From nobody Sat Jun 11 14:27:00 2022 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 49B548406E2; Sat, 11 Jun 2022 14:27:01 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4LL0X516trz4tj5; Sat, 11 Jun 2022 14:27:01 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1654957621; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=IB/5kFI4lv8xqaq5AXhS5/6N0aoeGSvmhZGdOBtWZeg=; b=uNcWFBJvp/j6r8NsPUgFRidJ3Riw4lnMmZaR+cl1fhIxxSOxSWXkHYAaE93aIRgIbLmYfl Rts6SM5xVJpp4i5pcwgFXnO3siT2GY9NCXwGQaaIWbEFHT1eLntXHgTOA6Xkod97zqvCot 3pXxkjqOwk004//aGEhxh4+g2xHQ23UulznNIIaMKI2Wo8koos+MYLx0SKPYPBuafOjlNA UGEzlsRZW3mmKbWJlf15QGJf1cLJ3mmFLaxmIWPtTPz3WUie4E7uAfTiv7bPBfLExqpFue 9FHuT42hDdK1P8dh/1mTFZNxxh99eaLAbJoHdI265AUTgxdPjp2bzxOZfrY87g== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id E803F6C8A; Sat, 11 Jun 2022 14:27:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 25BER0lW023547; Sat, 11 Jun 2022 14:27:00 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 25BER0Qv023546; Sat, 11 Jun 2022 14:27:00 GMT (envelope-from git) Date: Sat, 11 Jun 2022 14:27:00 GMT Message-Id: <202206111427.25BER0Qv023546@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 603571cd3226 - main - biology/biolibc: Update to 0.2.3 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 603571cd3226aa0b353aceb61aeaf275b2973c6b Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1654957621; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=IB/5kFI4lv8xqaq5AXhS5/6N0aoeGSvmhZGdOBtWZeg=; b=otIJAkLCPjR88hQGc46DUW0lDhuW5mEzFLakqSNucvhTpt3RgWLoK8JUfkNJ7ysR7+Y3Hh hScMrWr6Q8rjbCC+lSQ5uuJrfE9vgPqQBKCUhoXUnhTnNd+ZcTNPqFAoU5+ZiHSkPvD0sv +W7y/z5LVKKkbIUXg4vFtrrKqwiqQkwDpFqfJQd9Hhj1/McWPqVQaz6a3Ht9TvH9WRgg9x eJggTDeyb+oddAj3uY1OW1V4CsgyZpxDjPn2vb4ULW1ORhP4Wgu/pq91n8ikXBSK+krh1f Si0oTSMnOKgSBQi5Rh6hesNRUG7Zj9dB368ayt396sayIc3wIIv2qm4iP/YjEA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1654957621; a=rsa-sha256; cv=none; b=G8Zi4WtZN7X6/+cJh0z/rmiLW51vDhKrat9YWMwV4xlQKWNaTSTOO8uDdAlkCjc+zxPtiR hyLwnpP+FwL553pMccb87m3kMUL74TlG08JQ0XiX8rR/KF2yEmBKHOmnJGso+6TpVX027/ 1cFmR3vNrwJMwpTOM2RM84X8Ei1Hm9vRL6Yh3GGogMe7vrUMHPiuK7tLyzTx2P2OeyGVB/ NOI8/RZHpWazfma7ZWS7ZlC/5qHh6T8V5Zw8Iy1Tq6aRQDFLtgj1E6qQBSf9Y+kEDenFEi bvzl7hqxc8a7650MA5jNfi9c6PE9TCRmRtK4zS705P8jwqV+SYrj5Fr6KXcrdA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=603571cd3226aa0b353aceb61aeaf275b2973c6b commit 603571cd3226aa0b353aceb61aeaf275b2973c6b Author: Jason W. Bacon AuthorDate: 2022-06-11 14:06:10 +0000 Commit: Jason W. Bacon CommitDate: 2022-06-11 14:26:56 +0000 biology/biolibc: Update to 0.2.3 Expand use of tsv_read_field_malloc() to improve memory efficiency Add SAM bit flag constants Import SAM-GFF compare functions from diffanal Updates for libxtend DSV API changes Numerous minor bug fixes and enhancements Changes: https://github.com/auerlab/biolibc/tags --- biology/biolibc/Makefile | 2 +- biology/biolibc/distinfo | 6 ++--- biology/biolibc/pkg-plist | 59 ++++++++++++++++++++++++++++++++++++++++++----- 3 files changed, 57 insertions(+), 10 deletions(-) diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile index 465f7ea9a665..f828f7e98752 100644 --- a/biology/biolibc/Makefile +++ b/biology/biolibc/Makefile @@ -1,5 +1,5 @@ PORTNAME= biolibc -DISTVERSION= 0.2.2 +DISTVERSION= 0.2.3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo index c319bf83d1ed..32220523e8e5 100644 --- a/biology/biolibc/distinfo +++ b/biology/biolibc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1647347323 -SHA256 (auerlab-biolibc-0.2.2_GH0.tar.gz) = b2d8ef23ce93321cc624fb1c7851e1353b12ac89ec0bac6a4f9ae0f3648869e4 -SIZE (auerlab-biolibc-0.2.2_GH0.tar.gz) = 129251 +TIMESTAMP = 1654950759 +SHA256 (auerlab-biolibc-0.2.3_GH0.tar.gz) = f3c99684a1b8a54497b190e9057e509d9a669295300025ead2ef29aa148ad750 +SIZE (auerlab-biolibc-0.2.3_GH0.tar.gz) = 140008 diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist index c0167ab0df06..dfbe6a49d997 100644 --- a/biology/biolibc/pkg-plist +++ b/biology/biolibc/pkg-plist @@ -104,11 +104,15 @@ man/man3/BL_FASTX_UNION.3.gz man/man3/BL_FASTX_}.3.gz man/man3/BL_GFF_ATTRIBUTES.3.gz man/man3/BL_GFF_ATTRIBUTES_AE.3.gz +man/man3/BL_GFF_ATTRIBUTES_ARRAY_SIZE.3.gz +man/man3/BL_GFF_ATTRIBUTES_LEN.3.gz man/man3/BL_GFF_END.3.gz man/man3/BL_GFF_FEATURE_ID.3.gz man/man3/BL_GFF_FEATURE_ID_AE.3.gz man/man3/BL_GFF_FEATURE_NAME.3.gz man/man3/BL_GFF_FEATURE_NAME_AE.3.gz +man/man3/BL_GFF_FEATURE_PARENT.3.gz +man/man3/BL_GFF_FEATURE_PARENT_AE.3.gz man/man3/BL_GFF_FILE_POS.3.gz man/man3/BL_GFF_INDEX_ARRAY_SIZE.3.gz man/man3/BL_GFF_INDEX_COUNT.3.gz @@ -166,6 +170,8 @@ man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3.gz man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3.gz man/man3/BL_SAM_CIGAR.3.gz man/man3/BL_SAM_CIGAR_AE.3.gz +man/man3/BL_SAM_CIGAR_ARRAY_SIZE.3.gz +man/man3/BL_SAM_CIGAR_LEN.3.gz man/man3/BL_SAM_FLAG.3.gz man/man3/BL_SAM_MAPQ.3.gz man/man3/BL_SAM_PNEXT.3.gz @@ -174,6 +180,7 @@ man/man3/BL_SAM_QNAME.3.gz man/man3/BL_SAM_QNAME_AE.3.gz man/man3/BL_SAM_QUAL.3.gz man/man3/BL_SAM_QUAL_AE.3.gz +man/man3/BL_SAM_QUAL_ARRAY_SIZE.3.gz man/man3/BL_SAM_QUAL_LEN.3.gz man/man3/BL_SAM_RNAME.3.gz man/man3/BL_SAM_RNAME_AE.3.gz @@ -181,6 +188,7 @@ man/man3/BL_SAM_RNEXT.3.gz man/man3/BL_SAM_RNEXT_AE.3.gz man/man3/BL_SAM_SEQ.3.gz man/man3/BL_SAM_SEQ_AE.3.gz +man/man3/BL_SAM_SEQ_ARRAY_SIZE.3.gz man/man3/BL_SAM_SEQ_LEN.3.gz man/man3/BL_SAM_TLEN.3.gz man/man3/BL_VCF_ALT.3.gz @@ -192,16 +200,22 @@ man/man3/BL_VCF_FILTER.3.gz man/man3/BL_VCF_FILTER_AE.3.gz man/man3/BL_VCF_FORMAT.3.gz man/man3/BL_VCF_FORMAT_AE.3.gz +man/man3/BL_VCF_FORMAT_ARRAY_SIZE.3.gz man/man3/BL_VCF_FORMAT_LEN.3.gz -man/man3/BL_VCF_FORMAT_MAX.3.gz man/man3/BL_VCF_ID.3.gz man/man3/BL_VCF_ID_AE.3.gz man/man3/BL_VCF_INFO.3.gz