[med-svn] [Git][med-team/htslib][master] 3 commits: Fix check for config.mk.
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Dec 13 10:35:28 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / htslib
Commits:
11a677cf by Michael R. Crusoe at 2019-12-13T09:54:41Z
Fix check for config.mk.
- - - - -
b03a6b14 by Michael R. Crusoe at 2019-12-13T10:00:08Z
Simplified arch-independent build
- - - - -
52415fa2 by Michael R. Crusoe at 2019-12-13T10:33:20Z
rename libhts2 to libht3 & release 1.10-2
- - - - -
6 changed files:
- debian/changelog
- debian/control
- − debian/libhts2.symbols
- debian/libhts2.install → debian/libhts3.install
- + debian/libhts3.symbols
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+htslib (1.10-2) unstable; urgency=medium
+
+ * Fix check for config.mk.
+ * Simplified arch-independent build
+ * libhts2 -> libhts3 to match the new SONAME
+ * Update the symbols as well
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 13 Dec 2019 11:04:33 +0100
+
htslib (1.10-1) unstable; urgency=medium
* New upstream release.
=====================================
debian/control
=====================================
@@ -13,12 +13,12 @@ Build-Depends: debhelper (>= 11~),
libssl-dev,
zlib1g-dev,
libdeflate-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/htslib
Vcs-Git: https://salsa.debian.org/med-team/htslib.git
Homepage: https://github.com/samtools/htslib
-Package: libhts2
+Package: libhts3
Architecture: any
Multi-Arch: same
Section: libs
@@ -42,7 +42,7 @@ Package: libhts-dev
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libhts2 (= ${binary:Version}),
+Depends: libhts3 (= ${binary:Version}),
liblzma-dev,
zlib1g-dev,
${misc:Depends}
=====================================
debian/libhts2.symbols deleted
=====================================
@@ -1,749 +0,0 @@
-libhts.so.2 libhts2 #MINVER#
- _reader_next_line at Base 1.0
- _regidx_build_index at Base 1.2.1
- bam_aux2A at Base 1.0
- bam_aux2Z at Base 1.0
- bam_aux2f at Base 1.0
- bam_aux2i at Base 1.0
- bam_auxB2f at Base 1.4.1
- bam_auxB2i at Base 1.4.1
- bam_auxB_len at Base 1.4.1
- bam_aux_append at Base 1.0
- bam_aux_del at Base 1.0
- bam_aux_get at Base 1.0
- bam_aux_update_array at Base 1.9
- bam_aux_update_float at Base 1.9
- bam_aux_update_int at Base 1.9
- bam_aux_update_str at Base 1.4.1
- bam_cigar2qlen at Base 1.0
- bam_cigar2rlen at Base 1.0
- bam_cigar2rqlens at Base 1.7
- bam_construct_seq at Base 1.0
- bam_copy1 at Base 1.0
- bam_destroy1 at Base 1.0
- bam_dup1 at Base 1.0
- bam_endpos at Base 1.0
- bam_flag2str at Base 1.0
- bam_hdr_destroy at Base 1.0
- bam_hdr_dup at Base 1.0
- bam_hdr_init at Base 1.0
- bam_hdr_read at Base 1.0
- bam_hdr_write at Base 1.0
- bam_header_to_cram at Base 1.0
- bam_index_build at Base 1.0
- bam_init1 at Base 1.0
- bam_mplp_auto at Base 1.0
- bam_mplp_constructor at Base 1.4.1
- bam_mplp_destroy at Base 1.0
- bam_mplp_destructor at Base 1.4.1
- bam_mplp_init at Base 1.0
- bam_mplp_init_overlaps at Base 1.0
- bam_mplp_reset at Base 1.4.1
- bam_mplp_set_maxcnt at Base 1.0
- bam_name2id at Base 1.0
- bam_plp_auto at Base 1.0
- bam_plp_constructor at Base 1.4.1
- bam_plp_destroy at Base 1.0
- bam_plp_destructor at Base 1.4.1
- bam_plp_init at Base 1.0
- bam_plp_init_overlaps at Base 1.0
- bam_plp_next at Base 1.0
- bam_plp_push at Base 1.0
- bam_plp_reset at Base 1.0
- bam_plp_set_maxcnt at Base 1.0
- bam_read1 at Base 1.0
- bam_str2flag at Base 1.0
- bam_write1 at Base 1.0
- bcf_add_filter at Base 1.0
- bcf_add_id at Base 1.3
- bcf_calc_ac at Base 1.0
- bcf_clear at Base 1.0
- bcf_copy at Base 1.2.1
- bcf_destroy at Base 1.0
- bcf_dup at Base 1.0
- bcf_empty at Base 1.3
- bcf_enc_vchar at Base 1.0
- bcf_enc_vfloat at Base 1.0
- bcf_enc_vint at Base 1.0
- bcf_float_missing at Base 1.0
- bcf_float_vector_end at Base 1.0
- bcf_fmt_array at Base 1.0
- bcf_fmt_sized_array at Base 1.0
- bcf_get_fmt at Base 1.0
- bcf_get_fmt_id at Base 1.1
- bcf_get_format_string at Base 1.0
- bcf_get_format_values at Base 1.0
- bcf_get_info at Base 1.0
- bcf_get_info_id at Base 1.1
- bcf_get_info_values at Base 1.0
- bcf_get_variant_type at Base 1.0
- bcf_get_variant_types at Base 1.0
- bcf_gt_type at Base 1.0
- bcf_has_filter at Base 1.0
- bcf_hdr_add_hrec at Base 1.0
- bcf_hdr_add_sample at Base 1.0
- bcf_hdr_append at Base 1.0
- bcf_hdr_check_sanity at Base 1.0
- bcf_hdr_combine at Base 1.0
- bcf_hdr_destroy at Base 1.0
- bcf_hdr_dup at Base 1.0
- bcf_hdr_fmt_text at Base 1.0
- bcf_hdr_format at Base 1.4.1
- bcf_hdr_get_hrec at Base 1.0
- bcf_hdr_get_version at Base 1.0
- bcf_hdr_id2int at Base 1.0
- bcf_hdr_init at Base 1.0
- bcf_hdr_merge at Base 1.3
- bcf_hdr_parse at Base 1.0
- bcf_hdr_parse_line at Base 1.0
- bcf_hdr_parse_sample_line at Base 1.0
- bcf_hdr_printf at Base 1.0
- bcf_hdr_read at Base 1.0
- bcf_hdr_register_hrec at Base 1.0
