 1.17 + bam_cigar2rlen@HTSLIB_1.0 1.17 + bam_cigar_table@HTSLIB_1.10 1.17 + bam_copy1@HTSLIB_1.0 1.17 + bam_destroy1@HTSLIB_1.0 1.17 + bam_dup1@HTSLIB_1.0 1.17 + bam_endpos@HTSLIB_1.0 1.17 + bam_flag2str@HTSLIB_1.0 1.17 + bam_hdr_read@HTSLIB_1.0 1.17 + bam_hdr_write@HTSLIB_1.0 1.17 + bam_index_build@Base 1.16 + bam_init1@HTSLIB_1.0 1.17 + bam_mods_at_next_pos@HTSLIB_1.14 1.17 + bam_mods_at_qpos@HTSLIB_1.14 1.17 + bam_mods_query_type@HTSLIB_1.16 1.17 + bam_mods_queryi@HTSLIB_1.18 1.18 + bam_mods_recorded@HTSLIB_1.16 1.17 + bam_mplp64_auto@HTSLIB_1.10 1.17 + bam_mplp_auto@HTSLIB_1.0 1.17 + bam_mplp_constructor@HTSLIB_1.4 1.17 + bam_mplp_destroy@HTSLIB_1.0 1.17 + bam_mplp_destructor@HTSLIB_1.4 1.17 + bam_mplp_init@HTSLIB_1.0 1.17 + bam_mplp_init_overlaps@HTSLIB_1.0 1.17 + bam_mplp_reset@HTSLIB_1.4 1.17 + bam_mplp_set_maxcnt@HTSLIB_1.0 1.17 + bam_next_basemod@HTSLIB_1.14 1.17 + bam_parse_basemod2@HTSLIB_1.18 1.18 + bam_parse_basemod@HTSLIB_1.14 1.17 + bam_parse_cigar@HTSLIB_1.12 1.17 + bam_plp64_auto@HTSLIB_1.10 1.17 + bam_plp64_next@HTSLIB_1.10 1.17 + bam_plp_auto@HTSLIB_1.0 1.17 + bam_plp_constructor@HTSLIB_1.4 1.17 + bam_plp_destroy@HTSLIB_1.0 1.17 + bam_plp_destructor@HTSLIB_1.4 1.17 + bam_plp_init@HTSLIB_1.0 1.17 + bam_plp_init_overlaps@Base 1.16 + bam_plp_insertion@HTSLIB_1.10 1.17 + bam_plp_insertion_mod@HTSLIB_1.14 1.17 + bam_plp_next@HTSLIB_1.0 1.17 + bam_plp_push@HTSLIB_1.0 1.17 + bam_plp_reset@HTSLIB_1.0 1.17 + bam_plp_set_maxcnt@HTSLIB_1.0 1.17 + bam_read1@HTSLIB_1.0 1.17 + bam_set1@HTSLIB_1.12 1.17 + bam_set_qname@HTSLIB_1.10 1.17 + bam_str2flag@HTSLIB_1.0 1.17 + bam_write1@HTSLIB_1.0 1.17 + bcf_add_filter@HTSLIB_1.0 1.17 + bcf_add_id@HTSLIB_1.3 1.17 + bcf_calc_ac@HTSLIB_1.0 1.17 + bcf_clear@HTSLIB_1.0 1.17 + bcf_copy@HTSLIB_1.2.1 1.17 + bcf_destroy@HTSLIB_1.0 1.17 + bcf_dup@HTSLIB_1.0 1.17 + bcf_empty@HTSLIB_1.3 1.17 + bcf_enc_vchar@HTSLIB_1.0 1.17 + bcf_enc_vfloat@HTSLIB_1.0 1.17 + bcf_enc_vint@HTSLIB_1.0 1.17 + bcf_float_missing@HTSLIB_1.0 1.17 + bcf_float_vector_end@HTSLIB_1.0 1.17 + bcf_fmt_array@HTSLIB_1.0 1.17 + bcf_fmt_sized_array@HTSLIB_1.0 1.17 + bcf_get_fmt@HTSLIB_1.0 1.17 + bcf_get_fmt_id@HTSLIB_1.1 1.17 + bcf_get_format_string@HTSLIB_1.0 1.17 + bcf_get_format_values@HTSLIB_1.0 1.17 + bcf_get_info@HTSLIB_1.0 1.17 + bcf_get_info_id@HTSLIB_1.1 1.17 + bcf_get_info_values@HTSLIB_1.0 1.17 + bcf_get_variant_type@HTSLIB_1.0 1.17 + bcf_get_variant_types@HTSLIB_1.0 1.17 + bcf_gt_type@HTSLIB_1.0 1.17 + bcf_has_filter@HTSLIB_1.0 1.17 + bcf_has_variant_type@HTSLIB_1.16 1.17 + bcf_has_variant_types@HTSLIB_1.16 1.17 + bcf_hdr_add_hrec@HTSLIB_1.0 1.17 + bcf_hdr_add_sample@HTSLIB_1.0 1.17 + bcf_hdr_append@HTSLIB_1.0 1.17 + bcf_hdr_check_sanity@Base 1.16 + bcf_hdr_combine@HTSLIB_1.0 1.17 + bcf_hdr_destroy@HTSLIB_1.0 1.17 + bcf_hdr_dup@HTSLIB_1.0 1.17 + bcf_hdr_fmt_text@HTSLIB_1.0 1.17 + bcf_hdr_format@HTSLIB_1.4 1.17 + bcf_hdr_get_hrec@HTSLIB_1.0 1.17 + bcf_hdr_get_version@HTSLIB_1.0 1.17 + bcf_hdr_id2int@HTSLIB_1.0 1.17 + bcf_hdr_init@HTSLIB_1.0 1.17 + bcf_hdr_merge@HTSLIB_1.3 1.17 + bcf_hdr_parse@HTSLIB_1.0 1.17 + bcf_hdr_parse_line@HTSLIB_1.0 1.17 + bcf_hdr_parse_sample_line@Base 1.16 + bcf_hdr_printf@HTSLIB_1.0 1.17 + bcf_hdr_read@HTSLIB_1.0 1.17 + bcf_hdr_remove@HTSLIB_1.0 1.17 + bcf_hdr_seqnames@HTSLIB_1.0 1.17 + bcf_hdr_set@HTSLIB_1.0 1.17 + bcf_hdr_set_samples@HTSLIB_1.0 1.17 + bcf_hdr_set_version@HTSLIB_1.0 1.17 + bcf_hdr_subset@HTSLIB_1.0 1.17 + bcf_hdr_sync@HTSLIB_1.0 1.17 + bcf_hdr_update_hrec@Base 1.17 + bcf_hdr_write@HTSLIB_1.0 1.17 + bcf_header_debug@Base 1.16 + bcf_hrec_add_key@HTSLIB_1.0 1.17 + bcf_hrec_debug@Base 1.16 + bcf_hrec_destroy@HTSLIB_1.0 1.17 + bcf_hrec_dup@HTSLIB_1.0 1.17 + bcf_hrec_find_key@HTSLIB_1.0 1.17 + bcf_hrec_format@HTSLIB_1.0 1.17 + bcf_hrec_set_val@HTSLIB_1.0 1.17 + bcf_idx_init@HTSLIB_1.10 1.17 + bcf_idx_save@HTSLIB_1.10 1.17 + bcf_index@Base 1.16 + bcf_index_build2@HTSLIB_1.3 1.17 + bcf_index_build3@HTSLIB_1.4 1.17 + bcf_index_build@HTSLIB_1.0 1.17 + bcf_index_load2@HTSLIB_1.3 1.17 + bcf_index_load3@HTSLIB_1.10 1.17 + bcf_init@HTSLIB_1.0 1.17 + bcf_is_snp@HTSLIB_1.0 1.17 + bcf_read@HTSLIB_1.0 1.17 + bcf_readrec@HTSLIB_1.0 1.17 + bcf_remove_allele_set@HTSLIB_1.3 1.17 + bcf_remove_alleles@HTSLIB_1.0 1.17 + bcf_remove_filter@HTSLIB_1.0 1.17 + bcf_sr_add_reader@HTSLIB_1.0 1.17 + bcf_sr_destroy@HTSLIB_1.0 1.17 + bcf_sr_destroy_threads@HTSLIB_1.4 1.17 + bcf_sr_init@HTSLIB_1.0 1.17 + bcf_sr_next_line@HTSLIB_1.0 1.17 + bcf_sr_regions_destroy@HTSLIB_1.0 1.17 + bcf_sr_regions_flush@HTSLIB_1.0 1.17 + bcf_sr_regions_init@HTSLIB_1.0 1.17 + bcf_sr_regions_next@HTSLIB_1.0 1.17 + bcf_sr_regions_overlap@HTSLIB_1.0 1.17 + bcf_sr_regions_seek@HTSLIB_1.0 1.17 + bcf_sr_remove_reader@HTSLIB_1.0 1.17 + bcf_sr_seek@HTSLIB_1.0 1.17 + bcf_sr_set_opt@HTSLIB_1.4 1.17 + bcf_sr_set_regions@HTSLIB_1.0 1.17 + bcf_sr_set_samples@HTSLIB_1.0 1.17 + bcf_sr_set_targets@HTSLIB_1.0 1.17 + bcf_sr_set_threads@HTSLIB_1.4 1.17 + bcf_sr_sort_add_active@Base 1.16 + bcf_sr_sort_destroy@Base 1.16 + bcf_sr_sort_init@Base 1.16 + bcf_sr_sort_next@Base 1.16 + bcf_sr_sort_remove_reader@Base 1.16 + bcf_sr_sort_reset@Base 1.16 + bcf_sr_sort_set_active@Base 1.16 + bcf_sr_strerror@HTSLIB_1.2.1 1.17 + bcf_strerror@HTSLIB_1.17 1.17 + bcf_subset@HTSLIB_1.0 1.17 + bcf_subset_format@HTSLIB_1.0 1.17 + bcf_sweep_bwd@HTSLIB_1.0 1.17 + bcf_sweep_destroy@HTSLIB_1.0 1.17 + bcf_sweep_fwd@HTSLIB_1.0 1.17 + bcf_sweep_hdr@HTSLIB_1.0 1.17 + bcf_sweep_init@HTSLIB_1.0 1.17 + bcf_translate@HTSLIB_1.0 1.17 + bcf_trim_alleles@HTSLIB_1.0 1.17 + bcf_type_shift@HTSLIB_1.0 1.17 + bcf_unpack@HTSLIB_1.0 1.17 + bcf_update_alleles@HTSLIB_1.0 1.17 + bcf_update_alleles_str@HTSLIB_1.0 1.17 + bcf_update_filter@HTSLIB_1.0 1.17 + bcf_update_format@HTSLIB_1.0 1.17 + bcf_update_format_string@HTSLIB_1.0 1.17 + bcf_update_id@HTSLIB_1.0 1.17 + bcf_update_info@HTSLIB_1.0 1.17 + bcf_variant_length@HTSLIB_1.16 1.17 + bcf_write@HTSLIB_1.0 1.17 + bgzf_block_write@HTSLIB_1.4 1.17 + bgzf_check_EOF@HTSLIB_1.0 1.17 + bgzf_close@HTSLIB_1.0 1.17 + bgzf_compress@HTSLIB_1.3 1.17 + bgzf_compression@HTSLIB_1.4 1.17 + bgzf_dopen@HTSLIB_1.0 1.17 + bgzf_flush@HTSLIB_1.0 1.17 + bgzf_flush_try@HTSLIB_1.0 1.17 + bgzf_getc@HTSLIB_1.0 1.17 + bgzf_getline@HTSLIB_1.0 1.17 + bgzf_hfile@Base 1.16 + bgzf_hopen@HTSLIB_1.0 1.17 + bgzf_idx_push@Base 1.16 + bgzf_index_add_block@Base 1.16 + bgzf_index_build_init@HTSLIB_1.0 1.17 + bgzf_index_destroy@Base 1.16 + bgzf_index_dump@HTSLIB_1.0 1.17 + bgzf_index_dump_hfile@HTSLIB_1.4 1.17 + bgzf_index_load@HTSLIB_1.0 1.17 + bgzf_index_load_hfile@HTSLIB_1.4 1.17 + bgzf_is_bgzf@HTSLIB_1.0 1.17 + bgzf_mt@HTSLIB_1.0 1.17 + bgzf_mt_read_block@Base 1.16 + bgzf_open@HTSLIB_1.0 1.17 + bgzf_peek@HTSLIB_1.10 1.17 + bgzf_raw_read@HTSLIB_1.0 1.17 + bgzf_raw_write@HTSLIB_1.0 1.17 + bgzf_read@HTSLIB_1.0 1.17 + bgzf_read_block@HTSLIB_1.0 1.17 + bgzf_seek@HTSLIB_1.0 1.17 + bgzf_set_cache_size@HTSLIB_1.0 1.17 + bgzf_thread_pool@HTSLIB_1.4 1.17 + bgzf_useek@HTSLIB_1.0 1.17 + bgzf_utell@HTSLIB_1.0 1.17 + bgzf_write@HTSLIB_1.0 1.17 + close_plugin@Base 1.16 + cram_beta_decode_char@Base 1.16 + cram_beta_decode_free@Base 1.16 + cram_beta_decode_init@Base 1.16 + cram_beta_decode_int@Base 1.16 + cram_beta_decode_long@Base 1.16 + cram_beta_describe@Base 1.17 + cram_beta_encode_char@Base 1.16 + cram_beta_encode_free@Base 1.16 + cram_beta_encode_init@Base 1.16 + cram_beta_encode_int@Base 1.16 + cram_beta_encode_long@Base 1.16 + cram_beta_encode_store@Base 1.16 + cram_block_append@HTSLIB_1.3 1.17 + cram_block_compression_hdr_decoder2encoder@Base 1.16 + cram_block_compression_hdr_set_rg@Base 1.16 + cram_block_get_comp_size@HTSLIB_1.3 1.17 + cram_block_get_content_id@HTSLIB_1.3 1.17 + cram_block_get_content_type@HTSLIB_1.3 1.17 + cram_block_get_crc32@HTSLIB_1.3 1.17 + cram_block_get_data@HTSLIB_1.3 1.17 + cram_block_get_method@HTSLIB_1.17 1.17 + cram_block_get_offset@HTSLIB_1.3 1.17 + cram_block_get_size@Base 1.16 + cram_block_get_uncomp_size@HTSLIB_1.3 