Received: from mail.netbsd.org (mail.netbsd.org [199.233.217.200]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) (Client CN "mail.NetBSD.org", Issuer "mail.NetBSD.org CA" (not verified)) by mollari.NetBSD.org (Postfix) with ESMTPS id BFA781A9239 for ; Tue, 14 Dec 2021 18:59:00 +0000 (UTC) Received: by mail.netbsd.org (Postfix, from userid 605) id D4AAF84F12; Tue, 14 Dec 2021 18:58:59 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 189BA84EAE for ; Tue, 14 Dec 2021 18:58:59 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id ec5xtu5AuFW9 for ; Tue, 14 Dec 2021 18:58:57 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 5315C84D58 for ; Tue, 14 Dec 2021 18:58:57 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 4C7CFFAEC; Tue, 14 Dec 2021 18:58:57 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_163950833782330" MIME-Version: 1.0 Date: Tue, 14 Dec 2021 18:58:57 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/biolibc To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20211214185857.4C7CFFAEC@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_163950833782330 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Tue Dec 14 18:58:57 UTC 2021 Modified Files: pkgsrc/biology/biolibc: Makefile PLIST buildlink3.mk distinfo Removed Files: pkgsrc/biology/biolibc/files: plist-mods.sh Log Message: biology/biolibc: Update to 0.2.1 Add orf.c with start/stop codon locators Standardize BED and GFF APIs Implement VCF input filtering Eliminate mutator macros mirroring mutator functions Numerous minor bug fixes and enhancements Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1 To generate a diff of this commit: cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/biolibc/Makefile \ pkgsrc/biology/biolibc/PLIST pkgsrc/biology/biolibc/buildlink3.mk cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/biolibc/distinfo cvs rdiff -u -r1.1 -r0 pkgsrc/biology/biolibc/files/plist-mods.sh Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_163950833782330 Content-Disposition: inline Content-Length: 22599 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/biolibc/Makefile diff -u pkgsrc/biology/biolibc/Makefile:1.6 pkgsrc/biology/biolibc/Makefile:1.7 --- pkgsrc/biology/biolibc/Makefile:1.6 Sat Sep 18 00:42:39 2021 +++ pkgsrc/biology/biolibc/Makefile Tue Dec 14 18:58:56 2021 @@ -1,9 +1,8 @@ -# $NetBSD: Makefile,v 1.6 2021/09/18 00:42:39 bacon Exp $ +# $NetBSD: Makefile,v 1.7 2021/12/14 18:58:56 bacon Exp $ -DISTNAME= biolibc-0.2.0.11 +DISTNAME= biolibc-0.2.1 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/} -GITHUB_TAG= 65b3b132c813bb04b3a9886d08f51af8137a60e6 MAINTAINER= bacon@NetBSD.org HOMEPAGE= https://github.com/auerlab/biolibc @@ -17,11 +16,9 @@ BUILD_TARGET= apple INSTALL_TARGET= apple-install .else INSTALL_TARGET= install-strip -PLIST.cs= yes .endif MAKE_ENV+= DYLIB_PATH=${PREFIX}/lib MANDIR=${PREFIX}/${PKGMANDIR} -PLIST_VARS= cs pre-build: cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend Index: pkgsrc/biology/biolibc/PLIST diff -u pkgsrc/biology/biolibc/PLIST:1.6 pkgsrc/biology/biolibc/PLIST:1.7 --- pkgsrc/biology/biolibc/PLIST:1.6 Sat Sep 18 00:42:39 2021 +++ pkgsrc/biology/biolibc/PLIST Tue Dec 