- bcf_hdr_remove at Base 1.0
- bcf_hdr_seqnames at Base 1.0
- bcf_hdr_set at Base 1.0
- bcf_hdr_set_samples at Base 1.0
- bcf_hdr_set_version at Base 1.0
- bcf_hdr_subset at Base 1.0
- bcf_hdr_sync at Base 1.0
- bcf_hdr_write at Base 1.0
- bcf_header_debug at Base 1.0
- bcf_hrec_add_key at Base 1.0
- bcf_hrec_debug at Base 1.0
- bcf_hrec_destroy at Base 1.0
- bcf_hrec_dup at Base 1.0
- bcf_hrec_find_key at Base 1.0
- bcf_hrec_format at Base 1.0
- bcf_hrec_set_val at Base 1.0
- bcf_index at Base 1.0
- bcf_index_build2 at Base 1.3
- bcf_index_build3 at Base 1.4.1
- bcf_index_build at Base 1.0
- bcf_index_load2 at Base 1.3
- bcf_init at Base 1.0
- bcf_is_snp at Base 1.0
- bcf_read at Base 1.0
- bcf_readrec at Base 1.0
- bcf_remove_allele_set at Base 1.3
- bcf_remove_alleles at Base 1.0
- bcf_remove_filter at Base 1.0
- bcf_sr_add_reader at Base 1.0
- bcf_sr_destroy at Base 1.0
- bcf_sr_destroy_threads at Base 1.4.1
- bcf_sr_init at Base 1.0
- bcf_sr_next_line at Base 1.0
- bcf_sr_regions_destroy at Base 1.0
- bcf_sr_regions_flush at Base 1.0
- bcf_sr_regions_init at Base 1.0
- bcf_sr_regions_next at Base 1.0
- bcf_sr_regions_overlap at Base 1.0
- bcf_sr_regions_seek at Base 1.0
- bcf_sr_remove_reader at Base 1.0
- bcf_sr_seek at Base 1.0
- bcf_sr_set_opt at Base 1.4.1
- bcf_sr_set_regions at Base 1.0
- bcf_sr_set_samples at Base 1.0
- bcf_sr_set_targets at Base 1.0
- bcf_sr_set_threads at Base 1.4.1
- bcf_sr_sort_add_active at Base 1.7
- bcf_sr_sort_destroy at Base 1.4.1
- bcf_sr_sort_init at Base 1.4.1
- bcf_sr_sort_next at Base 1.4.1
- bcf_sr_sort_remove_reader at Base 1.4.1
- bcf_sr_sort_reset at Base 1.9
- bcf_sr_sort_set_active at Base 1.7
- bcf_sr_strerror at Base 1.2.1
- bcf_subset at Base 1.0
- bcf_subset_format at Base 1.0
- bcf_sweep_bwd at Base 1.0
- bcf_sweep_destroy at Base 1.0
- bcf_sweep_fwd at Base 1.0
- bcf_sweep_hdr at Base 1.0
- bcf_sweep_init at Base 1.0
- bcf_translate at Base 1.0
- bcf_trim_alleles at Base 1.0
- bcf_type_shift at Base 1.0
- bcf_unpack at Base 1.0
- bcf_update_alleles at Base 1.0
- bcf_update_alleles_str at Base 1.0
- bcf_update_filter at Base 1.0
- bcf_update_format at Base 1.0
- bcf_update_format_string at Base 1.0
- bcf_update_id at Base 1.0
- bcf_update_info at Base 1.0
- bcf_write at Base 1.0
- bgzf_block_write at Base 1.4.1
- bgzf_check_EOF at Base 1.0
- bgzf_close at Base 1.0
- bgzf_compress at Base 1.3
- bgzf_compression at Base 1.4.1
- bgzf_decode_func at Base 1.4.1
- bgzf_dopen at Base 1.0
- bgzf_encode_func at Base 1.4.1
- bgzf_encode_level0_func at Base 1.9
- bgzf_flush at Base 1.0
- bgzf_flush_try at Base 1.0
- bgzf_getc at Base 1.0
- bgzf_getline at Base 1.0
- bgzf_hfile at Base 1.5
- bgzf_hopen at Base 1.0
- bgzf_index_add_block at Base 1.0
- bgzf_index_build_init at Base 1.0
- bgzf_index_destroy at Base 1.0
- bgzf_index_dump at Base 1.0
- bgzf_index_dump_hfile at Base 1.4.1
- bgzf_index_load at Base 1.0
- bgzf_index_load_hfile at Base 1.4.1
- bgzf_is_bgzf at Base 1.0
- bgzf_mt at Base 1.0
- bgzf_mt_read_block at Base 1.4.1
- bgzf_nul_func at Base 1.4.1
- bgzf_open at Base 1.0
- bgzf_raw_read at Base 1.0
- bgzf_raw_write at Base 1.0
- bgzf_read at Base 1.0
- bgzf_read_block at Base 1.0
- bgzf_seek at Base 1.0
- bgzf_set_cache_size at Base 1.0
- bgzf_thread_pool at Base 1.4.1
- bgzf_useek at Base 1.0
- bgzf_utell at Base 1.0
- bgzf_write at Base 1.0
- cram_beta_decode_char at Base 1.0
- cram_beta_decode_free at Base 1.0
- cram_beta_decode_init at Base 1.0
- cram_beta_decode_int at Base 1.0
- cram_beta_encode_char at Base 1.0
- cram_beta_encode_free at Base 1.0
- cram_beta_encode_init at Base 1.0
- cram_beta_encode_int at Base 1.0
- cram_beta_encode_store at Base 1.0
- cram_block_append at Base 1.3
- cram_block_compression_hdr_decoder2encoder at Base 1.3
- cram_block_compression_hdr_set_rg at Base 1.3
- cram_block_get_comp_size at Base 1.3
- cram_block_get_content_id at Base 1.3
- cram_block_get_content_type at Base 1.3
- cram_block_get_crc32 at Base 1.3
- cram_block_get_data at Base 1.3
- cram_block_get_offset at Base 1.3
- cram_block_get_size at Base 1.3
- cram_block_get_uncomp_size at Base 1.3
- cram_block_method2str at Base 1.0
- cram_block_set_comp_size at Base 1.3
- cram_block_set_content_id at Base 1.3
- cram_block_set_crc32 at Base 1.3
- cram_block_set_data at Base 1.3
- cram_block_set_offset at Base 1.3
- cram_block_set_size at Base 1.3
- cram_block_set_uncomp_size at Base 1.3
- cram_block_size at Base 1.3
- cram_block_update_size at Base 1.3
- cram_byte_array_len_decode at Base 1.0
- cram_byte_array_len_decode_free at Base 1.0
- cram_byte_array_len_decode_init at Base 1.0
- cram_byte_array_len_encode at Base 1.0
- cram_byte_array_len_encode_free at Base 1.0
- cram_byte_array_len_encode_init at Base 1.0
- cram_byte_array_len_encode_store at Base 1.0