1.17 + cram_block_method2str@Base 1.16 + cram_block_set_comp_size@HTSLIB_1.3 1.17 + cram_block_set_content_id@HTSLIB_1.3 1.17 + cram_block_set_crc32@HTSLIB_1.3 1.17 + cram_block_set_data@HTSLIB_1.3 1.17 + cram_block_set_offset@HTSLIB_1.3 1.17 + cram_block_set_size@Base 1.16 + cram_block_set_uncomp_size@HTSLIB_1.3 1.17 + cram_block_size@HTSLIB_1.3 1.17 + cram_block_update_size@HTSLIB_1.3 1.17 + cram_byte_array_len_decode@Base 1.16 + cram_byte_array_len_decode_free@Base 1.16 + cram_byte_array_len_decode_init@Base 1.16 + cram_byte_array_len_describe@Base 1.17 + cram_byte_array_len_encode@Base 1.16 + cram_byte_array_len_encode_free@Base 1.16 + cram_byte_array_len_encode_init@Base 1.16 + cram_byte_array_len_encode_store@Base 1.16 + cram_byte_array_stop_decode_block@Base 1.16 + cram_byte_array_stop_decode_free@Base 1.16 + cram_byte_array_stop_decode_init@Base 1.16 + cram_byte_array_stop_describe@Base 1.17 + cram_byte_array_stop_encode@Base 1.16 + cram_byte_array_stop_encode_free@Base 1.16 + cram_byte_array_stop_encode_init@Base 1.16 + cram_byte_array_stop_encode_store@Base 1.16 + cram_check_EOF@HTSLIB_1.4 1.17 + cram_cid2ds_free@HTSLIB_1.17 1.17 + cram_cid2ds_query@HTSLIB_1.17 1.17 + cram_close@HTSLIB_1.0 1.17 + cram_codec_decoder2encoder@Base 1.16 + cram_codec_describe@HTSLIB_1.17 1.17 + cram_codec_get_content_ids@HTSLIB_1.17 1.17 + cram_codec_to_id@Base 1.16 + cram_compress_block2@Base 1.16 + cram_compress_block@HTSLIB_1.0 1.17 + cram_const_decode_byte@Base 1.16 + cram_const_decode_free@Base 1.16 + cram_const_decode_init@Base 1.16 + cram_const_decode_int@Base 1.16 + cram_const_decode_long@Base 1.16 + cram_const_decode_size@Base 1.16 + cram_const_describe@Base 1.17 + cram_const_encode@Base 1.16 + cram_const_encode_init@Base 1.16 + cram_const_encode_store@Base 1.16 + cram_container_get_landmarks@HTSLIB_1.3 1.17 + cram_container_get_length@HTSLIB_1.3 1.17 + cram_container_get_num_bases@HTSLIB_1.17 1.17 + cram_container_get_num_blocks@HTSLIB_1.3 1.17 + cram_container_get_num_records@HTSLIB_1.17 1.17 + cram_container_is_empty@HTSLIB_1.3 1.17 + cram_container_set_landmarks@HTSLIB_1.3 1.17 + cram_container_set_length@HTSLIB_1.3 1.17 + cram_container_set_num_blocks@HTSLIB_1.3 1.17 + cram_container_size@HTSLIB_1.3 1.17 + cram_content_type2str@Base 1.16 + cram_copy_slice@HTSLIB_1.3 1.17 + cram_decode_TD@Base 1.16 + cram_decode_compression_header@HTSLIB_1.17 1.17 + cram_decode_estimate_sizes@Base 1.16 + cram_decode_slice@Base 1.16 + cram_decode_slice_header@HTSLIB_1.16 1.17 + cram_decode_slice_mt@Base 1.16 + cram_decode_slice_thread@Base 1.16 + cram_decoder_init@Base 1.16 + cram_dependent_data_series@Base 1.16 + cram_describe_encodings@HTSLIB_1.17 1.17 + cram_dopen@HTSLIB_1.0 1.17 + cram_drain_rqueue@Base 1.16 + cram_encode_compression_header@Base 1.16 + cram_encode_container@Base 1.16 + cram_encode_slice_header@Base 1.16 + cram_encoder_init@Base 1.16 + cram_encoding2str@Base 1.16 + cram_eof@HTSLIB_1.0 1.17 + cram_expand_method@HTSLIB_1.17 1.17 + cram_external_decode_char@Base 1.16 + cram_external_decode_free@Base 1.16 + cram_external_decode_init@Base 1.16 + cram_external_decode_int@Base 1.16 + cram_external_decode_long@Base 1.16 + cram_external_decode_size@Base 1.16 + cram_external_describe@Base 1.17 + cram_external_encode_char@Base 1.16 + cram_external_encode_free@Base 1.16 + cram_external_encode_init@Base 1.16 + cram_external_encode_int@Base 1.16 + cram_external_encode_long@Base 1.16 + cram_external_encode_sint@Base 1.16 + cram_external_encode_slong@Base 1.16 + cram_external_encode_store@Base 1.16 + cram_external_get_block@Base 1.16 + cram_fd_get_fp@HTSLIB_1.3 1.17 + cram_fd_get_header@HTSLIB_1.3 1.17 + cram_fd_get_version@HTSLIB_1.3 1.17 + cram_fd_set_fp@HTSLIB_1.3 1.17 + cram_fd_set_header@HTSLIB_1.3 1.17 + cram_fd_set_version@HTSLIB_1.3 1.17 + cram_flush@HTSLIB_1.0 1.17 + cram_flush_container@Base 1.16 + cram_flush_container_mt@Base 1.16 + cram_flush_thread@Base 1.16 + cram_free_block@HTSLIB_1.0 1.17 + cram_free_compression_header@HTSLIB_1.17 1.17 + cram_free_container@HTSLIB_1.0 1.17 + cram_free_file_def@Base 1.16 + cram_free_slice@Base 1.16 + cram_free_slice_header@HTSLIB_1.16 1.17 + cram_gamma_decode@Base 1.16 + cram_gamma_decode_free@Base 1.16 + cram_gamma_decode_init@Base 1.16 + cram_gamma_describe@Base 1.17 + cram_get_bam_seq@Base 1.16 + cram_get_ref@Base 1.16 + cram_get_refs@HTSLIB_1.4 1.17 + cram_get_seq@Base 1.16 + cram_huffman_decode_char0@Base 1.16 + cram_huffman_decode_char@Base 1.16 + cram_huffman_decode_free@Base 1.16 + cram_huffman_decode_init@Base 1.16 + cram_huffman_decode_int0@Base 1.16 + cram_huffman_decode_int@Base 1.16 + cram_huffman_decode_long0@Base 1.16 + cram_huffman_decode_long@Base 1.16 + cram_huffman_decode_null@Base 1.16 + cram_huffman_describe@Base 1.17 + cram_huffman_encode_char0@Base 1.16 + cram_huffman_encode_char@Base 1.16 + cram_huffman_encode_free@Base 1.16 + cram_huffman_encode_init@Base 1.16 + cram_huffman_encode_int0@Base 1.16 + cram_huffman_encode_int@Base 1.16 + cram_huffman_encode_long0@Base 1.16 + cram_huffman_encode_long@Base 1.16 + cram_huffman_encode_store@Base 1.16 + cram_index_build@Base 1.16 + cram_index_free@Base 1.16 + cram_index_last@Base 1.16 + cram_index_load@Base 1.16 + cram_index_query@Base 1.16 + cram_index_query_last@Base 1.16 + cram_index_slice@Base 