man/man3/BL_VCF_INFO_AE.3.gz +man/man3/BL_VCF_INFO_ARRAY_SIZE.3.gz man/man3/BL_VCF_INFO_LEN.3.gz -man/man3/BL_VCF_INFO_MAX.3.gz man/man3/BL_VCF_MULTI_SAMPLES.3.gz man/man3/BL_VCF_MULTI_SAMPLES_AE.3.gz +man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES.3.gz +man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES_AE.3.gz +man/man3/BL_VCF_MULTI_SAMPLE_COUNT.3.gz +man/man3/BL_VCF_MULTI_SAMPLE_LENS.3.gz +man/man3/BL_VCF_MULTI_SAMPLE_LENS_AE.3.gz +man/man3/BL_VCF_MULTI_SAMPLE_POINTER_ARRAY_SIZE.3.gz man/man3/BL_VCF_OTHER_COUNT.3.gz man/man3/BL_VCF_PHREDS.3.gz man/man3/BL_VCF_PHREDS_AE.3.gz @@ -213,9 +227,13 @@ man/man3/BL_VCF_QUAL_AE.3.gz man/man3/BL_VCF_REF.3.gz man/man3/BL_VCF_REF_AE.3.gz man/man3/BL_VCF_REF_COUNT.3.gz +man/man3/BL_VCF_SAMPLE_ARRAY_SIZE.3.gz +man/man3/BL_VCF_SAMPLE_LEN.3.gz man/man3/BL_VCF_SAMPLE_MAX.3.gz man/man3/BL_VCF_SINGLE_SAMPLE.3.gz man/man3/BL_VCF_SINGLE_SAMPLE_AE.3.gz +man/man3/BL_VCF_SINGLE_SAMPLE_ARRAY_SIZE.3.gz +man/man3/BL_VCF_SINGLE_SAMPLE_LEN.3.gz man/man3/biolibc.3.gz man/man3/bl_align_map_seq_exact.3.gz man/man3/bl_align_map_seq_sub.3.gz @@ -303,7 +321,9 @@ man/man3/bl_fastx_set_fasta.3.gz man/man3/bl_fastx_set_fastq.3.gz man/man3/bl_fastx_set_format.3.gz man/man3/bl_fastx_write.3.gz +man/man3/bl_gff_copy.3.gz man/man3/bl_gff_copy_header.3.gz +man/man3/bl_gff_dup.3.gz man/man3/bl_gff_extract_attribute.3.gz man/man3/bl_gff_free.3.gz man/man3/bl_gff_index_add.3.gz @@ -324,9 +344,13 @@ man/man3/bl_gff_index_set_start_ae.3.gz man/man3/bl_gff_index_set_start_cpy.3.gz man/man3/bl_gff_init.3.gz man/man3/bl_gff_read.3.gz +man/man3/bl_gff_sam_cmp.3.gz +man/man3/bl_gff_sam_overlap.3.gz man/man3/bl_gff_set_attributes.3.gz man/man3/bl_gff_set_attributes_ae.3.gz +man/man3/bl_gff_set_attributes_array_size.3.gz man/man3/bl_gff_set_attributes_cpy.3.gz +man/man3/bl_gff_set_attributes_len.3.gz man/man3/bl_gff_set_end.3.gz man/man3/bl_gff_set_feature_id.3.gz man/man3/bl_gff_set_feature_id_ae.3.gz @@ -334,6 +358,9 @@ man/man3/bl_gff_set_feature_id_cpy.3.gz man/man3/bl_gff_set_feature_name.3.gz man/man3/bl_gff_set_feature_name_ae.3.gz man/man3/bl_gff_set_feature_name_cpy.3.gz +man/man3/bl_gff_set_feature_parent.3.gz +man/man3/bl_gff_set_feature_parent_ae.3.gz +man/man3/bl_gff_set_feature_parent_cpy.3.gz man/man3/bl_gff_set_file_pos.3.gz man/man3/bl_gff_set_gene_name_cpy.3.gz man/man3/bl_gff_set_phase.3.gz @@ -399,11 +426,19 @@ man/man3/bl_sam_buff_set_trailing_alignments.3.gz man/man3/bl_sam_buff_set_unmapped_alignments.3.gz man/man3/bl_sam_buff_shift.3.gz man/man3/bl_sam_copy.3.gz +man/man3/bl_sam_copy_header.3.gz +man/man3/bl_sam_fclose.3.gz +man/man3/bl_sam_fopen.3.gz man/man3/bl_sam_free.3.gz +man/man3/bl_sam_gff_cmp.3.gz +man/man3/bl_sam_gff_overlap.3.gz man/man3/bl_sam_init.3.gz man/man3/bl_sam_read.3.gz +man/man3/bl_sam_set_cigar.3.gz man/man3/bl_sam_set_cigar_ae.3.gz +man/man3/bl_sam_set_cigar_array_size.3.gz