- cram_byte_array_stop_decode_block at Base 1.0
- cram_byte_array_stop_decode_free at Base 1.0
- cram_byte_array_stop_decode_init at Base 1.0
- cram_byte_array_stop_encode at Base 1.0
- cram_byte_array_stop_encode_free at Base 1.0
- cram_byte_array_stop_encode_init at Base 1.0
- cram_byte_array_stop_encode_store at Base 1.0
- cram_check_EOF at Base 1.4.1
- cram_close at Base 1.0
- cram_codec_decoder2encoder at Base 1.3
- cram_codec_to_id at Base 1.2.1
- cram_compress_block at Base 1.0
- cram_container_get_landmarks at Base 1.3
- cram_container_get_length at Base 1.3
- cram_container_get_num_blocks at Base 1.3
- cram_container_is_empty at Base 1.3
- cram_container_set_landmarks at Base 1.3
- cram_container_set_length at Base 1.3
- cram_container_set_num_blocks at Base 1.3
- cram_container_size at Base 1.3
- cram_content_type2str at Base 1.0
- cram_copy_slice at Base 1.3
- cram_decode_TD at Base 1.0
- cram_decode_compression_header at Base 1.0
- cram_decode_estimate_sizes at Base 1.3
- cram_decode_slice at Base 1.0
- cram_decode_slice_header at Base 1.0
- cram_decode_slice_mt at Base 1.0
- cram_decode_slice_thread at Base 1.0
- cram_decoder_init at Base 1.0
- cram_dependent_data_series at Base 1.2.1
- cram_dopen at Base 1.0
- cram_drain_rqueue at Base 1.8
- cram_encode_compression_header at Base 1.0
- cram_encode_container at Base 1.0
- cram_encode_slice_header at Base 1.0
- cram_encoder_init at Base 1.0
- cram_encoding2str at Base 1.0
- cram_eof at Base 1.0
- cram_external_decode_char at Base 1.0
- cram_external_decode_free at Base 1.0
- cram_external_decode_init at Base 1.0
- cram_external_decode_int at Base 1.0
- cram_external_encode_char at Base 1.2.1
- cram_external_encode_free at Base 1.0
- cram_external_encode_init at Base 1.0
- cram_external_encode_int at Base 1.2.1
- cram_external_encode_store at Base 1.0
- cram_fd_get_fp at Base 1.3
- cram_fd_get_header at Base 1.3
- cram_fd_get_version at Base 1.3
- cram_fd_set_fp at Base 1.3
- cram_fd_set_header at Base 1.3
- cram_fd_set_version at Base 1.3
- cram_flush at Base 1.0
- cram_flush_container at Base 1.0
- cram_flush_container_mt at Base 1.0
- cram_flush_thread at Base 1.0
- cram_free_block at Base 1.0
- cram_free_compression_header at Base 1.0
- cram_free_container at Base 1.0
- cram_free_file_def at Base 1.0
- cram_free_slice at Base 1.0
- cram_free_slice_header at Base 1.0
- cram_gamma_decode at Base 1.0
- cram_gamma_decode_free at Base 1.0
- cram_gamma_decode_init at Base 1.0
- cram_get_bam_seq at Base 1.0
- cram_get_ref at Base 1.0
- cram_get_refs at Base 1.4.1
- cram_get_seq at Base 1.0
- cram_header_to_bam at Base 1.0
- cram_huffman_decode_char0 at Base 1.0
- cram_huffman_decode_char at Base 1.0
- cram_huffman_decode_free at Base 1.0
- cram_huffman_decode_init at Base 1.0
- cram_huffman_decode_int0 at Base 1.0
- cram_huffman_decode_int at Base 1.0
- cram_huffman_decode_null at Base 1.3
- cram_huffman_encode_char0 at Base 1.0
- cram_huffman_encode_char at Base 1.0
- cram_huffman_encode_free at Base 1.0
- cram_huffman_encode_init at Base 1.0
- cram_huffman_encode_int0 at Base 1.0
- cram_huffman_encode_int at Base 1.0
- cram_huffman_encode_store at Base 1.0
- cram_index_build at Base 1.0
- cram_index_free at Base 1.0
- cram_index_last at Base 1.7
- cram_index_load at Base 1.0
- cram_index_query at Base 1.0
- cram_load_reference at Base 1.0
- cram_major_vers at Base 1.3
- cram_minor_vers at Base 1.3
- cram_new_block at Base 1.0
- cram_new_compression_header at Base 1.0
- cram_new_container at Base 1.0
- cram_new_metrics at Base 1.0
- cram_new_slice at Base 1.0
- cram_open at Base 1.0
- cram_put_bam_seq at Base 1.0
- cram_read_SAM_hdr at Base 1.0
- cram_read_block at Base 1.0
- cram_read_container at Base 1.0
- cram_read_file_def at Base 1.0
- cram_read_slice at Base 1.0
- cram_ref_decr at Base 1.0
- cram_ref_incr at Base 1.0
- cram_ref_load at Base 1.0
- cram_seek at Base 1.0
- cram_seek_to_refpos at Base 1.0
- cram_set_header at Base 1.0
- cram_set_option at Base 1.0
- cram_set_voption at Base 1.0
- cram_slice_hdr_get_num_blocks at Base 1.3
- cram_stats_add at Base 1.0
- cram_stats_create at Base 1.0
- cram_stats_del at Base 1.0
- cram_stats_encoding at Base 1.0
- cram_stats_free at Base 1.0
- cram_store_container at Base 1.3
- cram_subexp_decode at Base 1.0
- cram_subexp_decode_free at Base 1.0
- cram_subexp_decode_init at Base 1.0
-#MISSING: 1.9# cram_to_bam at Base 1.4.1
- cram_transcode_rg at Base 1.3
- cram_uncompress_block at Base 1.0
- cram_update_curr_slice at Base 1.4.1
- cram_write_SAM_hdr at Base 1.0
- cram_write_block at Base 1.0
- cram_write_container at Base 1.0
- cram_write_file_def at Base 1.0
- debug_buffer at Base 1.0
- debug_buffers at Base 1.0
- errmod_cal at Base 1.4.1
- errmod_destroy at Base 1.4.1
- errmod_init at Base 1.4.1