1.16 + cram_load_reference@Base 1.16 + cram_major_vers@HTSLIB_1.3 1.17 + cram_minor_vers@HTSLIB_1.3 1.17 + cram_new_block@HTSLIB_1.0 1.17 + cram_new_compression_header@Base 1.16 + cram_new_container@HTSLIB_1.0 1.17 + cram_new_metrics@Base 1.16 + cram_new_slice@Base 1.16 + cram_open@HTSLIB_1.0 1.17 + cram_put_bam_seq@Base 1.16 + cram_read_SAM_hdr@Base 1.16 + cram_read_block@HTSLIB_1.0 1.17 + cram_read_container@HTSLIB_1.0 1.17 + cram_read_file_def@Base 1.16 + cram_read_slice@Base 1.16 + cram_ref_decr@Base 1.16 + cram_ref_incr@Base 1.16 + cram_ref_load@Base 1.16 + cram_seek@HTSLIB_1.0 1.17 + cram_seek_to_refpos@Base 1.16 + cram_set_header2@Base 1.16 + cram_set_header@HTSLIB_1.0 1.17 + cram_set_option@HTSLIB_1.0 1.17 + cram_set_voption@HTSLIB_1.0 1.17 + cram_slice_hdr_get_coords@HTSLIB_1.16 1.17 + cram_slice_hdr_get_embed_ref_id@HTSLIB_1.16 1.17 + cram_slice_hdr_get_num_blocks@HTSLIB_1.16 1.17 + cram_stats_add@Base 1.16 + cram_stats_create@Base 1.16 + cram_stats_del@Base 1.16 + cram_stats_encoding@Base 1.16 + cram_stats_free@Base 1.16 + cram_store_container@HTSLIB_1.3 1.17 + cram_subexp_decode@Base 1.16 + cram_subexp_decode_free@Base 1.16 + cram_subexp_decode_init@Base 1.16 + cram_subexp_describe@Base 1.17 + cram_to_bam@Base 1.16 + cram_transcode_rg@HTSLIB_1.3 1.17 + cram_uncompress_block@HTSLIB_1.0 1.17 + cram_update_cid2ds_map@HTSLIB_1.17 1.17 + cram_update_curr_slice@Base 1.16 + cram_varint_decode_free@Base 1.16 + cram_varint_decode_init@Base 1.16 + cram_varint_decode_int@Base 1.16 + cram_varint_decode_long@Base 1.16 + cram_varint_decode_sint@Base 1.16 + cram_varint_decode_size@Base 1.16 + cram_varint_decode_slong@Base 1.16 + cram_varint_describe@Base 1.17 + cram_varint_encode_free@Base 1.16 + cram_varint_encode_init@Base 1.16 + cram_varint_encode_int@Base 1.16 + cram_varint_encode_long@Base 1.16 + cram_varint_encode_sint@Base 1.16 + cram_varint_encode_slong@Base 1.16 + cram_varint_encode_store@Base 1.16 + cram_varint_get_block@Base 1.16 + cram_write_SAM_hdr@Base 1.16 + cram_write_block@HTSLIB_1.0 1.17 + cram_write_container@HTSLIB_1.0 1.17 + cram_write_eof_block@Base 1.16 + cram_write_file_def@Base 1.16 + cram_xdelta_decode_block@Base 1.16 + cram_xdelta_decode_char@Base 1.16 + cram_xdelta_decode_free@Base 1.16 + cram_xdelta_decode_init@Base 1.16 + cram_xdelta_decode_int@Base 1.16 + cram_xdelta_decode_long@Base 1.16 + cram_xdelta_decode_size@Base 1.16 + cram_xdelta_encode_char@Base 1.16 + cram_xdelta_encode_flush@Base 1.16 + cram_xdelta_encode_free@Base 1.16 + cram_xdelta_encode_init@Base 1.16 + cram_xdelta_encode_int@Base 1.16 + cram_xdelta_encode_long@Base 1.16 + cram_xdelta_encode_store@Base 