From 7d56a8f23a79fb2aa75d32120d3b5584ce467854 Mon Sep 17 00:00:00 2001 From: Lea Evers Date: Tue, 26 Aug 2025 13:33:07 +0200 Subject: [PATCH 1/3] HTSlib: Add at 1.22.1 --- common/CI/config.yaml | 1 + packages/h/htslib/abi_libs | 1 + packages/h/htslib/abi_symbols | 616 +++++++++++++++++++++++++++++ packages/h/htslib/abi_used_libs | 7 + packages/h/htslib/abi_used_symbols | 242 ++++++++++++ packages/h/htslib/monitoring.yaml | 7 + packages/h/htslib/package.yml | 24 ++ packages/h/htslib/pspec_x86_64.xml | 93 +++++ 8 files changed, 991 insertions(+) create mode 100644 packages/h/htslib/abi_libs create mode 100644 packages/h/htslib/abi_symbols create mode 100644 packages/h/htslib/abi_used_libs create mode 100644 packages/h/htslib/abi_used_symbols create mode 100644 packages/h/htslib/monitoring.yaml create mode 100644 packages/h/htslib/package.yml create mode 100644 packages/h/htslib/pspec_x86_64.xml 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/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 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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 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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 From 9277487142112514a72dadc83649af2983bcbc4c Mon Sep 17 00:00:00 2001 From: Lea Evers Date: Tue, 26 Aug 2025 13:44:39 +0200 Subject: [PATCH 2/3] bcftools: add at 1.22 --- packages/b/bcftools/abi_libs | 42 + packages/b/bcftools/abi_symbols | 1239 ++++++++++++++++++++++++++ packages/b/bcftools/abi_used_libs | 5 + packages/b/bcftools/abi_used_symbols | 336 +++++++ packages/b/bcftools/monitoring.yaml | 6 + packages/b/bcftools/package.yml | 20 + packages/b/bcftools/pspec_x86_64.xml | 84 ++ 7 files changed, 1732 insertions(+) create mode 100644 packages/b/bcftools/abi_libs create mode 100644 packages/b/bcftools/abi_symbols create mode 100644 packages/b/bcftools/abi_used_libs create mode 100644 packages/b/bcftools/abi_used_symbols create mode 100644 packages/b/bcftools/monitoring.yaml create mode 100644 packages/b/bcftools/package.yml create mode 100644 packages/b/bcftools/pspec_x86_64.xml 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 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/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 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+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 From 29d480dfa7a987ec2ec66d6603e192b811fdcaf6 Mon Sep 17 00:00:00 2001 From: Lea Evers Date: Tue, 26 Aug 2025 13:53:40 +0200 Subject: [PATCH 3/3] samtools: add at 1.22.1 --- packages/s/samtools/abi_used_libs | 5 + packages/s/samtools/abi_used_symbols | 389 +++++++++++++++++++++++++++ packages/s/samtools/monitoring.yaml | 7 + packages/s/samtools/package.yml | 21 ++ packages/s/samtools/pspec_x86_64.xml | 99 +++++++ 5 files changed, 521 insertions(+) create mode 100644 packages/s/samtools/abi_used_libs create mode 100644 packages/s/samtools/abi_used_symbols create mode 100644 packages/s/samtools/monitoring.yaml create mode 100644 packages/s/samtools/package.yml create mode 100644 packages/s/samtools/pspec_x86_64.xml 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 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+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 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+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 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+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