- expand_cache_path at Base 1.0
- fai_build3 at Base 1.4.1
- fai_build at Base 1.0
-#MISSING: 1.9# fai_build_core at Base 1.0
- fai_destroy at Base 1.0
- fai_fetch at Base 1.0
- fai_fetchqual at Base 1.9
- fai_load3 at Base 1.4.1
- fai_load3_format at Base 1.9
- fai_load at Base 1.0
- fai_load_format at Base 1.9
- faidx_fetch_nseq at Base 1.2.1
- faidx_fetch_qual at Base 1.9
- faidx_fetch_seq at Base 1.0
- faidx_has_seq at Base 1.0
- faidx_iseq at Base 1.1
- faidx_nseq at Base 1.1
- faidx_seq_len at Base 1.1
- file_exists at Base 1.0
- file_size at Base 1.0
- find_file_url at Base 1.0
- find_path at Base 1.3
- grp_create_key at Base 1.4.1
- hclose at Base 1.0
- hclose_abruptly at Base 1.0
- hdopen at Base 1.0
- hfile_add_scheme_handler at Base 1.3
- hfile_always_local at Base 1.3
- hfile_always_remote at Base 1.3
- hfile_destroy at Base 1.0
- hfile_init at Base 1.0
- hfile_init_fixed at Base 1.4.1
- hfile_mem_get_buffer at Base 1.7
- hfile_mem_steal_buffer at Base 1.7
- hfile_oflags at Base 1.0
- hfile_plugin_init_gcs at Base 1.4.1
- hfile_plugin_init_libcurl at Base 1.3.1
- hfile_plugin_init_mem at Base 1.7
- hfile_plugin_init_net at Base 1.3
- hfile_plugin_init_s3 at Base 1.4.1
- hfile_set_blksize at Base 1.5
- hflush at Base 1.0
- hgetc2 at Base 1.0
- hgetdelim at Base 1.4.1
- hgets at Base 1.4.1
- hisremote at Base 1.2.1
- hopen at Base 1.0
- hopen_htsget_redirect at Base 1.6
- hopen_net at Base 1.0
- hopenv_mem at Base 1.7
- hpeek at Base 1.0
- hputc2 at Base 1.0
- hputs2 at Base 1.0
- hread2 at Base 1.0
- hrec_add_idx at Base 1.0
- hseek at Base 1.0
- hts_base64_decoded_length at Base 1.4.1
- hts_check_EOF at Base 1.4.1
- hts_close at Base 1.0
- hts_decode_base64 at Base 1.4.1
- hts_decode_percent at Base 1.4.1
- hts_detect_format at Base 1.2.1
- hts_drand48 at Base 1.6
- hts_erand48 at Base 1.6
- hts_file_type at Base 1.0
- hts_format_description at Base 1.2.1
- hts_format_file_extension at Base 1.3
- hts_get_bgzfp at Base 1.0
- hts_get_format at Base 1.2.1
- hts_get_log_level at Base 1.5
- hts_getline at Base 1.0
- hts_hopen at Base 1.2.1
- hts_idx_destroy at Base 1.0
- hts_idx_finish at Base 1.0
- hts_idx_get_meta at Base 1.0
- hts_idx_get_n_no_coor at Base 1.0
- hts_idx_get_stat at Base 1.0
- hts_idx_getfn at Base 1.0
- hts_idx_init at Base 1.0
- hts_idx_load2 at Base 1.3
- hts_idx_load at Base 1.0
- hts_idx_push at Base 1.0
- hts_idx_save at Base 1.0
- hts_idx_save_as at Base 1.3
- hts_idx_seqnames at Base 1.0
- hts_idx_set_meta at Base 1.0
- hts_itr_destroy at Base 1.0
- hts_itr_multi_bam at Base 1.7
- hts_itr_multi_cram at Base 1.7
- hts_itr_multi_destroy at Base 1.7
- hts_itr_multi_next at Base 1.7
- hts_itr_next at Base 1.0
- hts_itr_off at Base 1.7
- hts_itr_query at Base 1.0
- hts_itr_querys at Base 1.0
- hts_itr_regions at Base 1.7
- hts_json_alloc_token at Base 1.7
- hts_json_fnext at Base 1.4.1
- hts_json_free_token at Base 1.7
- hts_json_fskip_value at Base 1.4.1
- hts_json_snext at Base 1.4.1
- hts_json_sskip_value at Base 1.4.1
- hts_json_token_str at Base 1.7
- hts_json_token_type at Base 1.7
- hts_log at Base 1.5
- hts_lrand48 at Base 1.6
- hts_md5_destroy at Base 1.3
- hts_md5_final at Base 1.3
- hts_md5_hex at Base 1.3
- hts_md5_init at Base 1.3
- hts_md5_reset at Base 1.3
- hts_md5_update at Base 1.3
- hts_open at Base 1.0
- hts_open_format at Base 1.3
- hts_opt_add at Base 1.3
- hts_opt_apply at Base 1.3
- hts_opt_free at Base 1.3
- hts_parse_decimal at Base 1.3
- hts_parse_format at Base 1.3
- hts_parse_opt_list at Base 1.3
- hts_parse_reg at Base 1.0
- hts_readlines at Base 1.0
- hts_readlist at Base 1.0
- hts_realloc_or_die at Base 1.4.1
- hts_reglist_free at Base 1.7
- hts_set_cache_size at Base 1.4.1
- hts_set_fai_filename at Base 1.0
- hts_set_log_level at Base 1.5
- hts_set_opt at Base 1.2.1
- hts_set_thread_pool at Base 1.4.1
- hts_set_threads at Base 1.0
- hts_srand48 at Base 1.6
- hts_tpool_delete_result at Base 1.4.1
- hts_tpool_destroy at Base 1.4.1
- hts_tpool_dispatch2 at Base 1.4.1
- hts_tpool_dispatch at Base 1.4.1
- hts_tpool_init at Base 1.4.1
- hts_tpool_kill at Base 1.4.1
- hts_tpool_next_result at Base 1.4.1
- hts_tpool_next_result_wait at Base 1.4.1
- hts_tpool_process_attach at Base 1.4.1
- hts_tpool_process_destroy at Base 1.4.1
- hts_tpool_process_detach at Base 1.4.1
- hts_tpool_process_empty at Base 1.4.1
- hts_tpool_process_flush at Base 1.4.1
- hts_tpool_process_init at Base 1.4.1
- hts_tpool_process_len at Base 1.4.1
- hts_tpool_process_qsize at Base 1.4.1
- hts_tpool_process_ref_decr at Base 1.4.1
- hts_tpool_process_ref_incr at Base 1.4.1
- hts_tpool_process_reset at Base 1.4.1
- hts_tpool_process_shutdown at Base 1.4.1
- hts_tpool_process_sz at Base 1.4.1
- hts_tpool_result_data at Base 1.4.1
- hts_tpool_size at Base 1.4.1
- hts_tpool_wake_dispatch at Base 1.4.1