1.16 + cram_xdelta_get_block@Base 1.16 + cram_xpack_decode_char@Base 1.16 + cram_xpack_decode_free@Base 1.16 + cram_xpack_decode_init@Base 1.16 + cram_xpack_decode_int@Base 1.16 + cram_xpack_decode_long@Base 1.16 + cram_xpack_decode_size@Base 1.16 + cram_xpack_encode_char@Base 1.16 + cram_xpack_encode_flush@Base 1.16 + cram_xpack_encode_free@Base 1.16 + cram_xpack_encode_init@Base 1.16 + cram_xpack_encode_int@Base 1.16 + cram_xpack_encode_long@Base 1.16 + cram_xpack_encode_store@Base 1.16 + cram_xpack_get_block@Base 1.16 + cram_xrle_decode_char@Base 1.16 + cram_xrle_decode_free@Base 1.16 + cram_xrle_decode_init@Base 1.16 + cram_xrle_decode_int@Base 1.16 + cram_xrle_decode_long@Base 1.16 + cram_xrle_decode_size@Base 1.16 + cram_xrle_encode_char@Base 1.16 + cram_xrle_encode_flush@Base 1.16 + cram_xrle_encode_free@Base 1.16 + cram_xrle_encode_init@Base 1.16 + cram_xrle_encode_int@Base 1.16 + cram_xrle_encode_long@Base 1.16 + cram_xrle_encode_store@Base 1.16 + cram_xrle_get_block@Base 1.16 + errmod_cal@HTSLIB_1.4 1.17 + errmod_destroy@HTSLIB_1.4 1.17 + errmod_init@HTSLIB_1.4 1.17 + fai_adjust_region@HTSLIB_1.17 1.17 + fai_build3@HTSLIB_1.4 1.17 + fai_build@HTSLIB_1.0 1.17 + fai_destroy@HTSLIB_1.0 1.17 + fai_fetch64@HTSLIB_1.10 1.17 + fai_fetch@HTSLIB_1.0 1.17 + fai_fetchqual64@HTSLIB_1.10 1.17 + fai_fetchqual@HTSLIB_1.9 1.17 + fai_line_length@HTSLIB_1.17 1.17 + fai_load3@HTSLIB_1.4 1.17 + fai_load3_format@HTSLIB_1.9 1.17 + fai_load@HTSLIB_1.0 1.17 + fai_load_format@HTSLIB_1.9 1.17 + fai_parse_region@HTSLIB_1.10 1.17 + fai_path@HTSLIB_1.11 1.17 + fai_set_cache_size@HTSLIB_1.10 1.17 + fai_thread_pool@HTSLIB_1.18 1.18 + faidx_fetch_nseq@HTSLIB_1.0 1.17 + faidx_fetch_qual64@HTSLIB_1.10 1.17 + faidx_fetch_qual@HTSLIB_1.9 1.17 + faidx_fetch_seq64@HTSLIB_1.10 1.17 + faidx_fetch_seq@HTSLIB_1.0 1.17 + faidx_has_seq@HTSLIB_1.0 1.17 + faidx_iseq@HTSLIB_1.1 1.17 + faidx_nseq@HTSLIB_1.1 1.17 + faidx_seq_len64@HTSLIB_1.17 1.17 + faidx_seq_len@HTSLIB_1.1 1.17 + fastq_format1@Base 1.16 + fastq_state_destroy@Base 1.16 + fastq_state_set@Base 1.16 + find_file_url@Base 1.16 + find_path@Base 1.16 + haddextension@HTSLIB_1.10 1.17 + hclose@HTSLIB_1.0 1.17 + hclose_abruptly@HTSLIB_1.0 1.17 + hdopen@HTSLIB_1.0 1.17 + hfile_add_scheme_handler@HTSLIB_1.3 1.17 + hfile_always_local@HTSLIB_1.3 1.17 + hfile_always_remote@HTSLIB_1.3 1.17 + hfile_destroy@HTSLIB_1.0 1.17 + hfile_has_plugin@HTSLIB_1.12 1.17 + hfile_init@HTSLIB_1.0 1.17 + hfile_init_fixed@Base 1.16 + hfile_list_plugins@HTSLIB_1.12 1.17 + hfile_list_schemes@HTSLIB_1.12 1.17 + 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signature.asc
Description: PGP signature