man/man3/bl_sam_set_cigar_cpy.3.gz +man/man3/bl_sam_set_cigar_len.3.gz man/man3/bl_sam_set_flag.3.gz man/man3/bl_sam_set_mapq.3.gz man/man3/bl_sam_set_pnext.3.gz @@ -412,6 +447,7 @@ man/man3/bl_sam_set_qname_ae.3.gz man/man3/bl_sam_set_qname_cpy.3.gz man/man3/bl_sam_set_qual.3.gz man/man3/bl_sam_set_qual_ae.3.gz +man/man3/bl_sam_set_qual_array_size.3.gz man/man3/bl_sam_set_qual_cpy.3.gz man/man3/bl_sam_set_qual_len.3.gz man/man3/bl_sam_set_rname_ae.3.gz @@ -420,9 +456,11 @@ man/man3/bl_sam_set_rnext_ae.3.gz man/man3/bl_sam_set_rnext_cpy.3.gz man/man3/bl_sam_set_seq.3.gz man/man3/bl_sam_set_seq_ae.3.gz +man/man3/bl_sam_set_seq_array_size.3.gz man/man3/bl_sam_set_seq_cpy.3.gz man/man3/bl_sam_set_seq_len.3.gz man/man3/bl_sam_set_tlen.3.gz +man/man3/bl_sam_skip_header.3.gz man/man3/bl_sam_write.3.gz man/man3/bl_vcf_call_downstream_of_alignment.3.gz man/man3/bl_vcf_call_in_alignment.3.gz @@ -433,7 +471,6 @@ man/man3/bl_vcf_init.3.gz man/man3/bl_vcf_parse_field_spec.3.gz man/man3/bl_vcf_read_ss_call.3.gz man/man3/bl_vcf_read_static_fields.3.gz -man/man3/bl_vcf_sample_alloc.3.gz man/man3/bl_vcf_set_alt_ae.3.gz man/man3/bl_vcf_set_alt_count.3.gz man/man3/bl_vcf_set_alt_cpy.3.gz @@ -443,16 +480,24 @@ man/man3/bl_vcf_set_filter_ae.3.gz man/man3/bl_vcf_set_filter_cpy.3.gz man/man3/bl_vcf_set_format.3.gz man/man3/bl_vcf_set_format_ae.3.gz +man/man3/bl_vcf_set_format_array_size.3.gz man/man3/bl_vcf_set_format_cpy.3.gz man/man3/bl_vcf_set_format_len.3.gz -man/man3/bl_vcf_set_format_max.3.gz man/man3/bl_vcf_set_id_ae.3.gz man/man3/bl_vcf_set_id_cpy.3.gz man/man3/bl_vcf_set_info.3.gz man/man3/bl_vcf_set_info_ae.3.gz +man/man3/bl_vcf_set_info_array_size.3.gz man/man3/bl_vcf_set_info_cpy.3.gz man/man3/bl_vcf_set_info_len.3.gz -man/man3/bl_vcf_set_info_max.3.gz +man/man3/bl_vcf_set_multi_sample_array_sizes.3.gz +man/man3/bl_vcf_set_multi_sample_array_sizes_ae.3.gz +man/man3/bl_vcf_set_multi_sample_array_sizes_cpy.3.gz +man/man3/bl_vcf_set_multi_sample_count.3.gz +man/man3/bl_vcf_set_multi_sample_lens.3.gz +man/man3/bl_vcf_set_multi_sample_lens_ae.3.gz +man/man3/bl_vcf_set_multi_sample_lens_cpy.3.gz +man/man3/bl_vcf_set_multi_sample_pointer_array_size.3.gz man/man3/bl_vcf_set_multi_samples.3.gz man/man3/bl_vcf_set_multi_samples_ae.3.gz man/man3/bl_vcf_set_multi_samples_cpy.3.gz @@ -468,10 +513,12 @@ man/man3/bl_vcf_set_qual_cpy.3.gz man/man3/bl_vcf_set_ref_ae.3.gz man/man3/bl_vcf_set_ref_count.3.gz man/man3/bl_vcf_set_ref_cpy.3.gz -man/man3/bl_vcf_set_sample_max.3.gz man/man3/bl_vcf_set_single_sample.3.gz man/man3/bl_vcf_set_single_sample_ae.3.gz +man/man3/bl_vcf_set_single_sample_array_size.3.gz man/man3/bl_vcf_set_single_sample_cpy.3.gz +man/man3/bl_vcf_set_single_sample_len.3.gz +man/man3/bl_vcf_skip_header.3.gz man/man3/bl_vcf_skip_meta_data.3.gz man/man3/bl_vcf_write_ss_call.3.gz man/man3/bl_vcf_write_static_fields.3.gz