- hts_useek at Base 1.0
- hts_utell at Base 1.0
- hts_verbose at Base 1.0
- hts_version at Base 1.0
- hwrite2 at Base 1.0
- int32_decode at Base 1.0
- int32_encode at Base 1.0
- int32_get_blk at Base 1.3
- int32_put_blk at Base 1.3
- is_directory at Base 1.0
- is_file at Base 1.0
- itf8_bytes at Base 1.3
- itf8_decode at Base 1.0
- itf8_decode_crc at Base 1.3
- itf8_encode at Base 1.0
- itf8_put_blk at Base 1.0
- kf_betai at Base 1.0
- kf_erfc at Base 1.0
- kf_gammap at Base 1.0
- kf_gammaq at Base 1.0
- kf_lgamma at Base 1.0
- kftp_connect at Base 1.0
- kftp_connect_file at Base 1.0
- kftp_parse_url at Base 1.0
- kftp_reconnect at Base 1.0
- kgetline at Base 1.3
- kh_clear_s2i at Base 1.0
- kh_del_s2i at Base 1.0
- kh_destroy_s2i at Base 1.0
- kh_get_s2i at Base 1.0
- kh_init_s2i at Base 1.0
- kh_put_s2i at Base 1.0
- kh_resize_s2i at Base 1.0
- khttp_connect_file at Base 1.0
- khttp_parse_url at Base 1.0
- kmemmem at Base 1.0
- knet_close at Base 1.0
- knet_dopen at Base 1.0
- knet_open at Base 1.0
- knet_read at Base 1.0
- knet_seek at Base 1.0
- kputd at Base 1.4.1
- ks_combsort__off at Base 1.0
- ks_combsort__off_max at Base 1.7
- ks_combsort_uint16_t at Base 1.4.1
- ks_heapadjust__off at Base 1.0
- ks_heapadjust__off_max at Base 1.7
- ks_heapadjust_uint16_t at Base 1.4.1
- ks_heapmake__off at Base 1.0
- ks_heapmake__off_max at Base 1.7
- ks_heapmake_uint16_t at Base 1.4.1
- ks_heapsort__off at Base 1.0
- ks_heapsort__off_max at Base 1.7
- ks_heapsort_uint16_t at Base 1.4.1
- ks_introsort__off at Base 1.0
- ks_introsort__off_max at Base 1.7
- ks_introsort_uint16_t at Base 1.4.1
- ks_ksmall__off at Base 1.0
- ks_ksmall__off_max at Base 1.7
- ks_ksmall_uint16_t at Base 1.4.1
- ks_mergesort__off at Base 1.0
- ks_mergesort__off_max at Base 1.7
- ks_mergesort_uint16_t at Base 1.4.1
- ks_shuffle__off at Base 1.0
- ks_shuffle__off_max at Base 1.7
- ks_shuffle_uint16_t at Base 1.4.1
- ksplit_core at Base 1.0
- ksprintf at Base 1.0
- kstrnstr at Base 1.0
- kstrstr at Base 1.0
- kstrtok at Base 1.0
- kt_fisher_exact at Base 1.0
- kvsprintf at Base 1.0
- ltf8_bytes at Base 1.4.1
- ltf8_decode at Base 1.0
- ltf8_decode_crc at Base 1.3
- merge_vsets at Base 1.4.1
- mfascii at Base 1.0
- mfclose at Base 1.0
- mfcreate at Base 1.0
- mfcreate_from at Base 1.0
- mfdestroy at Base 1.0
- mfdetach at Base 1.0
- mfeof at Base 1.0
- mfflush at Base 1.0
- mfgetc at Base 1.0
- mfgets at Base 1.0
- mfmmap at Base 1.3
- mfopen at Base 1.0
- mfread at Base 1.0
- mfrecreate at Base 1.0
- mfreopen at Base 1.0
- mfseek at Base 1.0
- mfsteal at Base 1.0
- mftell at Base 1.0
- mftruncate at Base 1.0
- mfwrite at Base 1.0
- mkdir_prefix at Base 1.0
- mrewind at Base 1.0
- mstderr at Base 1.0
- mstdin at Base 1.0
- mstdout at Base 1.0
- mungetc at Base 1.0
- open_path_mfile at Base 1.0
- pairing_score at Base 1.4.1
- pool_alloc at Base 1.0
- pool_create at Base 1.0
- pool_destroy at Base 1.0
- pool_free at Base 1.0
- probaln_glocal at Base 1.4.1
- push_vset at Base 1.4.1
- rans_compress at Base 1.2.1
- rans_compress_O0 at Base 1.2.1
- rans_compress_O1 at Base 1.2.1
- rans_uncompress at Base 1.2.1
- rans_uncompress_O0 at Base 1.2.1
- rans_uncompress_O1 at Base 1.2.1
- refs2id at Base 1.0
- refs_free at Base 1.0
- regidx_destroy at Base 1.2.1
- regidx_init at Base 1.2.1
- regidx_insert at Base 1.2.1
- regidx_nregs at Base 1.2.1
- regidx_overlap at Base 1.2.1
- regidx_parse_bed at Base 1.2.1
- regidx_parse_tab at Base 1.2.1
- regidx_seq_names at Base 1.2.1
- regidx_seq_nregs at Base 1.2.1
- remove_vset at Base 1.4.1
- sam_cap_mapq at Base 1.4.1
- sam_format1 at Base 1.0
- sam_hdr_PG_ID at Base 1.0
- sam_hdr_add at Base 1.0
- sam_hdr_add_PG at Base 1.0
- sam_hdr_add_lines at Base 1.0
- sam_hdr_change_HD at Base 1.7
- sam_hdr_decr_ref at Base 1.0
- sam_hdr_dump at Base 1.0
- sam_hdr_dup at Base 1.0
- sam_hdr_find at Base 1.0
- sam_hdr_find_key at Base 1.0
- sam_hdr_find_line at Base 1.0
- sam_hdr_find_rg at Base 1.0
- sam_hdr_free at Base 1.0
- sam_hdr_incr_ref at Base 1.0
- sam_hdr_length at Base 1.0
- sam_hdr_link_pg at Base 1.0
- sam_hdr_name2ref at Base 1.0
- sam_hdr_new at Base 1.0
- sam_hdr_parse at Base 1.0
- sam_hdr_parse_ at Base 1.0
- sam_hdr_read at Base 1.0
- sam_hdr_rebuild at Base 1.0
- sam_hdr_sort_order at Base 1.3
- sam_hdr_str at Base 1.0
- sam_hdr_update at Base 1.0
- sam_hdr_vadd at Base 1.0
- sam_hdr_write at Base 1.0
- sam_index_build2 at Base 1.3
- sam_index_build3 at Base 1.4.1
- sam_index_build at Base 1.3
- sam_index_load2 at Base 1.3
- sam_index_load at Base 1.0
- sam_itr_queryi at Base 1.0
- sam_itr_querys at Base 1.0
- sam_itr_regions at Base 1.7
- sam_open_mode at Base 1.0
- sam_open_mode_opts at Base 1.3
- sam_parse1 at Base 1.0
- sam_prob_realn at Base 1.4.1
- sam_read1 at Base 1.0
- sam_write1 at Base 1.0
- seq_nt16_int at Base 1.2.1
