diff --git a/common/CI/config.yaml b/common/CI/config.yaml index b265fb261620..3ab97aedddec 100644 --- a/common/CI/config.yaml +++ b/common/CI/config.yaml @@ -17,6 +17,7 @@ static_libs: - ghc - glibc - golang + - htslib - ispc - ldc - libboost diff --git a/packages/b/bcftools/abi_libs b/packages/b/bcftools/abi_libs new file mode 100644 index 000000000000..682b6fb286d6 --- /dev/null +++ b/packages/b/bcftools/abi_libs @@ -0,0 +1,42 @@ +GTisec.so +GTsubset.so +ad-bias.so +add-variantkey.so +af-dist.so +allele-length.so +bcftools +check-ploidy.so +check-sparsity.so +color-chrs.so +contrast.so +counts.so +dosage.so +fill-AN-AC.so +fill-from-fasta.so +fill-tags.so +fixploidy.so +fixref.so +frameshifts.so +guess-ploidy.so +gvcfz.so +impute-info.so +indel-stats.so +isecGT.so +mendelian2.so +missing2ref.so +parental-origin.so +prune.so +remove-overlaps.so +scatter.so +setGT.so +smpl-stats.so +split-vep.so +split.so +tag2tag.so +trio-dnm2.so +trio-stats.so +trio-switch-rate.so +variant-distance.so +variantkey-hex.so +vcf2table.so +vrfs.so diff --git a/packages/b/bcftools/abi_symbols b/packages/b/bcftools/abi_symbols new file mode 100644 index 000000000000..4e9a1312f737 --- /dev/null +++ b/packages/b/bcftools/abi_symbols @@ -0,0 +1,1239 @@ +GTisec.so:about +GTisec.so:apply_verbosity +GTisec.so:choose +GTisec.so:compute_bankers +GTisec.so:destroy +GTisec.so:error +GTisec.so:error_errno +GTisec.so:hts_bcf_wmode +GTisec.so:hts_bcf_wmode2 +GTisec.so:init +GTisec.so:init_index +GTisec.so:init_index2 +GTisec.so:parse_overlap_option +GTisec.so:process +GTisec.so:set_wmode +GTisec.so:usage +GTisec.so:version +GTisec.so:write_index_parse +GTsubset.so:about +GTsubset.so:apply_verbosity +GTsubset.so:destroy +GTsubset.so:error +GTsubset.so:error_errno +GTsubset.so:hts_bcf_wmode +GTsubset.so:hts_bcf_wmode2 +GTsubset.so:init +GTsubset.so:init_index +GTsubset.so:init_index2 +GTsubset.so:parse_overlap_option +GTsubset.so:process +GTsubset.so:set_wmode +GTsubset.so:usage +GTsubset.so:version +GTsubset.so:write_index_parse +ad-bias.so:about +ad-bias.so:apply_verbosity +ad-bias.so:args +ad-bias.so:convert_destroy +ad-bias.so:convert_header +ad-bias.so:convert_init +ad-bias.so:convert_is_tag_used +ad-bias.so:convert_line +ad-bias.so:convert_list_used_tags +ad-bias.so:convert_max_unpack +ad-bias.so:convert_set_option +ad-bias.so:destroy +ad-bias.so:error +ad-bias.so:error_errno +ad-bias.so:hts_bcf_wmode +ad-bias.so:hts_bcf_wmode2 +ad-bias.so:init +ad-bias.so:init_index +ad-bias.so:init_index2 +ad-bias.so:parse_overlap_option +ad-bias.so:parse_samples +ad-bias.so:process +ad-bias.so:set_wmode +ad-bias.so:usage +ad-bias.so:version +ad-bias.so:write_index_parse +add-variantkey.so:about +add-variantkey.so:apply_verbosity +add-variantkey.so:destroy +add-variantkey.so:error +add-variantkey.so:error_errno +add-variantkey.so:hts_bcf_wmode +add-variantkey.so:hts_bcf_wmode2 +add-variantkey.so:in_hdr +add-variantkey.so:init +add-variantkey.so:init_index +add-variantkey.so:init_index2 +add-variantkey.so:out_hdr +add-variantkey.so:parse_overlap_option +add-variantkey.so:process +add-variantkey.so:set_wmode +add-variantkey.so:usage +add-variantkey.so:version +add-variantkey.so:write_index_parse +af-dist.so:about +af-dist.so:apply_verbosity +af-dist.so:args +af-dist.so:bin_destroy +af-dist.so:bin_get_idx +af-dist.so:bin_get_size +af-dist.so:bin_get_value +af-dist.so:bin_init +af-dist.so:destroy +af-dist.so:error +af-dist.so:error_errno +af-dist.so:hts_bcf_wmode +af-dist.so:hts_bcf_wmode2 +af-dist.so:init +af-dist.so:init_index +af-dist.so:init_index2 +af-dist.so:parse_overlap_option +af-dist.so:process +af-dist.so:set_wmode +af-dist.so:usage +af-dist.so:version +af-dist.so:write_index_parse +allele-length.so:about +allele-length.so:apply_verbosity +allele-length.so:contain_non_base +allele-length.so:destroy +allele-length.so:error +allele-length.so:error_errno +allele-length.so:hts_bcf_wmode +allele-length.so:hts_bcf_wmode2 +allele-length.so:init +allele-length.so:init_index +allele-length.so:init_index2 +allele-length.so:parse_overlap_option +allele-length.so:process +allele-length.so:set_wmode +allele-length.so:usage +allele-length.so:version +allele-length.so:write_index_parse +bcftools:_IO_stdin_used +bcftools:__bss_start +bcftools:__data_start +bcftools:_abuf_split +bcftools:_edata +bcftools:_end +bcftools:_reglist_build_index +bcftools:_start +bcftools:abuf_destroy +bcftools:abuf_flush +bcftools:abuf_init +bcftools:abuf_push +bcftools:abuf_set +bcftools:annots_reader_close +bcftools:annots_reader_next +bcftools:annots_reader_reset +bcftools:append_cluster +bcftools:append_node +bcftools:apply_verbosity +bcftools:bam_smpl_add_bam +bcftools:bam_smpl_add_readgroups +bcftools:bam_smpl_add_samples +bcftools:bam_smpl_destroy +bcftools:bam_smpl_get_sample_id +bcftools:bam_smpl_get_samples +bcftools:bam_smpl_ignore_readgroups +bcftools:bam_smpl_init +bcftools:bcf_all_phased +bcftools:bcf_call2bcf +bcftools:bcf_call_combine +bcftools:bcf_call_destroy +bcftools:bcf_call_gap_prep +bcftools:bcf_call_glfgen +bcftools:bcf_call_init +bcftools:bcf_callaux_clean +bcftools:bcf_cgp_calc_cons +bcftools:bcf_cgp_l_run +bcftools:bcf_edlib_gap_prep +bcftools:bcf_em1 +bcftools:bcf_hdr_append_version +bcftools:bcf_iaux_destroy +bcftools:bcf_iaux_gap_prep +bcftools:bcf_p1_cal +bcftools:bcf_p1_call_gt +bcftools:bcf_p1_destroy +bcftools:bcf_p1_dump_afs +bcftools:bcf_p1_get_M +bcftools:bcf_p1_indel_prior +bcftools:bcf_p1_init +bcftools:bcf_p1_init_prior +bcftools:bcf_p1_init_subprior +bcftools:bcf_p1_set_n1 +bcftools:bcftools_version +bcftools:bin_destroy +bcftools:bin_get_idx +bcftools:bin_get_size +bcftools:bin_get_value +bcftools:bin_init +bcftools:blk_read +bcftools:bounded_gaussian_calc_df +bcftools:bounded_gaussian_calc_f +bcftools:bounded_gaussian_convert_get +bcftools:bounded_gaussian_convert_set +bcftools:bounded_gaussian_sprint_func +bcftools:buf_flush +bcftools:buf_push +bcftools:calc_Pkij +bcftools:calc_SegBias +bcftools:calc_chisq_bias +bcftools:calc_dev +bcftools:calc_mwu_bias +bcftools:calc_mwu_biasZ +bcftools:calc_mwu_bias_cdf +bcftools:calc_vdb +bcftools:call_init_pl2p +bcftools:can_merge +bcftools:ccall +bcftools:ccall_destroy +bcftools:ccall_init +bcftools:cds_translate +bcftools:clean_buffer +bcftools:clean_files +bcftools:clean_files_and_throw +bcftools:cluster_can_flush_ +bcftools:cmp_bcf_pos +bcftools:cmp_bcf_pos_ref_alt +bcftools:cmp_nodes +bcftools:cnt4 +bcftools:cols_append +bcftools:cols_clear +bcftools:cols_destroy +bcftools:cols_split +bcftools:cons_mark_STR +bcftools:convert_destroy +bcftools:convert_header +bcftools:convert_init +bcftools:convert_is_tag_used +bcftools:convert_line +bcftools:convert_list_used_tags +bcftools:convert_max_unpack +bcftools:convert_set_option +bcftools:copy_string_field +bcftools:count_plugins +bcftools:csq_push +bcftools:csq_stage +bcftools:csq_strings +bcftools:debug_als +bcftools:debug_maux +bcftools:debug_print_buffers +bcftools:debug_state +bcftools:destroy_data +bcftools:dist_destroy +bcftools:dist_get +bcftools:dist_init +bcftools:dist_insert +bcftools:dist_insert_n +bcftools:dist_nbins +bcftools:dist_nvalues +bcftools:do_partial_merge +bcftools:edlibAlign +bcftools:edlibDefaultAlignConfig +bcftools:edlibFreeAlignResult +bcftools:edlibNewAlignConfig +bcftools:edlib_glocal +bcftools:error +bcftools:error_errno +bcftools:est_indelreg +bcftools:estimate_AF_from_GT +bcftools:estimate_AF_from_PL +bcftools:exp_calc_df +bcftools:exp_calc_f +bcftools:exp_convert_get +bcftools:exp_sprint_func +bcftools:expand_path +bcftools:extsort_alloc +bcftools:extsort_destroy +bcftools:extsort_init +bcftools:extsort_push +bcftools:extsort_set +bcftools:extsort_shift +bcftools:extsort_sort +bcftools:filter_destroy +bcftools:filter_ext_types +bcftools:filter_get_doubles +bcftools:filter_init +bcftools:filter_list_undef_tags +bcftools:filter_list_used_tags +bcftools:filter_max_unpack +bcftools:filter_parse +bcftools:filter_set_samples +bcftools:filter_status +bcftools:filter_test +bcftools:filter_test_ext +bcftools:find_STR +bcftools:find_STR64 +bcftools:free_payload +bcftools:gaussian_calc_df +bcftools:gaussian_calc_f +bcftools:gaussian_convert_get +bcftools:gaussian_sprint_func +bcftools:gencode +bcftools:gencode_tables +bcftools:get_GT +bcftools:get_PL +bcftools:get_pos +bcftools:gf_type2gff_string +bcftools:gff_destroy +bcftools:gff_get +bcftools:gff_has_seq +bcftools:gff_id2string +bcftools:gff_init +bcftools:gff_iseq +bcftools:gff_nseq +bcftools:gff_parse +bcftools:gff_set +bcftools:gvcf_destroy +bcftools:gvcf_flush +bcftools:gvcf_init +bcftools:gvcf_set_alleles +bcftools:gvcf_stage +bcftools:gvcf_update_header +bcftools:gvcf_write +bcftools:gvcf_write_block +bcftools:hap_add_csq +bcftools:hap_destroy +bcftools:hap_finalize +bcftools:hap_flush +bcftools:hap_init +bcftools:hclust_create_dot +bcftools:hclust_create_list +bcftools:hclust_destroy +bcftools:hclust_destroy_list +bcftools:hclust_explain +bcftools:hclust_init +bcftools:hclust_set_threshold +bcftools:hdr_add_localized_tags +bcftools:hmm_destroy +bcftools:hmm_get_fwd_bwd_prob +bcftools:hmm_get_nstates +bcftools:hmm_get_tprob +bcftools:hmm_get_viterbi_path +bcftools:hmm_init +bcftools:hmm_init_states +bcftools:hmm_reset +bcftools:hmm_restore +bcftools:hmm_run_baum_welch +bcftools:hmm_run_fwd_bwd +bcftools:hmm_run_viterbi +bcftools:hmm_set_tprob +bcftools:hmm_set_tprob_func +bcftools:hmm_snapshot +bcftools:hts_bcf_wmode +bcftools:hts_bcf_wmode2 +bcftools:indel_ctx_destroy +bcftools:indel_ctx_init +bcftools:indel_ctx_type +bcftools:init_allele_trimming_maps +bcftools:init_chr_names +bcftools:init_data +bcftools:init_index +bcftools:init_index2 +bcftools:init_local_alleles +bcftools:init_ploidy +bcftools:init_sample2sex +bcftools:init_tmp_prefix +bcftools:isec_vcf +bcftools:khash_str2int_clear_free +bcftools:kmin_brent +bcftools:kmin_hj +bcftools:kprint_aa_prediction +bcftools:kput_vcsq +bcftools:ks_combsort_uint32_t +bcftools:ks_heapadjust_uint32_t +bcftools:ks_heapmake_uint32_t +bcftools:ks_heapsort_uint32_t +bcftools:ks_introsort_uint32_t +bcftools:ks_ksmall_uint32_t +bcftools:ks_mergesort_uint32_t +bcftools:ks_shuffle_uint32_t +bcftools:main +bcftools:main_consensus +bcftools:main_csq +bcftools:main_mpileup +bcftools:main_plugin +bcftools:main_polysomy +bcftools:main_reheader +bcftools:main_sort +bcftools:main_tabix +bcftools:main_vcfannotate +bcftools:main_vcfcall +bcftools:main_vcfcnv +bcftools:main_vcfconcat +bcftools:main_vcfconvert +bcftools:main_vcffilter +bcftools:main_vcfgtcheck +bcftools:main_vcfhead +bcftools:main_vcfindex +bcftools:main_vcfisec +bcftools:main_vcfmerge +bcftools:main_vcfnorm +bcftools:main_vcfquery +bcftools:main_vcfroh +bcftools:main_vcfsom +bcftools:main_vcfstats +bcftools:main_vcfview +bcftools:mann_whitney_1947 +bcftools:mann_whitney_1947_cdf +bcftools:maux_debug +bcftools:maux_destroy +bcftools:maux_expand1 +bcftools:maux_init +bcftools:maux_reset +bcftools:mcall +bcftools:mcall_destroy +bcftools:mcall_init +bcftools:mcall_trim_and_update_numberR +bcftools:merge_GT +bcftools:merge_alleles +bcftools:merge_blocks +bcftools:merge_chrom2qual +bcftools:merge_filter +bcftools:merge_format +bcftools:merge_format_field +bcftools:merge_format_string +bcftools:merge_headers +bcftools:merge_info +bcftools:merge_line +bcftools:merge_localized_numberAR_format_field +bcftools:merge_localized_numberG_format_field +bcftools:merge_to_output +bcftools:merge_vcf +bcftools:mkdir_p +bcftools:mpileup_alloc +bcftools:mpileup_destroy +bcftools:mpileup_get +bcftools:mpileup_init +bcftools:mpileup_next +bcftools:mpileup_set +bcftools:msprintf +bcftools:next_line +bcftools:normalize_alleles +bcftools:nt4 +bcftools:open_file +bcftools:open_tmp_file +bcftools:parse_format_flag +bcftools:parse_mem_string +bcftools:parse_novel_rate +bcftools:parse_overlap_option +bcftools:parse_tag_list +bcftools:parse_with_payload +bcftools:peakfit_add_bounded_gaussian +bcftools:peakfit_add_exp +bcftools:peakfit_add_gaussian +bcftools:peakfit_calc_df +bcftools:peakfit_calc_f +bcftools:peakfit_calc_fdf +bcftools:peakfit_destroy +bcftools:peakfit_evaluate +bcftools:peakfit_get_params +bcftools:peakfit_init +bcftools:peakfit_reset +bcftools:peakfit_run +bcftools:peakfit_set_mc +bcftools:peakfit_set_params +bcftools:peakfit_sprint_func +bcftools:peakfit_verbose +bcftools:ploidy_add_sex +bcftools:ploidy_destroy +bcftools:ploidy_format +bcftools:ploidy_id2sex +bcftools:ploidy_init +bcftools:ploidy_init_string +bcftools:ploidy_max +bcftools:ploidy_min +bcftools:ploidy_nsex +bcftools:ploidy_parse +bcftools:ploidy_query +bcftools:ploidy_regions +bcftools:ploidy_sex2id +bcftools:print_vcf_gz_header +bcftools:process_line +bcftools:qcall +bcftools:qcall_destroy +bcftools:qcall_init +bcftools:rcns_destroy +bcftools:rcns_get_consensus +bcftools:rcns_init +bcftools:rcns_reset +bcftools:rcns_set_reads +bcftools:read_AF +bcftools:read_file_list +bcftools:regidx_destroy +bcftools:regidx_init +bcftools:regidx_init_string +bcftools:regidx_insert +bcftools:regidx_insert_list +bcftools:regidx_nregs +bcftools:regidx_overlap +bcftools:regidx_parse_bed +bcftools:regidx_parse_reg +bcftools:regidx_parse_tab +bcftools:regidx_parse_vcf +bcftools:regidx_push +bcftools:regidx_seq_names +bcftools:regidx_seq_nregs +bcftools:regidx_set +bcftools:regitr_copy +bcftools:regitr_destroy +bcftools:regitr_init +bcftools:regitr_loop +bcftools:regitr_overlap +bcftools:regitr_reset +bcftools:remove_filter +bcftools:remove_format +bcftools:remove_format_tag +bcftools:remove_id +bcftools:remove_info +bcftools:remove_info_tag +bcftools:remove_node +bcftools:remove_qual +bcftools:set_allele_type +bcftools:set_pdg +bcftools:set_tprob_genmap +bcftools:set_tprob_rrate +bcftools:set_wmode +bcftools:shifted_del_synonymous +bcftools:smalloc +bcftools:smpl_ilist_destroy +bcftools:smpl_ilist_init +bcftools:smpl_ilist_map +bcftools:sort_blocks +bcftools:splice_init +bcftools:stage_line +bcftools:subset_vcf +bcftools:test16 +bcftools:test_cds +bcftools:test_cds_local +bcftools:test_prefix +bcftools:test_splice +bcftools:test_symbolic_alt +bcftools:test_tscript +bcftools:test_utr +bcftools:tpos2qpos +bcftools:tscript_init_ref +bcftools:tscript_splice_ref +bcftools:tsv_destroy +bcftools:tsv_init +bcftools:tsv_parse +bcftools:tsv_register +bcftools:tsv_setter_chrom +bcftools:tsv_setter_id +bcftools:tsv_setter_pos +bcftools:tsv_setter_ref_alt +bcftools:update_AN_AC +bcftools:update_local_alleles +bcftools:vbuf_flush +bcftools:vbuf_push +bcftools:vcf_index_stats +bcftools:vcfbuf_destroy +bcftools:vcfbuf_flush +bcftools:vcfbuf_get +bcftools:vcfbuf_init +bcftools:vcfbuf_ld +bcftools:vcfbuf_nsites +bcftools:vcfbuf_peek +bcftools:vcfbuf_push +bcftools:vcfbuf_remove +bcftools:vcfbuf_set +bcftools:vcmp_destroy +bcftools:vcmp_find_allele +bcftools:vcmp_init +bcftools:vcmp_map_ARvalues +bcftools:vcmp_map_dipGvalues +bcftools:vcmp_set_ref +bcftools:version +bcftools:write_index_parse +check-ploidy.so:about +check-ploidy.so:apply_verbosity +check-ploidy.so:destroy +check-ploidy.so:error +check-ploidy.so:error_errno +check-ploidy.so:hts_bcf_wmode +check-ploidy.so:hts_bcf_wmode2 +check-ploidy.so:init +check-ploidy.so:init_index +check-ploidy.so:init_index2 +check-ploidy.so:parse_overlap_option +check-ploidy.so:process +check-ploidy.so:set_wmode +check-ploidy.so:usage +check-ploidy.so:version +check-ploidy.so:write_index_parse +check-sparsity.so:about +check-sparsity.so:apply_verbosity +check-sparsity.so:error +check-sparsity.so:error_errno +check-sparsity.so:hts_bcf_wmode +check-sparsity.so:hts_bcf_wmode2 +check-sparsity.so:init_index +check-sparsity.so:init_index2 +check-sparsity.so:parse_overlap_option +check-sparsity.so:run +check-sparsity.so:set_wmode +check-sparsity.so:version +check-sparsity.so:write_index_parse +color-chrs.so:about +color-chrs.so:apply_verbosity +color-chrs.so:destroy +color-chrs.so:error +color-chrs.so:error_errno +color-chrs.so:flush_viterbi +color-chrs.so:hmm_destroy +color-chrs.so:hmm_get_fwd_bwd_prob +color-chrs.so:hmm_get_nstates +color-chrs.so:hmm_get_tprob +color-chrs.so:hmm_get_viterbi_path +color-chrs.so:hmm_init +color-chrs.so:hmm_init_states +color-chrs.so:hmm_reset +color-chrs.so:hmm_restore +color-chrs.so:hmm_run_baum_welch +color-chrs.so:hmm_run_fwd_bwd +color-chrs.so:hmm_run_viterbi +color-chrs.so:hmm_set_tprob +color-chrs.so:hmm_set_tprob_func +color-chrs.so:hmm_snapshot +color-chrs.so:hts_bcf_wmode +color-chrs.so:hts_bcf_wmode2 +color-chrs.so:init +color-chrs.so:init_index +color-chrs.so:init_index2 +color-chrs.so:parse_overlap_option +color-chrs.so:process +color-chrs.so:set_wmode +color-chrs.so:usage +color-chrs.so:version +color-chrs.so:write_index_parse +contrast.so:about +contrast.so:apply_verbosity +contrast.so:args +contrast.so:error +contrast.so:error_errno +contrast.so:hts_bcf_wmode +contrast.so:hts_bcf_wmode2 +contrast.so:init_index +contrast.so:init_index2 +contrast.so:parse_overlap_option +contrast.so:run +contrast.so:set_wmode +contrast.so:version +contrast.so:write_index_parse +counts.so:about +counts.so:apply_verbosity +counts.so:destroy +counts.so:error +counts.so:error_errno +counts.so:hts_bcf_wmode +counts.so:hts_bcf_wmode2 +counts.so:init +counts.so:init_index +counts.so:init_index2 +counts.so:nindels +counts.so:nmnps +counts.so:nothers +counts.so:nsamples +counts.so:nsites +counts.so:nsnps +counts.so:parse_overlap_option +counts.so:process +counts.so:set_wmode +counts.so:version +counts.so:write_index_parse +dosage.so:about +dosage.so:apply_verbosity +dosage.so:buf +dosage.so:calc_dosage_GL +dosage.so:calc_dosage_GT +dosage.so:calc_dosage_PL +dosage.so:destroy +dosage.so:dsg +dosage.so:error +dosage.so:error_errno +dosage.so:gl_type +dosage.so:handlers +dosage.so:hts_bcf_wmode +dosage.so:hts_bcf_wmode2 +dosage.so:in_hdr +dosage.so:init +dosage.so:init_index +dosage.so:init_index2 +dosage.so:mdsg +dosage.so:mvals +dosage.so:nbuf +dosage.so:nhandlers +dosage.so:ntags +dosage.so:parse_overlap_option +dosage.so:pl_type +dosage.so:process +dosage.so:set_wmode +dosage.so:split_list +dosage.so:tags +dosage.so:usage +dosage.so:vals +dosage.so:version +dosage.so:write_index_parse +fill-AN-AC.so:about +fill-AN-AC.so:apply_verbosity +fill-AN-AC.so:arr +fill-AN-AC.so:destroy +fill-AN-AC.so:error +fill-AN-AC.so:error_errno +fill-AN-AC.so:hts_bcf_wmode +fill-AN-AC.so:hts_bcf_wmode2 +fill-AN-AC.so:in_hdr +fill-AN-AC.so:init +fill-AN-AC.so:init_index +fill-AN-AC.so:init_index2 +fill-AN-AC.so:marr +fill-AN-AC.so:out_hdr +fill-AN-AC.so:parse_overlap_option +fill-AN-AC.so:process +fill-AN-AC.so:set_wmode +fill-AN-AC.so:version +fill-AN-AC.so:write_index_parse +fill-from-fasta.so:about +fill-from-fasta.so:anno +fill-from-fasta.so:apply_verbosity +fill-from-fasta.so:column +fill-from-fasta.so:destroy +fill-from-fasta.so:error +fill-from-fasta.so:error_errno +fill-from-fasta.so:expand_path +fill-from-fasta.so:faidx +fill-from-fasta.so:filter +fill-from-fasta.so:filter_destroy +fill-from-fasta.so:filter_ext_types +fill-from-fasta.so:filter_get_doubles +fill-from-fasta.so:filter_init +fill-from-fasta.so:filter_list_undef_tags +fill-from-fasta.so:filter_list_used_tags +fill-from-fasta.so:filter_logic +fill-from-fasta.so:filter_max_unpack +fill-from-fasta.so:filter_parse +fill-from-fasta.so:filter_set_samples +fill-from-fasta.so:filter_status +fill-from-fasta.so:filter_str +fill-from-fasta.so:filter_test +fill-from-fasta.so:filter_test_ext +fill-from-fasta.so:hts_bcf_wmode +fill-from-fasta.so:hts_bcf_wmode2 +fill-from-fasta.so:in_hdr +fill-from-fasta.so:init +fill-from-fasta.so:init_index +fill-from-fasta.so:init_index2 +fill-from-fasta.so:out_hdr +fill-from-fasta.so:parse_overlap_option +fill-from-fasta.so:parse_tag_list +fill-from-fasta.so:process +fill-from-fasta.so:replace_nonACGTN +fill-from-fasta.so:set_wmode +fill-from-fasta.so:usage +fill-from-fasta.so:version +fill-from-fasta.so:write_index_parse +fill-tags.so:about +fill-tags.so:apply_verbosity +fill-tags.so:calc_hwe +fill-tags.so:destroy +fill-tags.so:error +fill-tags.so:error_errno +fill-tags.so:ftf_destroy +fill-tags.so:ftf_filter_expr +fill-tags.so:hts_bcf_wmode +fill-tags.so:hts_bcf_wmode2 +fill-tags.so:init +fill-tags.so:init_index +fill-tags.so:init_index2 +fill-tags.so:init_pops +fill-tags.so:list_tags +fill-tags.so:parse_func +fill-tags.so:parse_func_pop +fill-tags.so:parse_overlap_option +fill-tags.so:parse_samples +fill-tags.so:parse_tags +fill-tags.so:process +fill-tags.so:set_wmode +fill-tags.so:usage +fill-tags.so:version +fill-tags.so:write_index_parse +fixploidy.so:_reglist_build_index +fixploidy.so:about +fixploidy.so:apply_verbosity +fixploidy.so:destroy +fixploidy.so:error +fixploidy.so:error_errno +fixploidy.so:hts_bcf_wmode +fixploidy.so:hts_bcf_wmode2 +fixploidy.so:init +fixploidy.so:init_index +fixploidy.so:init_index2 +fixploidy.so:parse_overlap_option +fixploidy.so:ploidy_add_sex +fixploidy.so:ploidy_destroy +fixploidy.so:ploidy_format +fixploidy.so:ploidy_id2sex +fixploidy.so:ploidy_init +fixploidy.so:ploidy_init_string +fixploidy.so:ploidy_max +fixploidy.so:ploidy_min +fixploidy.so:ploidy_nsex +fixploidy.so:ploidy_parse +fixploidy.so:ploidy_query +fixploidy.so:ploidy_regions +fixploidy.so:ploidy_sex2id +fixploidy.so:process +fixploidy.so:regidx_destroy +fixploidy.so:regidx_init +fixploidy.so:regidx_init_string +fixploidy.so:regidx_insert +fixploidy.so:regidx_insert_list +fixploidy.so:regidx_nregs +fixploidy.so:regidx_overlap +fixploidy.so:regidx_parse_bed +fixploidy.so:regidx_parse_reg +fixploidy.so:regidx_parse_tab +fixploidy.so:regidx_parse_vcf +fixploidy.so:regidx_push +fixploidy.so:regidx_seq_names +fixploidy.so:regidx_seq_nregs +fixploidy.so:regidx_set +fixploidy.so:regitr_copy +fixploidy.so:regitr_destroy +fixploidy.so:regitr_init +fixploidy.so:regitr_loop +fixploidy.so:regitr_overlap +fixploidy.so:regitr_reset +fixploidy.so:set_samples +fixploidy.so:set_wmode +fixploidy.so:usage +fixploidy.so:version +fixploidy.so:write_index_parse +fixref.so:about +fixref.so:apply_verbosity +fixref.so:args +fixref.so:bot_mask +fixref.so:destroy +fixref.so:error +fixref.so:error_errno +fixref.so:hts_bcf_wmode +fixref.so:hts_bcf_wmode2 +fixref.so:info_annots +fixref.so:init +fixref.so:init_index +fixref.so:init_index2 +fixref.so:parse_overlap_option +fixref.so:process +fixref.so:set_wmode +fixref.so:top_mask +fixref.so:usage +fixref.so:version +fixref.so:write_index_parse +frameshifts.so:about +frameshifts.so:apply_verbosity +frameshifts.so:destroy +frameshifts.so:error +frameshifts.so:error_errno +frameshifts.so:exons +frameshifts.so:frm +frameshifts.so:hts_bcf_wmode +frameshifts.so:hts_bcf_wmode2 +frameshifts.so:in_hdr +frameshifts.so:init +frameshifts.so:init_index +frameshifts.so:init_index2 +frameshifts.so:nfrm +frameshifts.so:out_hdr +frameshifts.so:parse_overlap_option +frameshifts.so:process +frameshifts.so:set_wmode +frameshifts.so:usage +frameshifts.so:version +frameshifts.so:write_index_parse +guess-ploidy.so:about +guess-ploidy.so:apply_verbosity +guess-ploidy.so:error +guess-ploidy.so:error_errno +guess-ploidy.so:hts_bcf_wmode +guess-ploidy.so:hts_bcf_wmode2 +guess-ploidy.so:init_index +guess-ploidy.so:init_index2 +guess-ploidy.so:parse_overlap_option +guess-ploidy.so:process_region_guess +guess-ploidy.so:run +guess-ploidy.so:set_wmode +guess-ploidy.so:version +guess-ploidy.so:write_index_parse +gvcfz.so:about +gvcfz.so:apply_verbosity +gvcfz.so:error +gvcfz.so:error_errno +gvcfz.so:hts_bcf_wmode +gvcfz.so:hts_bcf_wmode2 +gvcfz.so:init_index +gvcfz.so:init_index2 +gvcfz.so:parse_overlap_option +gvcfz.so:run +gvcfz.so:set_wmode +gvcfz.so:version +gvcfz.so:write_index_parse +impute-info.so:about +impute-info.so:apply_verbosity +impute-info.so:buf +impute-info.so:destroy +impute-info.so:error +impute-info.so:error_errno +impute-info.so:gp_type +impute-info.so:hts_bcf_wmode +impute-info.so:hts_bcf_wmode2 +impute-info.so:in_hdr +impute-info.so:init +impute-info.so:init_index +impute-info.so:init_index2 +impute-info.so:nbuf +impute-info.so:nrec +impute-info.so:nskip_dip +impute-info.so:nskip_gp +impute-info.so:out_hdr +impute-info.so:parse_overlap_option +impute-info.so:process +impute-info.so:set_wmode +impute-info.so:usage +impute-info.so:version +impute-info.so:write_index_parse +indel-stats.so:about +indel-stats.so:apply_verbosity +indel-stats.so:args +indel-stats.so:error +indel-stats.so:error_errno +indel-stats.so:hts_bcf_wmode +indel-stats.so:hts_bcf_wmode2 +indel-stats.so:init_index +indel-stats.so:init_index2 +indel-stats.so:parse_overlap_option +indel-stats.so:run +indel-stats.so:set_wmode +indel-stats.so:version +indel-stats.so:write_index_parse +isecGT.so:about +isecGT.so:apply_verbosity +isecGT.so:error +isecGT.so:error_errno +isecGT.so:hts_bcf_wmode +isecGT.so:hts_bcf_wmode2 +isecGT.so:init_index +isecGT.so:init_index2 +isecGT.so:parse_overlap_option +isecGT.so:run +isecGT.so:set_wmode +isecGT.so:smpl_ilist_destroy +isecGT.so:smpl_ilist_init +isecGT.so:smpl_ilist_map +isecGT.so:version +isecGT.so:write_index_parse +mendelian2.so:about +mendelian2.so:apply_verbosity +mendelian2.so:error +mendelian2.so:error_errno +mendelian2.so:hts_bcf_wmode +mendelian2.so:hts_bcf_wmode2 +mendelian2.so:init_index +mendelian2.so:init_index2 +mendelian2.so:init_rules +mendelian2.so:parse_overlap_option +mendelian2.so:run +mendelian2.so:set_wmode +mendelian2.so:version +mendelian2.so:write_index_parse +missing2ref.so:about +missing2ref.so:apply_verbosity +missing2ref.so:arr +missing2ref.so:destroy +missing2ref.so:error +missing2ref.so:error_errno +missing2ref.so:gts +missing2ref.so:hts_bcf_wmode +missing2ref.so:hts_bcf_wmode2 +missing2ref.so:in_hdr +missing2ref.so:init +missing2ref.so:init_index +missing2ref.so:init_index2 +missing2ref.so:marr +missing2ref.so:mgts +missing2ref.so:nchanged +missing2ref.so:new_gt +missing2ref.so:out_hdr +missing2ref.so:parse_overlap_option +missing2ref.so:process +missing2ref.so:set_wmode +missing2ref.so:usage +missing2ref.so:use_major +missing2ref.so:version +missing2ref.so:write_index_parse +parental-origin.so:about +parental-origin.so:apply_verbosity +parental-origin.so:args +parental-origin.so:error +parental-origin.so:error_errno +parental-origin.so:hts_bcf_wmode +parental-origin.so:hts_bcf_wmode2 +parental-origin.so:init_index +parental-origin.so:init_index2 +parental-origin.so:parse_overlap_option +parental-origin.so:run +parental-origin.so:set_wmode +parental-origin.so:version +parental-origin.so:write_index_parse +prune.so:about +prune.so:apply_verbosity +prune.so:error +prune.so:error_errno +prune.so:hts_bcf_wmode +prune.so:hts_bcf_wmode2 +prune.so:init_index +prune.so:init_index2 +prune.so:parse_overlap_option +prune.so:run +prune.so:set_wmode +prune.so:version +prune.so:write_index_parse +remove-overlaps.so:about +remove-overlaps.so:apply_verbosity +remove-overlaps.so:error +remove-overlaps.so:error_errno +remove-overlaps.so:hts_bcf_wmode +remove-overlaps.so:hts_bcf_wmode2 +remove-overlaps.so:init_index +remove-overlaps.so:init_index2 +remove-overlaps.so:parse_overlap_option +remove-overlaps.so:run +remove-overlaps.so:set_wmode +remove-overlaps.so:version +remove-overlaps.so:write_index_parse +scatter.so:about +scatter.so:apply_verbosity +scatter.so:error +scatter.so:error_errno +scatter.so:hts_bcf_wmode +scatter.so:hts_bcf_wmode2 +scatter.so:init_index +scatter.so:init_index2 +scatter.so:parse_overlap_option +scatter.so:regidx_parse_reg_name +scatter.so:run +scatter.so:set_wmode +scatter.so:version +scatter.so:write_index_parse +setGT.so:about +setGT.so:apply_verbosity +setGT.so:args +setGT.so:destroy +setGT.so:error +setGT.so:error_errno +setGT.so:hts_bcf_wmode +setGT.so:hts_bcf_wmode2 +setGT.so:init +setGT.so:init_index +setGT.so:init_index2 +setGT.so:parse_binom_expr +setGT.so:parse_overlap_option +setGT.so:process +setGT.so:set_wmode +setGT.so:usage +setGT.so:version +setGT.so:write_index_parse +smpl-stats.so:about +smpl-stats.so:apply_verbosity +smpl-stats.so:args +smpl-stats.so:error +smpl-stats.so:error_errno +smpl-stats.so:hts_bcf_wmode +smpl-stats.so:hts_bcf_wmode2 +smpl-stats.so:init_index +smpl-stats.so:init_index2 +smpl-stats.so:parse_overlap_option +smpl-stats.so:run +smpl-stats.so:set_wmode +smpl-stats.so:version +smpl-stats.so:write_index_parse +split-vep.so:about +split-vep.so:apply_verbosity +split-vep.so:args +split-vep.so:csq_rewrite_worst +split-vep.so:error +split-vep.so:error_errno +split-vep.so:hts_bcf_wmode +split-vep.so:hts_bcf_wmode2 +split-vep.so:init_index +split-vep.so:init_index2 +split-vep.so:init_select_tr_expr +split-vep.so:parse_overlap_option +split-vep.so:run +split-vep.so:set_wmode +split-vep.so:strdup_annot_prefix +split-vep.so:version +split-vep.so:write_index_parse +split.so:about +split.so:apply_verbosity +split.so:error +split.so:error_errno +split.so:hts_bcf_wmode +split.so:hts_bcf_wmode2 +split.so:init_index +split.so:init_index2 +split.so:init_subsets +split.so:parse_overlap_option +split.so:run +split.so:set_wmode +split.so:version +split.so:write_index_parse +tag2tag.so:about +tag2tag.so:apply_verbosity +tag2tag.so:destroy +tag2tag.so:error +tag2tag.so:error_errno +tag2tag.so:hts_bcf_wmode +tag2tag.so:hts_bcf_wmode2 +tag2tag.so:init +tag2tag.so:init_index +tag2tag.so:init_index2 +tag2tag.so:parse_defaults +tag2tag.so:parse_overlap_option +tag2tag.so:process +tag2tag.so:process_LXX +tag2tag.so:process_XX +tag2tag.so:set_wmode +tag2tag.so:tags +tag2tag.so:tags_LXX +tag2tag.so:tags_XX +tag2tag.so:usage +tag2tag.so:version +tag2tag.so:write_index_parse +trio-dnm2.so:about +trio-dnm2.so:apply_verbosity +trio-dnm2.so:error +trio-dnm2.so:error_errno +trio-dnm2.so:hts_bcf_wmode +trio-dnm2.so:hts_bcf_wmode2 +trio-dnm2.so:init_index +trio-dnm2.so:init_index2 +trio-dnm2.so:parse_overlap_option +trio-dnm2.so:run +trio-dnm2.so:set_wmode +trio-dnm2.so:version +trio-dnm2.so:write_index_parse +trio-stats.so:about +trio-stats.so:apply_verbosity +trio-stats.so:args +trio-stats.so:error +trio-stats.so:error_errno +trio-stats.so:hts_bcf_wmode +trio-stats.so:hts_bcf_wmode2 +trio-stats.so:init_index +trio-stats.so:init_index2 +trio-stats.so:parse_overlap_option +trio-stats.so:run +trio-stats.so:set_wmode +trio-stats.so:version +trio-stats.so:write_index_parse +trio-switch-rate.so:about +trio-switch-rate.so:apply_verbosity +trio-switch-rate.so:args +trio-switch-rate.so:destroy +trio-switch-rate.so:error +trio-switch-rate.so:error_errno +trio-switch-rate.so:hts_bcf_wmode +trio-switch-rate.so:hts_bcf_wmode2 +trio-switch-rate.so:init +trio-switch-rate.so:init_index +trio-switch-rate.so:init_index2 +trio-switch-rate.so:parse_genotype +trio-switch-rate.so:parse_overlap_option +trio-switch-rate.so:parse_ped +trio-switch-rate.so:process +trio-switch-rate.so:set_wmode +trio-switch-rate.so:usage +trio-switch-rate.so:version +trio-switch-rate.so:write_index_parse +variant-distance.so:about +variant-distance.so:apply_verbosity +variant-distance.so:error +variant-distance.so:error_errno +variant-distance.so:hts_bcf_wmode +variant-distance.so:hts_bcf_wmode2 +variant-distance.so:init_index +variant-distance.so:init_index2 +variant-distance.so:parse_overlap_option +variant-distance.so:run +variant-distance.so:set_wmode +variant-distance.so:version +variant-distance.so:write_index_parse +variantkey-hex.so:FILE_NRVK +variantkey-hex.so:FILE_RSVK +variantkey-hex.so:FILE_VKRS +variantkey-hex.so:about +variantkey-hex.so:apply_verbosity +variantkey-hex.so:destroy +variantkey-hex.so:error +variantkey-hex.so:error_errno +variantkey-hex.so:fp_nrvk +variantkey-hex.so:fp_rsvk +variantkey-hex.so:fp_vkrs +variantkey-hex.so:hts_bcf_wmode +variantkey-hex.so:hts_bcf_wmode2 +variantkey-hex.so:in_hdr +variantkey-hex.so:init +variantkey-hex.so:init_index +variantkey-hex.so:init_index2 +variantkey-hex.so:parse_overlap_option +variantkey-hex.so:process +variantkey-hex.so:set_wmode +variantkey-hex.so:usage +variantkey-hex.so:version +variantkey-hex.so:write_index_parse +vcf2table.so:COLOR_BLACK +vcf2table.so:COLOR_BLUE +vcf2table.so:COLOR_CYAN +vcf2table.so:COLOR_GREEN +vcf2table.so:COLOR_MAGENTA +vcf2table.so:COLOR_RED +vcf2table.so:COLOR_RESET +vcf2table.so:COLOR_WHITE +vcf2table.so:COLOR_YELLOW +vcf2table.so:StringListAt +vcf2table.so:StringListFree +vcf2table.so:about +vcf2table.so:apply_verbosity +vcf2table.so:destroy +vcf2table.so:error +vcf2table.so:error_errno +vcf2table.so:hts_bcf_wmode +vcf2table.so:hts_bcf_wmode2 +vcf2table.so:init +vcf2table.so:init_index +vcf2table.so:init_index2 +vcf2table.so:parse_overlap_option +vcf2table.so:process +vcf2table.so:set_wmode +vcf2table.so:version +vcf2table.so:write_index_parse +vrfs.so:about +vrfs.so:apply_verbosity +vrfs.so:error +vrfs.so:error_errno +vrfs.so:hts_bcf_wmode +vrfs.so:hts_bcf_wmode2 +vrfs.so:init_index +vrfs.so:init_index2 +vrfs.so:parse_overlap_option +vrfs.so:run +vrfs.so:set_wmode +vrfs.so:var2 +vrfs.so:version +vrfs.so:write_index_parse diff --git a/packages/b/bcftools/abi_used_libs b/packages/b/bcftools/abi_used_libs new file mode 100644 index 000000000000..aa6ef31b0ca0 --- /dev/null +++ b/packages/b/bcftools/abi_used_libs @@ -0,0 +1,5 @@ +UNKNOWN +libc.so.6 +libgsl.so.25 +libhts.so.3 +libm.so.6 diff --git a/packages/b/bcftools/abi_used_symbols b/packages/b/bcftools/abi_used_symbols new file mode 100644 index 000000000000..8949838c8383 --- /dev/null +++ b/packages/b/bcftools/abi_used_symbols @@ -0,0 +1,336 @@ +UNKNOWN:ceil +UNKNOWN:log10 +UNKNOWN:lroundf +UNKNOWN:round +UNKNOWN:sqrt +libc.so.6:__assert_fail +libc.so.6:__ctype_b_loc +libc.so.6:__ctype_tolower_loc +libc.so.6:__ctype_toupper_loc +libc.so.6:__errno_location +libc.so.6:__fprintf_chk +libc.so.6:__isoc23_sscanf +libc.so.6:__isoc23_strtol +libc.so.6:__isoc23_strtoul +libc.so.6:__isoc23_strtoull +libc.so.6:__libc_start_main +libc.so.6:__memset_chk +libc.so.6:__printf_chk +libc.so.6:__snprintf_chk +libc.so.6:__sprintf_chk +libc.so.6:__stack_chk_fail +libc.so.6:__stpcpy_chk +libc.so.6:__strcpy_chk +libc.so.6:__vfprintf_chk +libc.so.6:__vsnprintf_chk +libc.so.6:abort +libc.so.6:calloc +libc.so.6:chmod +libc.so.6:close +libc.so.6:closedir +libc.so.6:ctime +libc.so.6:dlclose +libc.so.6:dlerror +libc.so.6:dlopen +libc.so.6:dlsym +libc.so.6:exit +libc.so.6:fchmod +libc.so.6:fclose +libc.so.6:fgets +libc.so.6:fileno +libc.so.6:fopen +libc.so.6:fputc +libc.so.6:fputs +libc.so.6:fread +libc.so.6:free +libc.so.6:fwrite +libc.so.6:getcwd +libc.so.6:getenv +libc.so.6:getopt +libc.so.6:getopt_long +libc.so.6:getpwnam +libc.so.6:gettimeofday +libc.so.6:isatty +libc.so.6:lseek +libc.so.6:malloc +libc.so.6:memcmp +libc.so.6:memcpy +libc.so.6:memmove +libc.so.6:memset +libc.so.6:mkdir +libc.so.6:mkdtemp +libc.so.6:mkstemp +libc.so.6:open +libc.so.6:opendir +libc.so.6:optarg +libc.so.6:opterr +libc.so.6:optind +libc.so.6:putchar +libc.so.6:puts +libc.so.6:qsort +libc.so.6:rand +libc.so.6:random +libc.so.6:read +libc.so.6:readdir +libc.so.6:realloc +libc.so.6:regcomp +libc.so.6:regexec +libc.so.6:regfree +libc.so.6:rmdir +libc.so.6:setlocale +libc.so.6:srand +libc.so.6:srandom +libc.so.6:stat +libc.so.6:stderr +libc.so.6:stdin +libc.so.6:stdout +libc.so.6:strcasecmp +libc.so.6:strchr +libc.so.6:strcmp +libc.so.6:strcpy +libc.so.6:strcspn +libc.so.6:strdup +libc.so.6:strerror +libc.so.6:strlen +libc.so.6:strncasecmp +libc.so.6:strncmp +libc.so.6:strncpy +libc.so.6:strrchr +libc.so.6:strspn +libc.so.6:strstr +libc.so.6:strtod +libc.so.6:system +libc.so.6:time +libc.so.6:unlink +libc.so.6:write +libgsl.so.25:gsl_matrix_set +libgsl.so.25:gsl_multifit_fdfsolver_alloc +libgsl.so.25:gsl_multifit_fdfsolver_free +libgsl.so.25:gsl_multifit_fdfsolver_iterate +libgsl.so.25:gsl_multifit_fdfsolver_lmsder +libgsl.so.25:gsl_multifit_fdfsolver_set +libgsl.so.25:gsl_multifit_fdfsolver_test +libgsl.so.25:gsl_strerror +libgsl.so.25:gsl_vector_alloc +libgsl.so.25:gsl_vector_free +libgsl.so.25:gsl_vector_get +libgsl.so.25:gsl_vector_set +libgsl.so.25:gsl_vector_view_array +libhts.so.3:bam_aux2i +libhts.so.3:bam_aux_append +libhts.so.3:bam_aux_del +libhts.so.3:bam_aux_get +libhts.so.3:bam_cigar2qlen +libhts.so.3:bam_cigar2rlen +libhts.so.3:bam_destroy1 +libhts.so.3:bam_endpos +libhts.so.3:bam_flag2str +libhts.so.3:bam_init1 +libhts.so.3:bam_mplp_auto +libhts.so.3:bam_mplp_constructor +libhts.so.3:bam_mplp_destroy +libhts.so.3:bam_mplp_destructor +libhts.so.3:bam_mplp_init +libhts.so.3:bam_mplp_init_overlaps +libhts.so.3:bam_mplp_reset +libhts.so.3:bam_mplp_set_maxcnt +libhts.so.3:bam_str2flag +libhts.so.3:bcf_add_filter +libhts.so.3:bcf_add_id +libhts.so.3:bcf_calc_ac +libhts.so.3:bcf_clear +libhts.so.3:bcf_copy +libhts.so.3:bcf_destroy +libhts.so.3:bcf_dup +libhts.so.3:bcf_empty +libhts.so.3:bcf_float_missing +libhts.so.3:bcf_float_vector_end +libhts.so.3:bcf_fmt_array +libhts.so.3:bcf_format_gt_v2 +libhts.so.3:bcf_get_fmt +libhts.so.3:bcf_get_format_string +libhts.so.3:bcf_get_format_values +libhts.so.3:bcf_get_info +libhts.so.3:bcf_get_info_values +libhts.so.3:bcf_get_variant_type +libhts.so.3:bcf_get_variant_types +libhts.so.3:bcf_gt_type +libhts.so.3:bcf_has_filter +libhts.so.3:bcf_has_variant_type +libhts.so.3:bcf_has_variant_types +libhts.so.3:bcf_hdr_add_hrec +libhts.so.3:bcf_hdr_add_sample +libhts.so.3:bcf_hdr_append +libhts.so.3:bcf_hdr_destroy +libhts.so.3:bcf_hdr_dup +libhts.so.3:bcf_hdr_format +libhts.so.3:bcf_hdr_get_hrec +libhts.so.3:bcf_hdr_get_version +libhts.so.3:bcf_hdr_id2int +libhts.so.3:bcf_hdr_init +libhts.so.3:bcf_hdr_merge +libhts.so.3:bcf_hdr_parse +libhts.so.3:bcf_hdr_printf +libhts.so.3:bcf_hdr_read +libhts.so.3:bcf_hdr_remove +libhts.so.3:bcf_hdr_seqnames +libhts.so.3:bcf_hdr_set +libhts.so.3:bcf_hdr_set_samples +libhts.so.3:bcf_hdr_set_version +libhts.so.3:bcf_hdr_subset +libhts.so.3:bcf_hdr_sync +libhts.so.3:bcf_hdr_write +libhts.so.3:bcf_hrec_destroy +libhts.so.3:bcf_hrec_dup +libhts.so.3:bcf_hrec_find_key +libhts.so.3:bcf_hrec_format +libhts.so.3:bcf_idx_init +libhts.so.3:bcf_idx_save +libhts.so.3:bcf_index_build +libhts.so.3:bcf_index_build3 +libhts.so.3:bcf_index_load2 +libhts.so.3:bcf_init +libhts.so.3:bcf_is_snp +libhts.so.3:bcf_read +libhts.so.3:bcf_readrec +libhts.so.3:bcf_remove_allele_set +libhts.so.3:bcf_remove_filter +libhts.so.3:bcf_sr_add_reader +libhts.so.3:bcf_sr_destroy +libhts.so.3:bcf_sr_init +libhts.so.3:bcf_sr_next_line +libhts.so.3:bcf_sr_regions_destroy +libhts.so.3:bcf_sr_regions_init +libhts.so.3:bcf_sr_regions_next +libhts.so.3:bcf_sr_regions_overlap +libhts.so.3:bcf_sr_remove_reader +libhts.so.3:bcf_sr_seek +libhts.so.3:bcf_sr_set_opt +libhts.so.3:bcf_sr_set_regions +libhts.so.3:bcf_sr_set_samples +libhts.so.3:bcf_sr_set_targets +libhts.so.3:bcf_sr_set_threads +libhts.so.3:bcf_sr_strerror +libhts.so.3:bcf_subset +libhts.so.3:bcf_translate +libhts.so.3:bcf_trim_alleles +libhts.so.3:bcf_type_shift +libhts.so.3:bcf_unpack +libhts.so.3:bcf_update_alleles +libhts.so.3:bcf_update_alleles_str +libhts.so.3:bcf_update_filter +libhts.so.3:bcf_update_format +libhts.so.3:bcf_update_format_string +libhts.so.3:bcf_update_id +libhts.so.3:bcf_update_info +libhts.so.3:bcf_variant_length +libhts.so.3:bcf_write +libhts.so.3:bgzf_check_EOF +libhts.so.3:bgzf_close +libhts.so.3:bgzf_compression +libhts.so.3:bgzf_flush +libhts.so.3:bgzf_getline +libhts.so.3:bgzf_open +libhts.so.3:bgzf_raw_read +libhts.so.3:bgzf_raw_write +libhts.so.3:bgzf_read +libhts.so.3:bgzf_read_block +libhts.so.3:bgzf_thread_pool +libhts.so.3:bgzf_write +libhts.so.3:errmod_cal +libhts.so.3:errmod_destroy +libhts.so.3:errmod_init +libhts.so.3:fai_destroy +libhts.so.3:fai_load +libhts.so.3:fai_load3 +libhts.so.3:faidx_fetch_seq +libhts.so.3:faidx_fetch_seq64 +libhts.so.3:faidx_has_seq +libhts.so.3:faidx_iseq +libhts.so.3:faidx_nseq +libhts.so.3:faidx_seq_len +libhts.so.3:faidx_seq_len64 +libhts.so.3:hrec_add_idx +libhts.so.3:hts_close +libhts.so.3:hts_drand48 +libhts.so.3:hts_get_bgzfp +libhts.so.3:hts_get_format +libhts.so.3:hts_getline +libhts.so.3:hts_idx_destroy +libhts.so.3:hts_idx_get_stat +libhts.so.3:hts_idx_load +libhts.so.3:hts_idx_nseq +libhts.so.3:hts_idx_seqnames +libhts.so.3:hts_itr_destroy +libhts.so.3:hts_itr_multi_next +libhts.so.3:hts_itr_next +libhts.so.3:hts_itr_query +libhts.so.3:hts_itr_querys +libhts.so.3:hts_log +libhts.so.3:hts_lrand48 +libhts.so.3:hts_open +libhts.so.3:hts_opt_add +libhts.so.3:hts_opt_apply +libhts.so.3:hts_opt_free +libhts.so.3:hts_readlines +libhts.so.3:hts_readlist +libhts.so.3:hts_realloc_or_die +libhts.so.3:hts_resize_array_ +libhts.so.3:hts_set_fai_filename +libhts.so.3:hts_set_opt +libhts.so.3:hts_set_thread_pool +libhts.so.3:hts_set_threads +libhts.so.3:hts_srand48 +libhts.so.3:hts_tpool_destroy +libhts.so.3:hts_tpool_init +libhts.so.3:hts_verbose +libhts.so.3:hts_version +libhts.so.3:kf_betai +libhts.so.3:kf_erfc +libhts.so.3:kf_gammaq +libhts.so.3:kputd +libhts.so.3:ksplit_core +libhts.so.3:ksprintf +libhts.so.3:kt_fisher_exact +libhts.so.3:probaln_glocal +libhts.so.3:sam_cap_mapq +libhts.so.3:sam_hdr_destroy +libhts.so.3:sam_hdr_read +libhts.so.3:sam_hdr_tid2name +libhts.so.3:sam_index_load +libhts.so.3:sam_itr_querys +libhts.so.3:sam_itr_regarray +libhts.so.3:sam_prob_realn +libhts.so.3:sam_read1 +libhts.so.3:seq_nt16_int +libhts.so.3:seq_nt16_str +libhts.so.3:seq_nt16_table +libhts.so.3:tbx_conf_bed +libhts.so.3:tbx_conf_gff +libhts.so.3:tbx_conf_sam +libhts.so.3:tbx_conf_vcf +libhts.so.3:tbx_destroy +libhts.so.3:tbx_index_build +libhts.so.3:tbx_index_load +libhts.so.3:tbx_index_load2 +libhts.so.3:tbx_name2id +libhts.so.3:tbx_readrec +libhts.so.3:tbx_seqnames +libhts.so.3:vcf_format +libhts.so.3:vcf_parse +libhts.so.3:vcf_write_line +libm.so.6:acos +libm.so.6:cos +libm.so.6:erfc +libm.so.6:exp +libm.so.6:expl +libm.so.6:floor +libm.so.6:lgamma +libm.so.6:log +libm.so.6:log10 +libm.so.6:lroundf +libm.so.6:nearbyintf +libm.so.6:pow +libm.so.6:sincos +libm.so.6:sqrt +libm.so.6:sqrtf diff --git a/packages/b/bcftools/monitoring.yaml b/packages/b/bcftools/monitoring.yaml new file mode 100644 index 000000000000..8df6ed0ff026 --- /dev/null +++ b/packages/b/bcftools/monitoring.yaml @@ -0,0 +1,6 @@ +releases: + id: 13454 + rss: https://github.com/samtools/bcftools/releases.atom + # No known CPE, checked 2025-08-24 +security: + cpe: ~ diff --git a/packages/b/bcftools/package.yml b/packages/b/bcftools/package.yml new file mode 100644 index 000000000000..3f4be7570a5f --- /dev/null +++ b/packages/b/bcftools/package.yml @@ -0,0 +1,20 @@ +name : bcftools +version : 1.22 +release : 1 +source : + - https://github.com/samtools/bcftools/releases/download/1.22/bcftools-1.22.tar.bz2 : f2ab9e2f605b1203a7e9cbfb0a3eb7689322297f8c34b45dc5237fe57d98489f +homepage : https://www.htslib.org/ +license : GPL-3.0-or-later +component : programming.tools +summary : utilities for variant calling and working with VCF/BCF files +description: | + BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. +builddeps : + - pkgconfig(gsl) + - pkgconfig(htslib) +setup : | + %configure --with-htslib=system --enable-libgsl +build : | + %make +install : | + %make_install diff --git a/packages/b/bcftools/pspec_x86_64.xml b/packages/b/bcftools/pspec_x86_64.xml new file mode 100644 index 000000000000..e6db254b6a97 --- /dev/null +++ b/packages/b/bcftools/pspec_x86_64.xml @@ -0,0 +1,84 @@ + + + bcftools + https://www.htslib.org/ + + Lea Evers + lea.evers@mailbox.org + + GPL-3.0-or-later + programming.tools + utilities for variant calling and working with VCF/BCF files + BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. + + https://sources.getsol.us/README.Solus + + + bcftools + utilities for variant calling and working with VCF/BCF files + BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. + + programming.tools + + /usr/bin/bcftools + /usr/bin/color-chrs.pl + /usr/bin/gff2gff.py + /usr/bin/guess-ploidy.py + /usr/bin/plot-roh.py + /usr/bin/plot-vcfstats + /usr/bin/run-roh.pl + /usr/bin/vcfutils.pl + /usr/lib64/bcftools/bcftools/GTisec.so + /usr/lib64/bcftools/bcftools/GTsubset.so + /usr/lib64/bcftools/bcftools/ad-bias.so + /usr/lib64/bcftools/bcftools/add-variantkey.so + /usr/lib64/bcftools/bcftools/af-dist.so + /usr/lib64/bcftools/bcftools/allele-length.so + /usr/lib64/bcftools/bcftools/check-ploidy.so + /usr/lib64/bcftools/bcftools/check-sparsity.so + /usr/lib64/bcftools/bcftools/color-chrs.so + /usr/lib64/bcftools/bcftools/contrast.so + /usr/lib64/bcftools/bcftools/counts.so + /usr/lib64/bcftools/bcftools/dosage.so + /usr/lib64/bcftools/bcftools/fill-AN-AC.so + /usr/lib64/bcftools/bcftools/fill-from-fasta.so + /usr/lib64/bcftools/bcftools/fill-tags.so + /usr/lib64/bcftools/bcftools/fixploidy.so + /usr/lib64/bcftools/bcftools/fixref.so + /usr/lib64/bcftools/bcftools/frameshifts.so + /usr/lib64/bcftools/bcftools/guess-ploidy.so + /usr/lib64/bcftools/bcftools/gvcfz.so + /usr/lib64/bcftools/bcftools/impute-info.so + /usr/lib64/bcftools/bcftools/indel-stats.so + /usr/lib64/bcftools/bcftools/isecGT.so + /usr/lib64/bcftools/bcftools/mendelian2.so + /usr/lib64/bcftools/bcftools/missing2ref.so + /usr/lib64/bcftools/bcftools/parental-origin.so + /usr/lib64/bcftools/bcftools/prune.so + /usr/lib64/bcftools/bcftools/remove-overlaps.so + /usr/lib64/bcftools/bcftools/scatter.so + /usr/lib64/bcftools/bcftools/setGT.so + /usr/lib64/bcftools/bcftools/smpl-stats.so + /usr/lib64/bcftools/bcftools/split-vep.so + /usr/lib64/bcftools/bcftools/split.so + /usr/lib64/bcftools/bcftools/tag2tag.so + /usr/lib64/bcftools/bcftools/trio-dnm2.so + /usr/lib64/bcftools/bcftools/trio-stats.so + /usr/lib64/bcftools/bcftools/trio-switch-rate.so + /usr/lib64/bcftools/bcftools/variant-distance.so + /usr/lib64/bcftools/bcftools/variantkey-hex.so + /usr/lib64/bcftools/bcftools/vcf2table.so + /usr/lib64/bcftools/bcftools/vrfs.so + /usr/share/man/man1/bcftools.1.zst + + + + + 2025-09-17 + 1.22 + Packaging update + Lea Evers + lea.evers@mailbox.org + + + \ No newline at end of file diff --git a/packages/h/htslib/abi_libs b/packages/h/htslib/abi_libs new file mode 100644 index 000000000000..fbf8f13331bb --- /dev/null +++ b/packages/h/htslib/abi_libs @@ -0,0 +1 @@ +libhts.so.3 diff --git a/packages/h/htslib/abi_symbols b/packages/h/htslib/abi_symbols new file mode 100644 index 000000000000..bdde9a184973 --- /dev/null +++ b/packages/h/htslib/abi_symbols @@ -0,0 +1,616 @@ +libhts.so.3:HTSLIB_1.0 +libhts.so.3:HTSLIB_1.1 +libhts.so.3:HTSLIB_1.10 +libhts.so.3:HTSLIB_1.11 +libhts.so.3:HTSLIB_1.12 +libhts.so.3:HTSLIB_1.13 +libhts.so.3:HTSLIB_1.14 +libhts.so.3:HTSLIB_1.15 +libhts.so.3:HTSLIB_1.16 +libhts.so.3:HTSLIB_1.17 +libhts.so.3:HTSLIB_1.18 +libhts.so.3:HTSLIB_1.2.1 +libhts.so.3:HTSLIB_1.20 +libhts.so.3:HTSLIB_1.21 +libhts.so.3:HTSLIB_1.3 +libhts.so.3:HTSLIB_1.4 +libhts.so.3:HTSLIB_1.5 +libhts.so.3:HTSLIB_1.6 +libhts.so.3:HTSLIB_1.7 +libhts.so.3:HTSLIB_1.9 +libhts.so.3:bam_aux2A +libhts.so.3:bam_aux2Z +libhts.so.3:bam_aux2f +libhts.so.3:bam_aux2i +libhts.so.3:bam_auxB2f +libhts.so.3:bam_auxB2i +libhts.so.3:bam_auxB_len +libhts.so.3:bam_aux_append +libhts.so.3:bam_aux_del +libhts.so.3:bam_aux_first +libhts.so.3:bam_aux_get +libhts.so.3:bam_aux_next +libhts.so.3:bam_aux_remove +libhts.so.3:bam_aux_update_array +libhts.so.3:bam_aux_update_float +libhts.so.3:bam_aux_update_int +libhts.so.3:bam_aux_update_str +libhts.so.3:bam_cigar2qlen +libhts.so.3:bam_cigar2rlen +libhts.so.3:bam_cigar_table +libhts.so.3:bam_copy1 +libhts.so.3:bam_destroy1 +libhts.so.3:bam_dup1 +libhts.so.3:bam_endpos +libhts.so.3:bam_flag2str +libhts.so.3:bam_hdr_read +libhts.so.3:bam_hdr_write +libhts.so.3:bam_init1 +libhts.so.3:bam_mods_at_next_pos +libhts.so.3:bam_mods_at_qpos +libhts.so.3:bam_mods_query_type +libhts.so.3:bam_mods_queryi +libhts.so.3:bam_mods_recorded +libhts.so.3:bam_mplp64_auto +libhts.so.3:bam_mplp_auto +libhts.so.3:bam_mplp_constructor +libhts.so.3:bam_mplp_destroy +libhts.so.3:bam_mplp_destructor +libhts.so.3:bam_mplp_init +libhts.so.3:bam_mplp_init_overlaps +libhts.so.3:bam_mplp_reset +libhts.so.3:bam_mplp_set_maxcnt +libhts.so.3:bam_next_basemod +libhts.so.3:bam_parse_basemod +libhts.so.3:bam_parse_basemod2 +libhts.so.3:bam_parse_cigar +libhts.so.3:bam_plp64_auto +libhts.so.3:bam_plp64_next +libhts.so.3:bam_plp_auto +libhts.so.3:bam_plp_constructor +libhts.so.3:bam_plp_destroy +libhts.so.3:bam_plp_destructor +libhts.so.3:bam_plp_init +libhts.so.3:bam_plp_insertion +libhts.so.3:bam_plp_insertion_mod +libhts.so.3:bam_plp_next +libhts.so.3:bam_plp_push +libhts.so.3:bam_plp_reset +libhts.so.3:bam_plp_set_maxcnt +libhts.so.3:bam_read1 +libhts.so.3:bam_set1 +libhts.so.3:bam_set_qname +libhts.so.3:bam_str2flag +libhts.so.3:bam_write1 +libhts.so.3:bcf_add_filter +libhts.so.3:bcf_add_id +libhts.so.3:bcf_calc_ac +libhts.so.3:bcf_clear +libhts.so.3:bcf_copy +libhts.so.3:bcf_destroy +libhts.so.3:bcf_dup +libhts.so.3:bcf_empty +libhts.so.3:bcf_enc_vchar +libhts.so.3:bcf_enc_vfloat +libhts.so.3:bcf_enc_vint +libhts.so.3:bcf_float_missing +libhts.so.3:bcf_float_vector_end +libhts.so.3:bcf_fmt_array +libhts.so.3:bcf_fmt_sized_array +libhts.so.3:bcf_format_gt_v2 +libhts.so.3:bcf_get_fmt +libhts.so.3:bcf_get_fmt_id +libhts.so.3:bcf_get_format_string +libhts.so.3:bcf_get_format_values +libhts.so.3:bcf_get_info +libhts.so.3:bcf_get_info_id +libhts.so.3:bcf_get_info_values +libhts.so.3:bcf_get_variant_type +libhts.so.3:bcf_get_variant_types +libhts.so.3:bcf_gt_type +libhts.so.3:bcf_has_filter +libhts.so.3:bcf_has_variant_type +libhts.so.3:bcf_has_variant_types +libhts.so.3:bcf_hdr_add_hrec +libhts.so.3:bcf_hdr_add_sample +libhts.so.3:bcf_hdr_append +libhts.so.3:bcf_hdr_combine +libhts.so.3:bcf_hdr_destroy +libhts.so.3:bcf_hdr_dup +libhts.so.3:bcf_hdr_fmt_text +libhts.so.3:bcf_hdr_format +libhts.so.3:bcf_hdr_get_hrec +libhts.so.3:bcf_hdr_get_version +libhts.so.3:bcf_hdr_id2int +libhts.so.3:bcf_hdr_init +libhts.so.3:bcf_hdr_merge +libhts.so.3:bcf_hdr_parse +libhts.so.3:bcf_hdr_parse_line +libhts.so.3:bcf_hdr_printf +libhts.so.3:bcf_hdr_read +libhts.so.3:bcf_hdr_remove +libhts.so.3:bcf_hdr_seqnames +libhts.so.3:bcf_hdr_set +libhts.so.3:bcf_hdr_set_samples +libhts.so.3:bcf_hdr_set_version +libhts.so.3:bcf_hdr_subset +libhts.so.3:bcf_hdr_sync +libhts.so.3:bcf_hdr_write +libhts.so.3:bcf_hrec_add_key +libhts.so.3:bcf_hrec_destroy +libhts.so.3:bcf_hrec_dup +libhts.so.3:bcf_hrec_find_key +libhts.so.3:bcf_hrec_format +libhts.so.3:bcf_hrec_set_val +libhts.so.3:bcf_idx_init +libhts.so.3:bcf_idx_save +libhts.so.3:bcf_index_build +libhts.so.3:bcf_index_build2 +libhts.so.3:bcf_index_build3 +libhts.so.3:bcf_index_load2 +libhts.so.3:bcf_index_load3 +libhts.so.3:bcf_init +libhts.so.3:bcf_is_snp +libhts.so.3:bcf_read +libhts.so.3:bcf_readrec +libhts.so.3:bcf_remove_allele_set +libhts.so.3:bcf_remove_alleles +libhts.so.3:bcf_remove_filter +libhts.so.3:bcf_sr_add_hreader +libhts.so.3:bcf_sr_add_reader +libhts.so.3:bcf_sr_destroy +libhts.so.3:bcf_sr_destroy_threads +libhts.so.3:bcf_sr_init +libhts.so.3:bcf_sr_next_line +libhts.so.3:bcf_sr_regions_destroy +libhts.so.3:bcf_sr_regions_flush +libhts.so.3:bcf_sr_regions_init +libhts.so.3:bcf_sr_regions_next +libhts.so.3:bcf_sr_regions_overlap +libhts.so.3:bcf_sr_regions_seek +libhts.so.3:bcf_sr_remove_reader +libhts.so.3:bcf_sr_seek +libhts.so.3:bcf_sr_set_opt +libhts.so.3:bcf_sr_set_regions +libhts.so.3:bcf_sr_set_samples +libhts.so.3:bcf_sr_set_targets +libhts.so.3:bcf_sr_set_threads +libhts.so.3:bcf_sr_strerror +libhts.so.3:bcf_strerror +libhts.so.3:bcf_subset +libhts.so.3:bcf_subset_format +libhts.so.3:bcf_sweep_bwd +libhts.so.3:bcf_sweep_destroy +libhts.so.3:bcf_sweep_fwd +libhts.so.3:bcf_sweep_hdr +libhts.so.3:bcf_sweep_init +libhts.so.3:bcf_translate +libhts.so.3:bcf_trim_alleles +libhts.so.3:bcf_type_shift +libhts.so.3:bcf_unpack +libhts.so.3:bcf_update_alleles +libhts.so.3:bcf_update_alleles_str +libhts.so.3:bcf_update_filter +libhts.so.3:bcf_update_format +libhts.so.3:bcf_update_format_string +libhts.so.3:bcf_update_id +libhts.so.3:bcf_update_info +libhts.so.3:bcf_variant_length +libhts.so.3:bcf_write +libhts.so.3:bgzf_block_write +libhts.so.3:bgzf_check_EOF +libhts.so.3:bgzf_close +libhts.so.3:bgzf_compress +libhts.so.3:bgzf_compression +libhts.so.3:bgzf_dopen +libhts.so.3:bgzf_flush +libhts.so.3:bgzf_flush_try +libhts.so.3:bgzf_getc +libhts.so.3:bgzf_getline +libhts.so.3:bgzf_hopen +libhts.so.3:bgzf_index_build_init +libhts.so.3:bgzf_index_dump +libhts.so.3:bgzf_index_dump_hfile +libhts.so.3:bgzf_index_load +libhts.so.3:bgzf_index_load_hfile +libhts.so.3:bgzf_is_bgzf +libhts.so.3:bgzf_mt +libhts.so.3:bgzf_open +libhts.so.3:bgzf_peek +libhts.so.3:bgzf_raw_read +libhts.so.3:bgzf_raw_write +libhts.so.3:bgzf_read +libhts.so.3:bgzf_read_block +libhts.so.3:bgzf_seek +libhts.so.3:bgzf_set_cache_size +libhts.so.3:bgzf_thread_pool +libhts.so.3:bgzf_useek +libhts.so.3:bgzf_utell +libhts.so.3:bgzf_write +libhts.so.3:cram_block_append +libhts.so.3:cram_block_get_comp_size +libhts.so.3:cram_block_get_content_id +libhts.so.3:cram_block_get_content_type +libhts.so.3:cram_block_get_crc32 +libhts.so.3:cram_block_get_data +libhts.so.3:cram_block_get_method +libhts.so.3:cram_block_get_offset +libhts.so.3:cram_block_get_uncomp_size +libhts.so.3:cram_block_set_comp_size +libhts.so.3:cram_block_set_content_id +libhts.so.3:cram_block_set_crc32 +libhts.so.3:cram_block_set_data +libhts.so.3:cram_block_set_offset +libhts.so.3:cram_block_set_uncomp_size +libhts.so.3:cram_block_size +libhts.so.3:cram_block_update_size +libhts.so.3:cram_check_EOF +libhts.so.3:cram_cid2ds_free +libhts.so.3:cram_cid2ds_query +libhts.so.3:cram_close +libhts.so.3:cram_codec_describe +libhts.so.3:cram_codec_get_content_ids +libhts.so.3:cram_compress_block +libhts.so.3:cram_container_get_coords +libhts.so.3:cram_container_get_landmarks +libhts.so.3:cram_container_get_length +libhts.so.3:cram_container_get_num_bases +libhts.so.3:cram_container_get_num_blocks +libhts.so.3:cram_container_get_num_records +libhts.so.3:cram_container_is_empty +libhts.so.3:cram_container_num2offset +libhts.so.3:cram_container_offset2num +libhts.so.3:cram_container_set_landmarks +libhts.so.3:cram_container_set_length +libhts.so.3:cram_container_set_num_blocks +libhts.so.3:cram_container_size +libhts.so.3:cram_copy_slice +libhts.so.3:cram_decode_compression_header +libhts.so.3:cram_decode_slice_header +libhts.so.3:cram_describe_encodings +libhts.so.3:cram_dopen +libhts.so.3:cram_eof +libhts.so.3:cram_expand_method +libhts.so.3:cram_fd_get_fp +libhts.so.3:cram_fd_get_header +libhts.so.3:cram_fd_get_version +libhts.so.3:cram_fd_set_fp +libhts.so.3:cram_fd_set_header +libhts.so.3:cram_fd_set_version +libhts.so.3:cram_filter_container +libhts.so.3:cram_flush +libhts.so.3:cram_free_block +libhts.so.3:cram_free_compression_header +libhts.so.3:cram_free_container +libhts.so.3:cram_free_slice_header +libhts.so.3:cram_get_refs +libhts.so.3:cram_index_extents +libhts.so.3:cram_major_vers +libhts.so.3:cram_minor_vers +libhts.so.3:cram_new_block +libhts.so.3:cram_new_container +libhts.so.3:cram_num_containers +libhts.so.3:cram_num_containers_between +libhts.so.3:cram_open +libhts.so.3:cram_read_block +libhts.so.3:cram_read_container +libhts.so.3:cram_seek +libhts.so.3:cram_set_header +libhts.so.3:cram_set_option +libhts.so.3:cram_set_voption +libhts.so.3:cram_slice_hdr_get_coords +libhts.so.3:cram_slice_hdr_get_embed_ref_id +libhts.so.3:cram_slice_hdr_get_num_blocks +libhts.so.3:cram_store_container +libhts.so.3:cram_transcode_rg +libhts.so.3:cram_uncompress_block +libhts.so.3:cram_update_cid2ds_map +libhts.so.3:cram_write_block +libhts.so.3:cram_write_container +libhts.so.3:errmod_cal +libhts.so.3:errmod_destroy +libhts.so.3:errmod_init +libhts.so.3:fai_adjust_region +libhts.so.3:fai_build +libhts.so.3:fai_build3 +libhts.so.3:fai_destroy +libhts.so.3:fai_fetch +libhts.so.3:fai_fetch64 +libhts.so.3:fai_fetchqual +libhts.so.3:fai_fetchqual64 +libhts.so.3:fai_line_length +libhts.so.3:fai_load +libhts.so.3:fai_load3 +libhts.so.3:fai_load3_format +libhts.so.3:fai_load_format +libhts.so.3:fai_parse_region +libhts.so.3:fai_path +libhts.so.3:fai_set_cache_size +libhts.so.3:fai_thread_pool +libhts.so.3:faidx_fetch_nseq +libhts.so.3:faidx_fetch_qual +libhts.so.3:faidx_fetch_qual64 +libhts.so.3:faidx_fetch_seq +libhts.so.3:faidx_fetch_seq64 +libhts.so.3:faidx_has_seq +libhts.so.3:faidx_iseq +libhts.so.3:faidx_nseq +libhts.so.3:faidx_seq_len +libhts.so.3:faidx_seq_len64 +libhts.so.3:haddextension +libhts.so.3:hclose +libhts.so.3:hclose_abruptly +libhts.so.3:hdopen +libhts.so.3:hfile_add_scheme_handler +libhts.so.3:hfile_always_local +libhts.so.3:hfile_always_remote +libhts.so.3:hfile_destroy +libhts.so.3:hfile_has_plugin +libhts.so.3:hfile_init +libhts.so.3:hfile_list_plugins +libhts.so.3:hfile_list_schemes +libhts.so.3:hfile_mem_get_buffer +libhts.so.3:hfile_mem_steal_buffer +libhts.so.3:hfile_oflags +libhts.so.3:hfile_set_blksize +libhts.so.3:hflush +libhts.so.3:hgetc2 +libhts.so.3:hgetdelim +libhts.so.3:hgets +libhts.so.3:hisremote +libhts.so.3:hopen +libhts.so.3:hpeek +libhts.so.3:hputc2 +libhts.so.3:hputs2 +libhts.so.3:hread2 +libhts.so.3:hrec_add_idx +libhts.so.3:hseek +libhts.so.3:hts_base_mod_state_alloc +libhts.so.3:hts_base_mod_state_free +libhts.so.3:hts_check_EOF +libhts.so.3:hts_close +libhts.so.3:hts_crc32 +libhts.so.3:hts_detect_format +libhts.so.3:hts_detect_format2 +libhts.so.3:hts_drand48 +libhts.so.3:hts_erand48 +libhts.so.3:hts_feature_string +libhts.so.3:hts_features +libhts.so.3:hts_file_type +libhts.so.3:hts_filter_eval +libhts.so.3:hts_filter_eval2 +libhts.so.3:hts_filter_free +libhts.so.3:hts_filter_init +libhts.so.3:hts_flush +libhts.so.3:hts_format_description +libhts.so.3:hts_format_file_extension +libhts.so.3:hts_free +libhts.so.3:hts_get_bgzfp +libhts.so.3:hts_get_format +libhts.so.3:hts_get_log_level +libhts.so.3:hts_getline +libhts.so.3:hts_hopen +libhts.so.3:hts_idx_destroy +libhts.so.3:hts_idx_finish +libhts.so.3:hts_idx_fmt +libhts.so.3:hts_idx_get_meta +libhts.so.3:hts_idx_get_n_no_coor +libhts.so.3:hts_idx_get_stat +libhts.so.3:hts_idx_init +libhts.so.3:hts_idx_load +libhts.so.3:hts_idx_load2 +libhts.so.3:hts_idx_load3 +libhts.so.3:hts_idx_nseq +libhts.so.3:hts_idx_push +libhts.so.3:hts_idx_save +libhts.so.3:hts_idx_save_as +libhts.so.3:hts_idx_seqnames +libhts.so.3:hts_idx_set_meta +libhts.so.3:hts_idx_tbi_name +libhts.so.3:hts_itr_destroy +libhts.so.3:hts_itr_multi_bam +libhts.so.3:hts_itr_multi_cram +libhts.so.3:hts_itr_multi_next +libhts.so.3:hts_itr_next +libhts.so.3:hts_itr_query +libhts.so.3:hts_itr_querys +libhts.so.3:hts_itr_regions +libhts.so.3:hts_json_alloc_token +libhts.so.3:hts_json_fnext +libhts.so.3:hts_json_free_token +libhts.so.3:hts_json_fskip_value +libhts.so.3:hts_json_snext +libhts.so.3:hts_json_sskip_value +libhts.so.3:hts_json_token_str +libhts.so.3:hts_json_token_type +libhts.so.3:hts_lib_shutdown +libhts.so.3:hts_log +libhts.so.3:hts_lrand48 +libhts.so.3:hts_md5_destroy +libhts.so.3:hts_md5_final +libhts.so.3:hts_md5_hex +libhts.so.3:hts_md5_init +libhts.so.3:hts_md5_reset +libhts.so.3:hts_md5_update +libhts.so.3:hts_open +libhts.so.3:hts_open_format +libhts.so.3:hts_opt_add +libhts.so.3:hts_opt_apply +libhts.so.3:hts_opt_free +libhts.so.3:hts_parse_decimal +libhts.so.3:hts_parse_format +libhts.so.3:hts_parse_opt_list +libhts.so.3:hts_parse_reg +libhts.so.3:hts_parse_reg64 +libhts.so.3:hts_parse_region +libhts.so.3:hts_readlines +libhts.so.3:hts_readlist +libhts.so.3:hts_realloc_or_die +libhts.so.3:hts_reglist_create +libhts.so.3:hts_reglist_free +libhts.so.3:hts_resize_array_ +libhts.so.3:hts_set_cache_size +libhts.so.3:hts_set_fai_filename +libhts.so.3:hts_set_filter_expression +libhts.so.3:hts_set_log_level +libhts.so.3:hts_set_opt +libhts.so.3:hts_set_thread_pool +libhts.so.3:hts_set_threads +libhts.so.3:hts_srand48 +libhts.so.3:hts_test_feature +libhts.so.3:hts_tpool_delete_result +libhts.so.3:hts_tpool_destroy +libhts.so.3:hts_tpool_dispatch +libhts.so.3:hts_tpool_dispatch2 +libhts.so.3:hts_tpool_dispatch3 +libhts.so.3:hts_tpool_init +libhts.so.3:hts_tpool_kill +libhts.so.3:hts_tpool_next_result +libhts.so.3:hts_tpool_next_result_wait +libhts.so.3:hts_tpool_process_attach +libhts.so.3:hts_tpool_process_destroy +libhts.so.3:hts_tpool_process_detach +libhts.so.3:hts_tpool_process_empty +libhts.so.3:hts_tpool_process_flush +libhts.so.3:hts_tpool_process_init +libhts.so.3:hts_tpool_process_is_shutdown +libhts.so.3:hts_tpool_process_len +libhts.so.3:hts_tpool_process_qsize +libhts.so.3:hts_tpool_process_ref_decr +libhts.so.3:hts_tpool_process_ref_incr +libhts.so.3:hts_tpool_process_reset +libhts.so.3:hts_tpool_process_shutdown +libhts.so.3:hts_tpool_process_sz +libhts.so.3:hts_tpool_result_data +libhts.so.3:hts_tpool_size +libhts.so.3:hts_tpool_wake_dispatch +libhts.so.3:hts_tpool_worker_id +libhts.so.3:hts_verbose +libhts.so.3:hts_version +libhts.so.3:hwrite2 +libhts.so.3:int32_put_blk +libhts.so.3:kf_betai +libhts.so.3:kf_erfc +libhts.so.3:kf_gammap +libhts.so.3:kf_gammaq +libhts.so.3:kf_lgamma +libhts.so.3:kgetline +libhts.so.3:kgetline2 +libhts.so.3:kmemmem +libhts.so.3:knet_close +libhts.so.3:knet_dopen +libhts.so.3:knet_open +libhts.so.3:knet_read +libhts.so.3:knet_seek +libhts.so.3:kputd +libhts.so.3:ksplit_core +libhts.so.3:ksprintf +libhts.so.3:kstrnstr +libhts.so.3:kstrstr +libhts.so.3:kstrtok +libhts.so.3:kt_fisher_exact +libhts.so.3:kvsprintf +libhts.so.3:probaln_glocal +libhts.so.3:regidx_destroy +libhts.so.3:regidx_init +libhts.so.3:regidx_init_string +libhts.so.3:regidx_insert +libhts.so.3:regidx_insert_list +libhts.so.3:regidx_nregs +libhts.so.3:regidx_overlap +libhts.so.3:regidx_parse_bed +libhts.so.3:regidx_parse_reg +libhts.so.3:regidx_parse_tab +libhts.so.3:regidx_parse_vcf +libhts.so.3:regidx_push +libhts.so.3:regidx_seq_names +libhts.so.3:regidx_seq_nregs +libhts.so.3:regitr_copy +libhts.so.3:regitr_destroy +libhts.so.3:regitr_init +libhts.so.3:regitr_loop +libhts.so.3:regitr_overlap +libhts.so.3:regitr_reset +libhts.so.3:sam_cap_mapq +libhts.so.3:sam_format1 +libhts.so.3:sam_hdr_add_line +libhts.so.3:sam_hdr_add_lines +libhts.so.3:sam_hdr_add_pg +libhts.so.3:sam_hdr_change_HD +libhts.so.3:sam_hdr_count_lines +libhts.so.3:sam_hdr_destroy +libhts.so.3:sam_hdr_dup +libhts.so.3:sam_hdr_find_line_id +libhts.so.3:sam_hdr_find_line_pos +libhts.so.3:sam_hdr_find_tag_id +libhts.so.3:sam_hdr_find_tag_pos +libhts.so.3:sam_hdr_incr_ref +libhts.so.3:sam_hdr_init +libhts.so.3:sam_hdr_length +libhts.so.3:sam_hdr_line_index +libhts.so.3:sam_hdr_line_name +libhts.so.3:sam_hdr_name2tid +libhts.so.3:sam_hdr_nref +libhts.so.3:sam_hdr_parse +libhts.so.3:sam_hdr_pg_id +libhts.so.3:sam_hdr_read +libhts.so.3:sam_hdr_remove_except +libhts.so.3:sam_hdr_remove_line_id +libhts.so.3:sam_hdr_remove_line_pos +libhts.so.3:sam_hdr_remove_lines +libhts.so.3:sam_hdr_remove_tag_id +libhts.so.3:sam_hdr_str +libhts.so.3:sam_hdr_tid2len +libhts.so.3:sam_hdr_tid2name +libhts.so.3:sam_hdr_update_line +libhts.so.3:sam_hdr_write +libhts.so.3:sam_idx_init +libhts.so.3:sam_idx_save +libhts.so.3:sam_index_build +libhts.so.3:sam_index_build2 +libhts.so.3:sam_index_build3 +libhts.so.3:sam_index_load +libhts.so.3:sam_index_load2 +libhts.so.3:sam_index_load3 +libhts.so.3:sam_itr_queryi +libhts.so.3:sam_itr_querys +libhts.so.3:sam_itr_regarray +libhts.so.3:sam_itr_regions +libhts.so.3:sam_open_mode +libhts.so.3:sam_open_mode_opts +libhts.so.3:sam_parse1 +libhts.so.3:sam_parse_cigar +libhts.so.3:sam_parse_region +libhts.so.3:sam_passes_filter +libhts.so.3:sam_prob_realn +libhts.so.3:sam_read1 +libhts.so.3:sam_write1 +libhts.so.3:seq_nt16_int +libhts.so.3:seq_nt16_str +libhts.so.3:seq_nt16_table +libhts.so.3:stringify_argv +libhts.so.3:tbx_conf_bed +libhts.so.3:tbx_conf_gaf +libhts.so.3:tbx_conf_gff +libhts.so.3:tbx_conf_psltbl +libhts.so.3:tbx_conf_sam +libhts.so.3:tbx_conf_vcf +libhts.so.3:tbx_destroy +libhts.so.3:tbx_index +libhts.so.3:tbx_index_build +libhts.so.3:tbx_index_build2 +libhts.so.3:tbx_index_build3 +libhts.so.3:tbx_index_load +libhts.so.3:tbx_index_load2 +libhts.so.3:tbx_index_load3 +libhts.so.3:tbx_name2id +libhts.so.3:tbx_readrec +libhts.so.3:tbx_seqnames +libhts.so.3:vcf_format +libhts.so.3:vcf_hdr_read +libhts.so.3:vcf_hdr_write +libhts.so.3:vcf_open_mode +libhts.so.3:vcf_parse +libhts.so.3:vcf_read +libhts.so.3:vcf_write +libhts.so.3:vcf_write_line diff --git a/packages/h/htslib/abi_used_libs b/packages/h/htslib/abi_used_libs new file mode 100644 index 000000000000..23d5143062fd --- /dev/null +++ b/packages/h/htslib/abi_used_libs @@ -0,0 +1,7 @@ +libbz2.so.1.0 +libc.so.6 +libcrypto.so.3 +libcurl.so.4 +liblzma.so.5 +libm.so.6 +libz.so.1 diff --git a/packages/h/htslib/abi_used_symbols b/packages/h/htslib/abi_used_symbols new file mode 100644 index 000000000000..1da1679e923f --- /dev/null +++ b/packages/h/htslib/abi_used_symbols @@ -0,0 +1,242 @@ +libbz2.so.1.0:BZ2_bzBuffToBuffCompress +libbz2.so.1.0:BZ2_bzBuffToBuffDecompress +libc.so.6:__assert_fail +libc.so.6:__ctype_b_loc +libc.so.6:__ctype_tolower_loc +libc.so.6:__ctype_toupper_loc +libc.so.6:__cxa_atexit +libc.so.6:__errno_location +libc.so.6:__fprintf_chk +libc.so.6:__isoc23_sscanf +libc.so.6:__isoc23_strtol +libc.so.6:__isoc23_strtoll +libc.so.6:__isoc23_strtoul +libc.so.6:__libc_start_main +libc.so.6:__memcpy_chk +libc.so.6:__memmove_chk +libc.so.6:__printf_chk +libc.so.6:__snprintf_chk +libc.so.6:__stack_chk_fail +libc.so.6:__strcpy_chk +libc.so.6:__strncpy_chk +libc.so.6:__vfprintf_chk +libc.so.6:__vsnprintf_chk +libc.so.6:_exit +libc.so.6:abort +libc.so.6:accept +libc.so.6:access +libc.so.6:bind +libc.so.6:calloc +libc.so.6:chmod +libc.so.6:clock +libc.so.6:close +libc.so.6:closedir +libc.so.6:connect +libc.so.6:dirfd +libc.so.6:drand48 +libc.so.6:dup +libc.so.6:dup2 +libc.so.6:epoll_create +libc.so.6:epoll_ctl +libc.so.6:epoll_wait +libc.so.6:erand48 +libc.so.6:exit +libc.so.6:fclose +libc.so.6:fcntl +libc.so.6:fdatasync +libc.so.6:fdopen +libc.so.6:feof +libc.so.6:ferror +libc.so.6:fflush +libc.so.6:fgets +libc.so.6:fileno +libc.so.6:fopen +libc.so.6:fork +libc.so.6:fputc +libc.so.6:fread +libc.so.6:free +libc.so.6:freeaddrinfo +libc.so.6:freopen +libc.so.6:fseek +libc.so.6:fstat +libc.so.6:fstatat +libc.so.6:ftell +libc.so.6:ftruncate +libc.so.6:fwrite +libc.so.6:gai_strerror +libc.so.6:getaddrinfo +libc.so.6:getcwd +libc.so.6:getenv +libc.so.6:getnameinfo +libc.so.6:getopt +libc.so.6:getopt_long +libc.so.6:getpid +libc.so.6:getrlimit +libc.so.6:getsockname +libc.so.6:getsockopt +libc.so.6:gettimeofday +libc.so.6:gmtime +libc.so.6:gmtime_r +libc.so.6:isatty +libc.so.6:listen +libc.so.6:lrand48 +libc.so.6:lseek +libc.so.6:malloc +libc.so.6:memchr +libc.so.6:memcmp +libc.so.6:memcpy +libc.so.6:memmove +libc.so.6:memset +libc.so.6:mkdir +libc.so.6:mkdirat +libc.so.6:mmap +libc.so.6:munmap +libc.so.6:nanosleep +libc.so.6:open +libc.so.6:openat +libc.so.6:opendir +libc.so.6:optarg +libc.so.6:optind +libc.so.6:perror +libc.so.6:pipe +libc.so.6:posix_memalign +libc.so.6:pthread_attr_destroy +libc.so.6:pthread_attr_getstacksize +libc.so.6:pthread_attr_init +libc.so.6:pthread_attr_setstacksize +libc.so.6:pthread_cond_broadcast +libc.so.6:pthread_cond_destroy +libc.so.6:pthread_cond_init +libc.so.6:pthread_cond_signal +libc.so.6:pthread_cond_timedwait +libc.so.6:pthread_cond_wait +libc.so.6:pthread_create +libc.so.6:pthread_getspecific +libc.so.6:pthread_join +libc.so.6:pthread_key_create +libc.so.6:pthread_kill +libc.so.6:pthread_mutex_destroy +libc.so.6:pthread_mutex_init +libc.so.6:pthread_mutex_lock +libc.so.6:pthread_mutex_unlock +libc.so.6:pthread_mutexattr_destroy +libc.so.6:pthread_mutexattr_init +libc.so.6:pthread_mutexattr_settype +libc.so.6:pthread_once +libc.so.6:pthread_self +libc.so.6:pthread_setspecific +libc.so.6:putc +libc.so.6:puts +libc.so.6:qsort +libc.so.6:read +libc.so.6:readdir +libc.so.6:readv +libc.so.6:realloc +libc.so.6:recv +libc.so.6:recvmsg +libc.so.6:regcomp +libc.so.6:regerror +libc.so.6:regexec +libc.so.6:regfree +libc.so.6:rename +libc.so.6:renameat +libc.so.6:select +libc.so.6:send +libc.so.6:sendfile +libc.so.6:sendmsg +libc.so.6:setsid +libc.so.6:setsockopt +libc.so.6:shutdown +libc.so.6:sigaction +libc.so.6:sigdelset +libc.so.6:sigemptyset +libc.so.6:sigfillset +libc.so.6:sigismember +libc.so.6:sigprocmask +libc.so.6:snprintf +libc.so.6:socket +libc.so.6:socketpair +libc.so.6:srand48 +libc.so.6:stat +libc.so.6:stderr +libc.so.6:stdin +libc.so.6:stdout +libc.so.6:stpcpy +libc.so.6:strcasecmp +libc.so.6:strchr +libc.so.6:strcmp +libc.so.6:strcpy +libc.so.6:strcspn +libc.so.6:strdup +libc.so.6:strerror +libc.so.6:strftime +libc.so.6:strlen +libc.so.6:strncasecmp +libc.so.6:strncmp +libc.so.6:strncpy +libc.so.6:strndup +libc.so.6:strpbrk +libc.so.6:strrchr +libc.so.6:strstr +libc.so.6:strtod +libc.so.6:time +libc.so.6:umask +libc.so.6:unlink +libc.so.6:unlinkat +libc.so.6:unsetenv +libc.so.6:utimes +libc.so.6:waitpid +libc.so.6:write +libcrypto.so.3:EVP_sha1 +libcrypto.so.3:EVP_sha256 +libcrypto.so.3:HMAC +libcrypto.so.3:SHA256 +libcurl.so.4:curl_easy_cleanup +libcurl.so.4:curl_easy_duphandle +libcurl.so.4:curl_easy_getinfo +libcurl.so.4:curl_easy_init +libcurl.so.4:curl_easy_pause +libcurl.so.4:curl_easy_perform +libcurl.so.4:curl_easy_reset +libcurl.so.4:curl_easy_setopt +libcurl.so.4:curl_easy_strerror +libcurl.so.4:curl_global_cleanup +libcurl.so.4:curl_global_init +libcurl.so.4:curl_multi_add_handle +libcurl.so.4:curl_multi_assign +libcurl.so.4:curl_multi_cleanup +libcurl.so.4:curl_multi_fdset +libcurl.so.4:curl_multi_info_read +libcurl.so.4:curl_multi_init +libcurl.so.4:curl_multi_perform +libcurl.so.4:curl_multi_remove_handle +libcurl.so.4:curl_multi_setopt +libcurl.so.4:curl_multi_socket_action +libcurl.so.4:curl_multi_strerror +libcurl.so.4:curl_multi_timeout +libcurl.so.4:curl_share_cleanup +libcurl.so.4:curl_share_init +libcurl.so.4:curl_share_setopt +libcurl.so.4:curl_slist_append +libcurl.so.4:curl_slist_free_all +libcurl.so.4:curl_version_info +liblzma.so.5:lzma_code +liblzma.so.5:lzma_easy_buffer_encode +liblzma.so.5:lzma_easy_decoder_memusage +liblzma.so.5:lzma_end +liblzma.so.5:lzma_stream_buffer_bound +liblzma.so.5:lzma_stream_decoder +libm.so.6:exp +libm.so.6:lgamma +libm.so.6:log +libm.so.6:log1p +libm.so.6:pow +libm.so.6:sqrt +libz.so.1:crc32 +libz.so.1:deflate +libz.so.1:deflateEnd +libz.so.1:deflateInit2_ +libz.so.1:inflate +libz.so.1:inflateEnd +libz.so.1:inflateInit2_ +libz.so.1:inflateReset diff --git a/packages/h/htslib/monitoring.yaml b/packages/h/htslib/monitoring.yaml new file mode 100644 index 000000000000..632bcfae99fb --- /dev/null +++ b/packages/h/htslib/monitoring.yaml @@ -0,0 +1,7 @@ +releases: + id: 13500 + rss: https://github.com/samtools/htslib/releases.atom +security: + cpe: + - vendor: htslib + product: htslib diff --git a/packages/h/htslib/package.yml b/packages/h/htslib/package.yml new file mode 100644 index 000000000000..ff271dc6b5eb --- /dev/null +++ b/packages/h/htslib/package.yml @@ -0,0 +1,24 @@ +name : htslib +version : 1.22.1 +release : 1 +source : + - https://github.com/samtools/htslib/releases/download/1.22.1/htslib-1.22.1.tar.bz2 : 3dfa6eeb71db719907fe3ef7c72cb2ec9965b20b58036547c858c89b58c342f7 +homepage : https://github.com/samtools/htslib +license : MIT +component : programming.library +summary : C library for high-throughput sequencing data formats +description: | + HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. +builddeps : + - pkgconfig(bzip2) + - pkgconfig(libcrypto) + - pkgconfig(libcurl) + - pkgconfig(liblzma) + - pkgconfig(zlib) + +setup : | + %configure +build : | + %make +install : | + %make_install diff --git a/packages/h/htslib/pspec_x86_64.xml b/packages/h/htslib/pspec_x86_64.xml new file mode 100644 index 000000000000..eaa6b146bb2d --- /dev/null +++ b/packages/h/htslib/pspec_x86_64.xml @@ -0,0 +1,93 @@ + + + htslib + https://github.com/samtools/htslib + + Lea Evers + lea.evers@mailbox.org + + GPL-2.0-or-later + programming.library + 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, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. + + https://sources.getsol.us/README.Solus + + + htslib + 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, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. + + programming.library + + /usr/bin/annot-tsv + /usr/bin/bgzip + /usr/bin/htsfile + /usr/bin/ref-cache + /usr/bin/tabix + /usr/lib64/libhts.so.1.22.1 + /usr/lib64/libhts.so.3 + /usr/share/man/man1/annot-tsv.1 + /usr/share/man/man1/bgzip.1 + /usr/share/man/man1/htsfile.1 + /usr/share/man/man1/ref-cache.1 + /usr/share/man/man1/tabix.1 + /usr/share/man/man5/faidx.5 + /usr/share/man/man5/sam.5 + /usr/share/man/man5/vcf.5 + /usr/share/man/man7/htslib-s3-plugin.7 + + + + htslib-devel + Development files for htslib + HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. + + programming.devel + + htslib + + + /usr/include/htslib/bgzf.h + /usr/include/htslib/cram.h + /usr/include/htslib/faidx.h + /usr/include/htslib/hfile.h + /usr/include/htslib/hts.h + /usr/include/htslib/hts_defs.h + /usr/include/htslib/hts_endian.h + /usr/include/htslib/hts_expr.h + /usr/include/htslib/hts_log.h + /usr/include/htslib/hts_os.h + /usr/include/htslib/kbitset.h + /usr/include/htslib/kfunc.h + /usr/include/htslib/khash.h + /usr/include/htslib/khash_str2int.h + /usr/include/htslib/klist.h + /usr/include/htslib/knetfile.h + /usr/include/htslib/kroundup.h + /usr/include/htslib/kseq.h + /usr/include/htslib/ksort.h + /usr/include/htslib/kstring.h + /usr/include/htslib/regidx.h + /usr/include/htslib/sam.h + /usr/include/htslib/synced_bcf_reader.h + /usr/include/htslib/tbx.h + /usr/include/htslib/thread_pool.h + /usr/include/htslib/vcf.h + /usr/include/htslib/vcf_sweep.h + /usr/include/htslib/vcfutils.h + /usr/lib64/libhts.a + /usr/lib64/libhts.so + /usr/lib64/pkgconfig/htslib.pc + + + + + 2025-07-15 + 1.22.1 + Packaging update + Lea Evers + lea.evers@mailbox.org + + + \ No newline at end of file diff --git a/packages/s/samtools/abi_used_libs b/packages/s/samtools/abi_used_libs new file mode 100644 index 000000000000..751af9f9f75b --- /dev/null +++ b/packages/s/samtools/abi_used_libs @@ -0,0 +1,5 @@ +libc.so.6 +libhts.so.3 +libm.so.6 +libncursesw.so.6 +libz.so.1 diff --git a/packages/s/samtools/abi_used_symbols b/packages/s/samtools/abi_used_symbols new file mode 100644 index 000000000000..63726a392025 --- /dev/null +++ b/packages/s/samtools/abi_used_symbols @@ -0,0 +1,389 @@ +libc.so.6:__assert_fail +libc.so.6:__ctype_b_loc +libc.so.6:__ctype_tolower_loc +libc.so.6:__ctype_toupper_loc +libc.so.6:__errno_location +libc.so.6:__fprintf_chk +libc.so.6:__isoc23_fscanf +libc.so.6:__isoc23_sscanf +libc.so.6:__isoc23_strtol +libc.so.6:__isoc23_strtoll +libc.so.6:__isoc23_strtoul +libc.so.6:__isoc23_strtoull +libc.so.6:__libc_start_main +libc.so.6:__memcpy_chk +libc.so.6:__printf_chk +libc.so.6:__snprintf_chk +libc.so.6:__sprintf_chk +libc.so.6:__stack_chk_fail +libc.so.6:__stpcpy_chk +libc.so.6:__strcat_chk +libc.so.6:__strcpy_chk +libc.so.6:__strncpy_chk +libc.so.6:__vfprintf_chk +libc.so.6:__vsnprintf_chk +libc.so.6:abort +libc.so.6:calloc +libc.so.6:clock +libc.so.6:drand48 +libc.so.6:dup +libc.so.6:exit +libc.so.6:fclose +libc.so.6:fdopen +libc.so.6:feof +libc.so.6:ferror +libc.so.6:fflush +libc.so.6:fgets +libc.so.6:fileno +libc.so.6:fopen +libc.so.6:fputc +libc.so.6:fputs +libc.so.6:fread +libc.so.6:free +libc.so.6:fwrite +libc.so.6:getenv +libc.so.6:getopt +libc.so.6:getopt_long +libc.so.6:getpid +libc.so.6:ioctl +libc.so.6:isatty +libc.so.6:lrand48 +libc.so.6:malloc +libc.so.6:memchr +libc.so.6:memcmp +libc.so.6:memcpy +libc.so.6:memmove +libc.so.6:memset +libc.so.6:mkstemp +libc.so.6:nanosleep +libc.so.6:open +libc.so.6:optarg +libc.so.6:opterr +libc.so.6:optind +libc.so.6:optopt +libc.so.6:pclose +libc.so.6:perror +libc.so.6:popen +libc.so.6:pthread_attr_init +libc.so.6:pthread_attr_setdetachstate +libc.so.6:pthread_create +libc.so.6:pthread_join +libc.so.6:putc +libc.so.6:putchar +libc.so.6:puts +libc.so.6:qsort +libc.so.6:rand +libc.so.6:realloc +libc.so.6:realpath +libc.so.6:regcomp +libc.so.6:regerror +libc.so.6:regexec +libc.so.6:regfree +libc.so.6:rewind +libc.so.6:srand +libc.so.6:stat +libc.so.6:stderr +libc.so.6:stdin +libc.so.6:stdout +libc.so.6:strcasecmp +libc.so.6:strchr +libc.so.6:strcmp +libc.so.6:strcpy +libc.so.6:strcspn +libc.so.6:strdup +libc.so.6:strerror +libc.so.6:strlen +libc.so.6:strncmp +libc.so.6:strncpy +libc.so.6:strrchr +libc.so.6:strspn +libc.so.6:strstr +libc.so.6:strtod +libc.so.6:strtok_r +libc.so.6:time +libc.so.6:unlink +libhts.so.3:bam_aux2A +libhts.so.3:bam_aux2Z +libhts.so.3:bam_aux2f +libhts.so.3:bam_aux2i +libhts.so.3:bam_aux_append +libhts.so.3:bam_aux_del +libhts.so.3:bam_aux_first +libhts.so.3:bam_aux_get +libhts.so.3:bam_aux_next +libhts.so.3:bam_aux_remove +libhts.so.3:bam_aux_update_int +libhts.so.3:bam_aux_update_str +libhts.so.3:bam_cigar2qlen +libhts.so.3:bam_cigar2rlen +libhts.so.3:bam_copy1 +libhts.so.3:bam_destroy1 +libhts.so.3:bam_dup1 +libhts.so.3:bam_endpos +libhts.so.3:bam_flag2str +libhts.so.3:bam_hdr_read +libhts.so.3:bam_hdr_write +libhts.so.3:bam_init1 +libhts.so.3:bam_mods_at_qpos +libhts.so.3:bam_mplp64_auto +libhts.so.3:bam_mplp_auto +libhts.so.3:bam_mplp_constructor +libhts.so.3:bam_mplp_destroy +libhts.so.3:bam_mplp_destructor +libhts.so.3:bam_mplp_init +libhts.so.3:bam_mplp_init_overlaps +libhts.so.3:bam_mplp_set_maxcnt +libhts.so.3:bam_next_basemod +libhts.so.3:bam_parse_basemod +libhts.so.3:bam_plp64_next +libhts.so.3:bam_plp_auto +libhts.so.3:bam_plp_destroy +libhts.so.3:bam_plp_init +libhts.so.3:bam_plp_insertion +libhts.so.3:bam_plp_insertion_mod +libhts.so.3:bam_plp_push +libhts.so.3:bam_plp_reset +libhts.so.3:bam_set1 +libhts.so.3:bam_str2flag +libhts.so.3:bgzf_close +libhts.so.3:bgzf_dopen +libhts.so.3:bgzf_flush +libhts.so.3:bgzf_index_build_init +libhts.so.3:bgzf_index_dump +libhts.so.3:bgzf_open +libhts.so.3:bgzf_raw_read +libhts.so.3:bgzf_raw_write +libhts.so.3:bgzf_thread_pool +libhts.so.3:bgzf_write +libhts.so.3:cram_block_append +libhts.so.3:cram_block_get_comp_size +libhts.so.3:cram_block_get_content_id +libhts.so.3:cram_block_get_data +libhts.so.3:cram_block_get_method +libhts.so.3:cram_block_get_offset +libhts.so.3:cram_block_get_uncomp_size +libhts.so.3:cram_block_set_comp_size +libhts.so.3:cram_block_set_offset +libhts.so.3:cram_block_size +libhts.so.3:cram_block_update_size +libhts.so.3:cram_cid2ds_free +libhts.so.3:cram_cid2ds_query +libhts.so.3:cram_compress_block +libhts.so.3:cram_container_get_coords +libhts.so.3:cram_container_get_landmarks +libhts.so.3:cram_container_get_length +libhts.so.3:cram_container_get_num_bases +libhts.so.3:cram_container_get_num_blocks +libhts.so.3:cram_container_get_num_records +libhts.so.3:cram_container_is_empty +libhts.so.3:cram_container_num2offset +libhts.so.3:cram_container_offset2num +libhts.so.3:cram_container_set_landmarks +libhts.so.3:cram_container_set_length +libhts.so.3:cram_container_set_num_blocks +libhts.so.3:cram_container_size +libhts.so.3:cram_copy_slice +libhts.so.3:cram_decode_compression_header +libhts.so.3:cram_decode_slice_header +libhts.so.3:cram_describe_encodings +libhts.so.3:cram_expand_method +libhts.so.3:cram_fd_get_fp +libhts.so.3:cram_fd_get_header +libhts.so.3:cram_fd_set_header +libhts.so.3:cram_filter_container +libhts.so.3:cram_free_block +libhts.so.3:cram_free_compression_header +libhts.so.3:cram_free_container +libhts.so.3:cram_free_slice_header +libhts.so.3:cram_get_refs +libhts.so.3:cram_index_extents +libhts.so.3:cram_major_vers +libhts.so.3:cram_minor_vers +libhts.so.3:cram_new_block +libhts.so.3:cram_num_containers +libhts.so.3:cram_num_containers_between +libhts.so.3:cram_read_block +libhts.so.3:cram_read_container +libhts.so.3:cram_seek +libhts.so.3:cram_set_option +libhts.so.3:cram_slice_hdr_get_coords +libhts.so.3:cram_slice_hdr_get_embed_ref_id +libhts.so.3:cram_slice_hdr_get_num_blocks +libhts.so.3:cram_store_container +libhts.so.3:cram_transcode_rg +libhts.so.3:cram_uncompress_block +libhts.so.3:cram_update_cid2ds_map +libhts.so.3:cram_write_block +libhts.so.3:cram_write_container +libhts.so.3:errmod_cal +libhts.so.3:errmod_destroy +libhts.so.3:errmod_init +libhts.so.3:fai_build3 +libhts.so.3:fai_destroy +libhts.so.3:fai_fetch64 +libhts.so.3:fai_fetchqual64 +libhts.so.3:fai_line_length +libhts.so.3:fai_load +libhts.so.3:fai_load3 +libhts.so.3:fai_load3_format +libhts.so.3:fai_parse_region +libhts.so.3:fai_path +libhts.so.3:fai_thread_pool +libhts.so.3:faidx_fetch_seq64 +libhts.so.3:faidx_has_seq +libhts.so.3:faidx_iseq +libhts.so.3:faidx_nseq +libhts.so.3:faidx_seq_len +libhts.so.3:hclose +libhts.so.3:hclose_abruptly +libhts.so.3:hdopen +libhts.so.3:hfile_list_plugins +libhts.so.3:hfile_list_schemes +libhts.so.3:hfile_set_blksize +libhts.so.3:hgets +libhts.so.3:hopen +libhts.so.3:hseek +libhts.so.3:hts_base_mod_state_alloc +libhts.so.3:hts_base_mod_state_free +libhts.so.3:hts_check_EOF +libhts.so.3:hts_close +libhts.so.3:hts_crc32 +libhts.so.3:hts_detect_format2 +libhts.so.3:hts_drand48 +libhts.so.3:hts_feature_string +libhts.so.3:hts_filter_free +libhts.so.3:hts_filter_init +libhts.so.3:hts_flush +libhts.so.3:hts_format_file_extension +libhts.so.3:hts_get_format +libhts.so.3:hts_get_log_level +libhts.so.3:hts_getline +libhts.so.3:hts_hopen +libhts.so.3:hts_idx_destroy +libhts.so.3:hts_idx_get_n_no_coor +libhts.so.3:hts_idx_get_stat +libhts.so.3:hts_itr_destroy +libhts.so.3:hts_itr_multi_next +libhts.so.3:hts_itr_next +libhts.so.3:hts_log +libhts.so.3:hts_md5_destroy +libhts.so.3:hts_md5_final +libhts.so.3:hts_md5_hex +libhts.so.3:hts_md5_init +libhts.so.3:hts_md5_reset +libhts.so.3:hts_md5_update +libhts.so.3:hts_open +libhts.so.3:hts_open_format +libhts.so.3:hts_opt_add +libhts.so.3:hts_opt_free +libhts.so.3:hts_parse_format +libhts.so.3:hts_parse_reg +libhts.so.3:hts_readlines +libhts.so.3:hts_realloc_or_die +libhts.so.3:hts_reglist_free +libhts.so.3:hts_resize_array_ +libhts.so.3:hts_set_fai_filename +libhts.so.3:hts_set_log_level +libhts.so.3:hts_set_opt +libhts.so.3:hts_set_thread_pool +libhts.so.3:hts_set_threads +libhts.so.3:hts_srand48 +libhts.so.3:hts_test_feature +libhts.so.3:hts_tpool_delete_result +libhts.so.3:hts_tpool_destroy +libhts.so.3:hts_tpool_dispatch2 +libhts.so.3:hts_tpool_init +libhts.so.3:hts_tpool_next_result +libhts.so.3:hts_tpool_process_destroy +libhts.so.3:hts_tpool_process_init +libhts.so.3:hts_tpool_result_data +libhts.so.3:hts_tpool_worker_id +libhts.so.3:hts_verbose +libhts.so.3:hts_version +libhts.so.3:hwrite2 +libhts.so.3:int32_put_blk +libhts.so.3:kgetline +libhts.so.3:ksprintf +libhts.so.3:sam_cap_mapq +libhts.so.3:sam_format1 +libhts.so.3:sam_hdr_add_line +libhts.so.3:sam_hdr_add_lines +libhts.so.3:sam_hdr_add_pg +libhts.so.3:sam_hdr_count_lines +libhts.so.3:sam_hdr_destroy +libhts.so.3:sam_hdr_dup +libhts.so.3:sam_hdr_find_line_id +libhts.so.3:sam_hdr_find_line_pos +libhts.so.3:sam_hdr_find_tag_id +libhts.so.3:sam_hdr_find_tag_pos +libhts.so.3:sam_hdr_init +libhts.so.3:sam_hdr_length +libhts.so.3:sam_hdr_line_index +libhts.so.3:sam_hdr_line_name +libhts.so.3:sam_hdr_name2tid +libhts.so.3:sam_hdr_nref +libhts.so.3:sam_hdr_parse +libhts.so.3:sam_hdr_read +libhts.so.3:sam_hdr_remove_except +libhts.so.3:sam_hdr_remove_line_id +libhts.so.3:sam_hdr_remove_lines +libhts.so.3:sam_hdr_remove_tag_id +libhts.so.3:sam_hdr_str +libhts.so.3:sam_hdr_tid2len +libhts.so.3:sam_hdr_tid2name +libhts.so.3:sam_hdr_update_line +libhts.so.3:sam_hdr_write +libhts.so.3:sam_idx_init +libhts.so.3:sam_idx_save +libhts.so.3:sam_index_build3 +libhts.so.3:sam_index_load +libhts.so.3:sam_index_load2 +libhts.so.3:sam_index_load3 +libhts.so.3:sam_itr_queryi +libhts.so.3:sam_itr_querys +libhts.so.3:sam_itr_regarray +libhts.so.3:sam_itr_regions +libhts.so.3:sam_open_mode +libhts.so.3:sam_parse_region +libhts.so.3:sam_passes_filter +libhts.so.3:sam_prob_realn +libhts.so.3:sam_read1 +libhts.so.3:sam_write1 +libhts.so.3:seq_nt16_int +libhts.so.3:seq_nt16_str +libhts.so.3:seq_nt16_table +libhts.so.3:stringify_argv +libm.so.6:exp +libm.so.6:log +libm.so.6:pow +libm.so.6:round +libm.so.6:sqrt +libncursesw.so.6:cbreak +libncursesw.so.6:delwin +libncursesw.so.6:endwin +libncursesw.so.6:getmaxx +libncursesw.so.6:getmaxy +libncursesw.so.6:init_pair +libncursesw.so.6:initscr +libncursesw.so.6:keypad +libncursesw.so.6:mvwprintw +libncursesw.so.6:newwin +libncursesw.so.6:noecho +libncursesw.so.6:set_escdelay +libncursesw.so.6:start_color +libncursesw.so.6:stdscr +libncursesw.so.6:vw_printw +libncursesw.so.6:waddch +libncursesw.so.6:wattr_off +libncursesw.so.6:wattr_on +libncursesw.so.6:wborder +libncursesw.so.6:wclear +libncursesw.so.6:wgetch +libncursesw.so.6:wmove +libncursesw.so.6:wrefresh +libz.so.1:crc32 +libz.so.1:gzclose +libz.so.1:gzdopen +libz.so.1:gzeof +libz.so.1:gzopen +libz.so.1:gzread diff --git a/packages/s/samtools/monitoring.yaml b/packages/s/samtools/monitoring.yaml new file mode 100644 index 000000000000..2aa21b5501ff --- /dev/null +++ b/packages/s/samtools/monitoring.yaml @@ -0,0 +1,7 @@ +releases: + id: 4759 + rss: https://github.com/samtools/samtools/releases.atom +security: + cpe: + - vendor: samtools + product: htsjdk diff --git a/packages/s/samtools/package.yml b/packages/s/samtools/package.yml new file mode 100644 index 000000000000..30725e4ef25f --- /dev/null +++ b/packages/s/samtools/package.yml @@ -0,0 +1,21 @@ +name : samtools +version : 1.22.1 +release : 1 +source : + - https://github.com/samtools/samtools/releases/download/1.22.1/samtools-1.22.1.tar.bz2 : 02aa5cd0ba52e06c2080054e059d7d77a885dfe9717c31cd89dfe7a4047eda0e +homepage : https://www.htslib.org/ +license : MIT +component : programming.tools +summary : Tools for manipulating SAM/BAM/CRAM sequencing data +description: | + Samtools is a suite of programs for interacting with high-throughput sequencing data. +builddeps : + - pkgconfig(htslib) + - pkgconfig(ncurses) + - pkgconfig(zlib) +setup : | + %configure --with-htslib=system +build : | + %make +install : | + %make_install diff --git a/packages/s/samtools/pspec_x86_64.xml b/packages/s/samtools/pspec_x86_64.xml new file mode 100644 index 000000000000..9e07e729d6f0 --- /dev/null +++ b/packages/s/samtools/pspec_x86_64.xml @@ -0,0 +1,99 @@ + + + samtools + https://www.htslib.org/ + + Lea Evers + lea.evers@mailbox.org + + MIT + programming.tools + Tools for manipulating SAM/BAM/CRAM sequencing data + Samtools is a suite of programs for interacting with high-throughput sequencing data. + + https://sources.getsol.us/README.Solus + + + samtools + Tools for manipulating SAM/BAM/CRAM sequencing data + Samtools is a suite of programs for interacting with high-throughput sequencing data. + + programming.tools + + /usr/bin/ace2sam + /usr/bin/blast2sam.pl + /usr/bin/bowtie2sam.pl + /usr/bin/export2sam.pl + /usr/bin/fasta-sanitize.pl + /usr/bin/interpolate_sam.pl + /usr/bin/maq2sam-long + /usr/bin/maq2sam-short + /usr/bin/md5fa + /usr/bin/md5sum-lite + /usr/bin/novo2sam.pl + /usr/bin/plot-ampliconstats + /usr/bin/plot-bamstats + /usr/bin/psl2sam.pl + /usr/bin/sam2vcf.pl + /usr/bin/samtools + /usr/bin/samtools.pl + /usr/bin/seq_cache_populate.pl + /usr/bin/soap2sam.pl + /usr/bin/wgsim + /usr/bin/wgsim_eval.pl + /usr/bin/zoom2sam.pl + /usr/share/man/man1/samtools-addreplacerg.1 + /usr/share/man/man1/samtools-ampliconclip.1 + /usr/share/man/man1/samtools-ampliconstats.1 + /usr/share/man/man1/samtools-bedcov.1 + /usr/share/man/man1/samtools-calmd.1 + /usr/share/man/man1/samtools-cat.1 + /usr/share/man/man1/samtools-checksum.1 + /usr/share/man/man1/samtools-collate.1 + /usr/share/man/man1/samtools-consensus.1 + /usr/share/man/man1/samtools-coverage.1 + /usr/share/man/man1/samtools-cram-size.1 + /usr/share/man/man1/samtools-depad.1 + /usr/share/man/man1/samtools-depth.1 + /usr/share/man/man1/samtools-dict.1 + /usr/share/man/man1/samtools-faidx.1 + /usr/share/man/man1/samtools-fasta.1 + /usr/share/man/man1/samtools-fastq.1 + /usr/share/man/man1/samtools-fixmate.1 + /usr/share/man/man1/samtools-flags.1 + /usr/share/man/man1/samtools-flagstat.1 + /usr/share/man/man1/samtools-fqidx.1 + /usr/share/man/man1/samtools-head.1 + /usr/share/man/man1/samtools-idxstats.1 + /usr/share/man/man1/samtools-import.1 + /usr/share/man/man1/samtools-index.1 + /usr/share/man/man1/samtools-markdup.1 + /usr/share/man/man1/samtools-merge.1 + /usr/share/man/man1/samtools-mpileup.1 + /usr/share/man/man1/samtools-phase.1 + /usr/share/man/man1/samtools-quickcheck.1 + /usr/share/man/man1/samtools-reference.1 + /usr/share/man/man1/samtools-reheader.1 + /usr/share/man/man1/samtools-reset.1 + /usr/share/man/man1/samtools-rmdup.1 + /usr/share/man/man1/samtools-samples.1 + /usr/share/man/man1/samtools-sort.1 + /usr/share/man/man1/samtools-split.1 + /usr/share/man/man1/samtools-stats.1 + /usr/share/man/man1/samtools-targetcut.1 + /usr/share/man/man1/samtools-tview.1 + /usr/share/man/man1/samtools-view.1 + /usr/share/man/man1/samtools.1 + /usr/share/man/man1/wgsim.1 + + + + + 2025-07-15 + 1.22.1 + Packaging update + Lea Evers + lea.evers@mailbox.org + + + \ No newline at end of file