- seq_nt16_str at Base 1.0
- seq_nt16_table at Base 1.0
- string_alloc at Base 1.0
- string_dup at Base 1.0
- string_ndup at Base 1.0
- string_pool_create at Base 1.0
- string_pool_destroy at Base 1.0
- stringify_argv at Base 1.0
- tbx_conf_bed at Base 1.0
- tbx_conf_gff at Base 1.0
- tbx_conf_psltbl at Base 1.0
- tbx_conf_sam at Base 1.0
- tbx_conf_vcf at Base 1.0
- tbx_destroy at Base 1.0
- tbx_index at Base 1.0
- tbx_index_build2 at Base 1.3
- tbx_index_build3 at Base 1.4.1
- tbx_index_build at Base 1.0
- tbx_index_load2 at Base 1.3
- tbx_index_load at Base 1.0
- tbx_name2id at Base 1.0
- tbx_parse1 at Base 1.0
- tbx_readrec at Base 1.0
- tbx_seqnames at Base 1.0
- tbx_set_meta at Base 1.0
- tokenise_search_path at Base 1.0
- vcf_format at Base 1.0
- vcf_hdr_read at Base 1.0
- vcf_hdr_write at Base 1.0
- vcf_parse at Base 1.0
- vcf_read at Base 1.0
- vcf_write at Base 1.0
- vcf_write_line at Base 1.0
- zlib_mem_inflate at Base 1.0
=====================================
debian/libhts2.install → debian/libhts3.install
=====================================
=====================================
debian/libhts3.symbols
=====================================
@@ -0,0 +1,758 @@
+libhts.so.3 libhts3 #MINVER#
+ 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_construct_seq 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
+ bam_index_build at Base 1.10
+ bam_init1 at Base 1.10
+ 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_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_plp_init_overlaps at Base 1.10
+ bam_plp_insertion at Base 1.10
+ 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_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_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 1.10
+ 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_parse_sample_line at Base 1.10
+ 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_header_debug at Base 1.10
+ bcf_hrec_add_key at Base 1.10
+ bcf_hrec_debug at Base 1.10
+ 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_index at Base 1.10
+ 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_sr_sort_add_active at Base 1.10
+ bcf_sr_sort_destroy at Base 1.10
+ bcf_sr_sort_init at Base 1.10
+ bcf_sr_sort_next at Base 1.10
+ bcf_sr_sort_remove_reader at Base 1.10
+ bcf_sr_sort_reset at Base 1.10
+ bcf_sr_sort_set_active at Base 1.10
+ 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_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
+ bgzf_hfile at Base 1.10
+ bgzf_hopen at Base 1.10
+ bgzf_idx_push at Base 1.10
+ bgzf_index_add_block at Base 1.10
+ bgzf_index_build_init at Base 1.10
+ bgzf_index_destroy at Base 1.10
+ 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 1.10
+ 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
+ cram_beta_decode_char at Base 1.10
+ cram_beta_decode_free at Base 1.10
+ cram_beta_decode_init at Base 1.10
+ cram_beta_decode_int at Base 1.10
+ cram_beta_decode_long at Base 1.10
+ cram_beta_encode_char at Base 1.10
+ cram_beta_encode_free at Base 1.10
+ cram_beta_encode_init at Base 1.10
+ cram_beta_encode_int at Base 1.10
+ cram_beta_encode_long at Base 1.10
+ cram_beta_encode_store at Base 1.10
+ cram_block_append at Base 1.10
+ cram_block_compression_hdr_decoder2encoder at Base 1.10
+ cram_block_compression_hdr_set_rg at Base 1.10
+ 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 1.10
+ cram_block_get_uncomp_size at Base 1.10
+ cram_block_method2str at Base 1.10
+ 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 1.10
+ 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 1.10
+ cram_byte_array_len_decode_free at Base 1.10
+ cram_byte_array_len_decode_init at Base 1.10
+ cram_byte_array_len_encode at Base 1.10
+ cram_byte_array_len_encode_free at Base 1.10
+ cram_byte_array_len_encode_init at Base 1.10
+ cram_byte_array_len_encode_store at Base 1.10
+ cram_byte_array_stop_decode_block at Base 1.10
+ cram_byte_array_stop_decode_free at Base 1.10
+ cram_byte_array_stop_decode_init at Base 1.10
+ cram_byte_array_stop_encode at Base 1.10
+ cram_byte_array_stop_encode_free at Base 1.10
+ cram_byte_array_stop_encode_init at Base 1.10
+ cram_byte_array_stop_encode_store at Base 1.10
+ cram_check_EOF at Base 1.10
+ cram_close at Base 1.10
+ cram_codec_decoder2encoder at Base 1.10
+ cram_codec_to_id at Base 1.10
+ cram_compress_block at Base 1.10
+ 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_content_type2str at Base 1.10
+ cram_copy_slice at Base 1.10
+ cram_decode_TD at Base 1.10
+ cram_decode_compression_header at Base 1.10
+ cram_decode_estimate_sizes at Base 1.10
+ cram_decode_slice at Base 1.10
+ cram_decode_slice_header at Base 1.10
+ cram_decode_slice_mt at Base 1.10
+ cram_decode_slice_thread at Base 1.10
+ cram_decoder_init at Base 1.10
+ cram_dependent_data_series at Base 1.10
+ cram_dopen at Base 1.10
+ cram_drain_rqueue at Base 1.10
+ cram_encode_compression_header at Base 1.10
+ cram_encode_container at Base 1.10
+ cram_encode_slice_header at Base 1.10
+ cram_encoder_init at Base 1.10
+ cram_encoding2str at Base 1.10
+ cram_eof at Base 1.10
+ cram_external_decode_char at Base 1.10
+ cram_external_decode_free at Base 1.10
+ cram_external_decode_init at Base 1.10
+ cram_external_decode_int at Base 1.10
+ cram_external_decode_long at Base 1.10
+ cram_external_encode_char at Base 1.10
+ cram_external_encode_free at Base 1.10
+ cram_external_encode_init at Base 1.10
+ cram_external_encode_int at Base 1.10
+ cram_external_encode_long at Base 1.10
+ cram_external_encode_store at Base 1.10
+ 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_flush_container at Base 1.10
+ cram_flush_container_mt at Base 1.10
+ cram_flush_thread at Base 1.10
+ cram_free_block at Base 1.10
+ cram_free_compression_header at Base 1.10
+ cram_free_container at Base 1.10
+ cram_free_file_def at Base 1.10
+ cram_free_slice at Base 1.10
+ cram_free_slice_header at Base 1.10
+ cram_gamma_decode at Base 1.10
+ cram_gamma_decode_free at Base 1.10
+ cram_gamma_decode_init at Base 1.10
+ cram_get_bam_seq at Base 1.10
+ cram_get_ref at Base 1.10
+ cram_get_refs at Base 1.10
+ cram_get_seq at Base 1.10
+ cram_huffman_decode_char0 at Base 1.10
+ cram_huffman_decode_char at Base 1.10
+ cram_huffman_decode_free at Base 1.10
+ cram_huffman_decode_init at Base 1.10
+ cram_huffman_decode_int0 at Base 1.10
+ cram_huffman_decode_int at Base 1.10
+ cram_huffman_decode_long0 at Base 1.10
+ cram_huffman_decode_long at Base 1.10
+ cram_huffman_decode_null at Base 1.10
+ cram_huffman_encode_char0 at Base 1.10
+ cram_huffman_encode_char at Base 1.10
+ cram_huffman_encode_free at Base 1.10
+ cram_huffman_encode_init at Base 1.10
+ cram_huffman_encode_int0 at Base 1.10
+ cram_huffman_encode_int at Base 1.10
+ cram_huffman_encode_long0 at Base 1.10
+ cram_huffman_encode_long at Base 1.10
+ cram_huffman_encode_store at Base 1.10
+ cram_index_build at Base 1.10
+ cram_index_free at Base 1.10
+ cram_index_last at Base 1.10
+ cram_index_load at Base 1.10
+ cram_index_query at Base 1.10
+ cram_index_slice at Base 1.10
+ cram_load_reference at Base 1.10
+ 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 1.10
+ cram_new_container at Base 1.10
+ cram_new_metrics at Base 1.10
+ cram_new_slice at Base 1.10
+ cram_open at Base 1.10
+ cram_put_bam_seq at Base 1.10
+ cram_read_SAM_hdr at Base 1.10
+ cram_read_block at Base 1.10
+ cram_read_container at Base 1.10
+ cram_read_file_def at Base 1.10
+ cram_read_slice at Base 1.10
+ cram_ref_decr at Base 1.10
+ cram_ref_incr at Base 1.10
+ cram_ref_load at Base 1.10
+ cram_seek at Base 1.10
+ cram_seek_to_refpos at Base 1.10
+ cram_set_header2 at Base 1.10
+ 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_num_blocks at Base 1.10
+ cram_stats_add at Base 1.10
+ cram_stats_create at Base 1.10
+ cram_stats_del at Base 1.10
+ cram_stats_encoding at Base 1.10
+ cram_stats_free at Base 1.10
+ cram_store_container at Base 1.10
+ cram_subexp_decode at Base 1.10
+ cram_subexp_decode_free at Base 1.10
+ cram_subexp_decode_init at Base 1.10
+ cram_transcode_rg at Base 1.10
+ cram_uncompress_block at Base 1.10
+ cram_update_curr_slice at Base 1.10
+ cram_write_SAM_hdr at Base 1.10
+ cram_write_block at Base 1.10
+ cram_write_container at Base 1.10
+ cram_write_file_def at Base 1.10
+ 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_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
+ find_file_url at Base 1.10
+ find_path at Base 1.10
+ 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_init at Base 1.10
+ hfile_init_fixed at Base 1.10
+ 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_gcs at Base 1.10
+ hfile_plugin_init_libcurl at Base 1.10
+ hfile_plugin_init_mem at Base 1.10
+ hfile_plugin_init_net at Base 1.10
+ hfile_plugin_init_s3 at Base 1.10
+ hfile_plugin_init_s3_write at Base 1.10
+ hfile_set_blksize at Base 1.10
+ 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 1.10
+ hopen_net at Base 1.10
+ 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 1.10
+ hts_check_EOF at Base 1.10
+ hts_close at Base 1.10
+ hts_decode_base64 at Base 1.10
+ hts_decode_percent at Base 1.10
+ hts_detect_format at Base 1.10
+ hts_drand48 at Base 1.10
+ hts_erand48 at Base 1.10
+ hts_file_type at Base 1.10
+ 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_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_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_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_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_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_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_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_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_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_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_verbose at Base 1.10
+ hts_version at Base 1.10
+ hwrite2 at Base 1.10
+ int32_get_blk at Base 1.10
+ int32_put_blk at Base 1.10
+ itf8_bytes at Base 1.10
+ itf8_decode at Base 1.10
+ itf8_decode_crc at Base 1.10
+ itf8_encode at Base 1.10
+ itf8_put_blk at Base 1.10
+ 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
+ kftp_connect at Base 1.10
+ kftp_connect_file at Base 1.10
+ kftp_parse_url at Base 1.10
+ kftp_reconnect at Base 1.10
+ kgetline2 at Base 1.10
+ kgetline at Base 1.10
+ khttp_connect_file at Base 1.10
+ khttp_parse_url at Base 1.10
+ 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
+ ltf8_bytes at Base 1.10
+ ltf8_decode at Base 1.10
+ ltf8_decode_crc at Base 1.10
+ ltf8_put_blk at Base 1.10
+ mfascii at Base 1.10
+ mfclose at Base 1.10
+ mfcreate at Base 1.10
+ mfcreate_from at Base 1.10
+ mfdestroy at Base 1.10
+ mfdetach at Base 1.10
+ mfeof at Base 1.10
+ mfflush at Base 1.10
+ mfgetc at Base 1.10
+ mfgets at Base 1.10
+ mfmmap at Base 1.10
+ mfopen at Base 1.10
+ mfread at Base 1.10
+ mfrecreate at Base 1.10
+ mfreopen at Base 1.10
+ mfseek at Base 1.10
+ mfsteal at Base 1.10
+ mftell at Base 1.10
+ mftruncate at Base 1.10
+ mfwrite at Base 1.10
+ mrewind at Base 1.10
+ mstderr at Base 1.10
+ mstdin at Base 1.10
+ mstdout at Base 1.10
+ mungetc at Base 1.10
+ open_path_mfile at Base 1.10
+ pool_alloc at Base 1.10
+ pool_create at Base 1.10
+ pool_destroy at Base 1.10
+ pool_free at Base 1.10
+ probaln_glocal at Base 1.10
+ rans_compress at Base 1.10
+ rans_compress_O0 at Base 1.10
+ rans_compress_O1 at Base 1.10
+ rans_uncompress at Base 1.10
+ rans_uncompress_O0 at Base 1.10
+ rans_uncompress_O1 at Base 1.10
+ refs2id at Base 1.10
+ refs_free at Base 1.10
+ 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
+ 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_hdr_dup_sdict at Base 1.10
+ sam_hdr_fill_hrecs at Base 1.10
+ 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_rebuild at Base 1.10
+ 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_update_target_arrays at Base 1.10
+ sam_hdr_write at Base 1.10
+ sam_hrecs_find_key at Base 1.10
+ sam_hrecs_find_rg at Base 1.10
+ sam_hrecs_find_type_id at Base 1.10
+ sam_hrecs_free at Base 1.10
+ sam_hrecs_group_order at Base 1.10
+ sam_hrecs_new at Base 1.10
+ sam_hrecs_rebuild_text at Base 1.10
+ sam_hrecs_remove_key at Base 1.10
+ sam_hrecs_sort_order at Base 1.10
+ 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_region at Base 1.10
+ sam_prob_realn at Base 1.10
+ sam_read1 at Base 1.10
+ sam_realloc_bam_data at Base 1.10
+ sam_set_thread_pool at Base 1.10
+ sam_set_threads at Base 1.10
+ sam_state_destroy at Base 1.10
+ 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 1.10
+ string_dup at Base 1.10
+ string_ndup at Base 1.10
+ string_pool_create at Base 1.10
+ string_pool_destroy at Base 1.10
+ 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
+ tbx_parse1 at Base 1.10
+ tbx_readrec at Base 1.10
+ tbx_seqnames at Base 1.10
+ tokenise_search_path at Base 1.10
+ vcf_format at Base 1.10
+ vcf_hdr_read at Base 1.10
+ vcf_hdr_write at Base 1.10
+ 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
+ zlib_mem_inflate at Base 1.10
=====================================
debian/rules
=====================================
@@ -27,7 +27,7 @@ endif
autoconf
dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3
-override_dh_auto_build:
+override_dh_auto_build-arch:
dh_auto_build -- \
CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
@@ -36,7 +36,9 @@ override_dh_auto_build:
libdir=/usr/lib/$(DEB_HOST_MULTIARCH)
# re-try later LDLIBS=-lhts \
-override_dh_auto_install:
+override_dh_auto_build-indep:
+
+override_dh_auto_install-arch:
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
rm $(CURDIR)/test/$${binary} ; \
done
@@ -46,12 +48,14 @@ override_dh_auto_install:
$(RM) -r test
mv test_backup test
-override_dh_install:
- dh_install
-ifeq (,$(wildcard ./debian/htslib-test/usr/share/htslib-test/config.mk))
+override_dh_auto_install-indep:
+
+override_dh_auto_test-indep:
+
+override_dh_install-indep:
+ dh_install --indep
sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk
sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk
-endif
override_dh_installchangelogs:
dh_installchangelogs NEWS
View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/bc910b7a1257cc17df26465f9d00eb0d3e92bc80...52415fa2e6ac93725e7c2edfe3d307011a3f8ee2
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/bc910b7a1257cc17df26465f9d00eb0d3e92bc80...52415fa2e6ac93725e7c2edfe3d307011a3f8ee2
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