14 18:58:56 2021 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.6 2021/09/18 00:42:39 bacon Exp $ +@comment $NetBSD: PLIST,v 1.7 2021/12/14 18:58:56 bacon Exp $ include/biolibc/bed.h include/biolibc/biolibc.h include/biolibc/biostring.h @@ -10,331 +10,155 @@ include/biolibc/overlap.h include/biolibc/pos-list.h include/biolibc/sam-buff.h include/biolibc/sam.h +include/biolibc/translate.h include/biolibc/vcf.h lib/libbiolibc.a lib/libbiolibc.so lib/libbiolibc.so.2 lib/libbiolibc.so.2.0 -${PLIST.cs}man/man3/BL_BED_BLOCK_COUNT.3 -${PLIST.cs}man/man3/BL_BED_BLOCK_SIZES.3 -${PLIST.cs}man/man3/BL_BED_BLOCK_SIZES_AE.3 -${PLIST.cs}man/man3/BL_BED_BLOCK_STARTS.3 -${PLIST.cs}man/man3/BL_BED_BLOCK_STARTS_AE.3 -${PLIST.cs}man/man3/BL_BED_CHROM.3 -${PLIST.cs}man/man3/BL_BED_CHROM_AE.3 -${PLIST.cs}man/man3/BL_BED_CHROM_END.3 -${PLIST.cs}man/man3/BL_BED_CHROM_START.3 -${PLIST.cs}man/man3/BL_BED_FIELDS.3 -${PLIST.cs}man/man3/BL_BED_ITEM_RGB.3 -${PLIST.cs}man/man3/BL_BED_ITEM_RGB_AE.3 -${PLIST.cs}man/man3/BL_BED_NAME.3 -${PLIST.cs}man/man3/BL_BED_NAME_AE.3 -${PLIST.cs}man/man3/BL_BED_SCORE.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_COUNT.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_SIZES.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_SIZES_AE.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_SIZES_CPY.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_STARTS.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_STARTS_AE.3 -${PLIST.cs}man/man3/BL_BED_SET_BLOCK_STARTS_CPY.3 -${PLIST.cs}man/man3/BL_BED_SET_CHROM.3 -${PLIST.cs}man/man3/BL_BED_SET_CHROM_AE.3 -${PLIST.cs}man/man3/BL_BED_SET_CHROM_CPY.3 -${PLIST.cs}man/man3/BL_BED_SET_CHROM_END.3 -${PLIST.cs}man/man3/BL_BED_SET_CHROM_START.3 -${PLIST.cs}man/man3/BL_BED_SET_FIELDS.3 -${PLIST.cs}man/man3/BL_BED_SET_ITEM_RGB.3 -${PLIST.cs}man/man3/BL_BED_SET_ITEM_RGB_AE.3 -${PLIST.cs}man/man3/BL_BED_SET_ITEM_RGB_CPY.3 -${PLIST.cs}man/man3/BL_BED_SET_NAME.3 -${PLIST.cs}man/man3/BL_BED_SET_NAME_AE.3 -${PLIST.cs}man/man3/BL_BED_SET_NAME_CPY.3 -${PLIST.cs}man/man3/BL_BED_SET_SCORE.3 -${PLIST.cs}man/man3/BL_BED_SET_STRAND.3 -${PLIST.cs}man/man3/BL_BED_SET_THICK_END.3 -${PLIST.cs}man/man3/BL_BED_SET_THICK_START.3 -${PLIST.cs}man/man3/BL_BED_STRAND.3 -${PLIST.cs}man/man3/BL_BED_THICK_END.3 -${PLIST.cs}man/man3/BL_BED_THICK_START.3 -${PLIST.cs}man/man3/BL_FASTA_DESC.3 -${PLIST.cs}man/man3/BL_FASTA_DESC_AE.3 -${PLIST.cs}man/man3/BL_FASTA_DESC_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTA_DESC_LEN.3 -${PLIST.cs}man/man3/BL_FASTA_SEQ.3 -${PLIST.cs}man/man3/BL_FASTA_SEQ_AE.3 -${PLIST.cs}man/man3/BL_FASTA_SEQ_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTA_SEQ_LEN.3 -${PLIST.cs}man/man3/BL_FASTA_SET_DESC.3 -${PLIST.cs}man/man3/BL_FASTA_SET_DESC_AE.3 -${PLIST.cs}man/man3/BL_FASTA_SET_DESC_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTA_SET_DESC_CPY.3 -${PLIST.cs}man/man3/BL_FASTA_SET_DESC_LEN.3 -${PLIST.cs}man/man3/BL_FASTA_SET_SEQ.3 -${PLIST.cs}man/man3/BL_FASTA_SET_SEQ_AE.3 -${PLIST.cs}man/man3/BL_FASTA_SET_SEQ_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTA_SET_SEQ_CPY.3 -${PLIST.cs}man/man3/BL_FASTA_SET_SEQ_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_DESC.3 -${PLIST.cs}man/man3/BL_FASTQ_DESC_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_DESC_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_DESC_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_PLUS.3 -${PLIST.cs}man/man3/BL_FASTQ_PLUS_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_PLUS_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_PLUS_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_QUAL.3 -${PLIST.cs}man/man3/BL_FASTQ_QUAL_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_QUAL_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_QUAL_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_SEQ.3 -${PLIST.cs}man/man3/BL_FASTQ_SEQ_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_SEQ_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_DESC.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_DESC_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_DESC_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_DESC_CPY.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_DESC_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_PLUS.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_PLUS_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_PLUS_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_PLUS_CPY.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_PLUS_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_QUAL.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_QUAL_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_QUAL_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_QUAL_CPY.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_QUAL_LEN.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_SEQ.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_SEQ_AE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_SEQ_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_SEQ_CPY.3 -${PLIST.cs}man/man3/BL_FASTQ_SET_SEQ_LEN.3 -${PLIST.cs}man/man3/BL_GFF_ATTRIBUTES.3 -${PLIST.cs}man/man3/BL_GFF_ATTRIBUTES_AE.3 -${PLIST.cs}man/man3/BL_GFF_END.3 -${PLIST.cs}man/man3/BL_GFF_FEATURE.3 -${PLIST.cs}man/man3/BL_GFF_FEATURE_AE.3 -${PLIST.cs}man/man3/BL_GFF_FEATURE_ID.3 -${PLIST.cs}man/man3/BL_GFF_FEATURE_ID_AE.3 -${PLIST.cs}man/man3/BL_GFF_GENE_NAME.3 -${PLIST.cs}man/man3/BL_GFF_GENE_NAME_AE.3 -${PLIST.cs}man/man3/BL_GFF_PHASE.3 -${PLIST.cs}man/man3/BL_GFF_SCORE.3 -${PLIST.cs}man/man3/BL_GFF_SEQUENCE.3 -${PLIST.cs}man/man3/BL_GFF_SEQUENCE_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_ATTRIBUTES.3 -${PLIST.cs}man/man3/BL_GFF_SET_ATTRIBUTES_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_ATTRIBUTES_CPY.3 -${PLIST.cs}man/man3/BL_GFF_SET_END.3 -${PLIST.cs}man/man3/BL_GFF_SET_FEATURE.3 -${PLIST.cs}man/man3/BL_GFF_SET_FEATURE_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_FEATURE_CPY.3 -${PLIST.cs}man/man3/BL_GFF_SET_FEATURE_ID.3 -${PLIST.cs}man/man3/BL_GFF_SET_FEATURE_ID_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_FEATURE_ID_CPY.3 -${PLIST.cs}man/man3/BL_GFF_SET_GENE_NAME.3 -${PLIST.cs}man/man3/BL_GFF_SET_GENE_NAME_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_GENE_NAME_CPY.3 -${PLIST.cs}man/man3/BL_GFF_SET_PHASE.3 -${PLIST.cs}man/man3/BL_GFF_SET_SCORE.3 -${PLIST.cs}man/man3/BL_GFF_SET_SEQUENCE.3 -${PLIST.cs}man/man3/BL_GFF_SET_SEQUENCE_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_SEQUENCE_CPY.3 -${PLIST.cs}man/man3/BL_GFF_SET_SOURCE.3 -${PLIST.cs}man/man3/BL_GFF_SET_SOURCE_AE.3 -${PLIST.cs}man/man3/BL_GFF_SET_SOURCE_CPY.3 -${PLIST.cs}man/man3/BL_GFF_SET_START.3 -${PLIST.cs}man/man3/BL_GFF_SET_STRAND.3 -${PLIST.cs}man/man3/BL_GFF_SOURCE.3 -${PLIST.cs}man/man3/BL_GFF_SOURCE_AE.3 -${PLIST.cs}man/man3/BL_GFF_START.3 -${PLIST.cs}man/man3/BL_GFF_STRAND.3 -${PLIST.cs}man/man3/BL_OVERLAP_FEATURE1_LEN.3 -${PLIST.cs}man/man3/BL_OVERLAP_FEATURE2_LEN.3 -${PLIST.cs}man/man3/BL_OVERLAP_OVERLAP_END.3 -${PLIST.cs}man/man3/BL_OVERLAP_OVERLAP_LEN.3 -${PLIST.cs}man/man3/BL_OVERLAP_OVERLAP_START.3 -${PLIST.cs}man/man3/BL_OVERLAP_SET_FEATURE1_LEN.3 -${PLIST.cs}man/man3/BL_OVERLAP_SET_FEATURE2_LEN.3 -${PLIST.cs}man/man3/BL_OVERLAP_SET_OVERLAP_END.3 -${PLIST.cs}man/man3/BL_OVERLAP_SET_OVERLAP_LEN.3 -${PLIST.cs}man/man3/BL_OVERLAP_SET_OVERLAP_START.3 -${PLIST.cs}man/man3/BL_POS_LIST_ARRAY_SIZE.3 -${PLIST.cs}man/man3/BL_POS_LIST_COUNT.3 -${PLIST.cs}man/man3/BL_POS_LIST_POSITIONS.3 -${PLIST.cs}man/man3/BL_POS_LIST_POSITIONS_AE.3 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-${PLIST.cs}man/man3/BL_SAM_QNAME_AE.3 -${PLIST.cs}man/man3/BL_SAM_QUAL.3 -${PLIST.cs}man/man3/BL_SAM_QUAL_AE.3 -${PLIST.cs}man/man3/BL_SAM_QUAL_LEN.3 -${PLIST.cs}man/man3/BL_SAM_RNAME.3 -${PLIST.cs}man/man3/BL_SAM_RNAME_AE.3 -${PLIST.cs}man/man3/BL_SAM_RNEXT.3 -${PLIST.cs}man/man3/BL_SAM_RNEXT_AE.3 -${PLIST.cs}man/man3/BL_SAM_SEQ.3 -${PLIST.cs}man/man3/BL_SAM_SEQ_AE.3 -${PLIST.cs}man/man3/BL_SAM_SEQ_LEN.3 -${PLIST.cs}man/man3/BL_SAM_SET_CIGAR.3 -${PLIST.cs}man/man3/BL_SAM_SET_CIGAR_AE.3 -${PLIST.cs}man/man3/BL_SAM_SET_CIGAR_CPY.3 -${PLIST.cs}man/man3/BL_SAM_SET_FLAG.3 -${PLIST.cs}man/man3/BL_SAM_SET_MAPQ.3 -${PLIST.cs}man/man3/BL_SAM_SET_PNEXT.3 -${PLIST.cs}man/man3/BL_SAM_SET_POS.3 -${PLIST.cs}man/man3/BL_SAM_SET_QNAME.3 -${PLIST.cs}man/man3/BL_SAM_SET_QNAME_AE.3 -${PLIST.cs}man/man3/BL_SAM_SET_QNAME_CPY.3 -${PLIST.cs}man/man3/BL_SAM_SET_QUAL.3 -${PLIST.cs}man/man3/BL_SAM_SET_QUAL_AE.3 -${PLIST.cs}man/man3/BL_SAM_SET_QUAL_CPY.3 -${PLIST.cs}man/man3/BL_SAM_SET_QUAL_LEN.3 -${PLIST.cs}man/man3/BL_SAM_SET_RNAME.3 -${PLIST.cs}man/man3/BL_SAM_SET_RNAME_AE.3 -${PLIST.cs}man/man3/BL_SAM_SET_RNAME_CPY.3 -${PLIST.cs}man/man3/BL_SAM_SET_RNEXT.3 -${PLIST.cs}man/man3/BL_SAM_SET_RNEXT_AE.3 -${PLIST.cs}man/man3/BL_SAM_SET_RNEXT_CPY.3 -${PLIST.cs}man/man3/BL_SAM_SET_SEQ.3 -${PLIST.cs}man/man3/BL_SAM_SET_SEQ_AE.3 -${PLIST.cs}man/man3/BL_SAM_SET_SEQ_CPY.3 -${PLIST.cs}man/man3/BL_SAM_SET_SEQ_LEN.3 -${PLIST.cs}man/man3/BL_SAM_SET_TLEN.3 -${PLIST.cs}man/man3/BL_SAM_TLEN.3 -${PLIST.cs}man/man3/BL_VCF_ALT.3 -${PLIST.cs}man/man3/BL_VCF_ALT_AE.3 -${PLIST.cs}man/man3/BL_VCF_ALT_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_CHROM.3 -${PLIST.cs}man/man3/BL_VCF_CHROM_AE.3 -${PLIST.cs}man/man3/BL_VCF_FILTER.3 -${PLIST.cs}man/man3/BL_VCF_FILTER_AE.3 -${PLIST.cs}man/man3/BL_VCF_FORMAT.3 -${PLIST.cs}man/man3/BL_VCF_FORMAT_AE.3 -${PLIST.cs}man/man3/BL_VCF_FORMAT_MAX.3 -${PLIST.cs}man/man3/BL_VCF_ID.3 -${PLIST.cs}man/man3/BL_VCF_ID_AE.3 -${PLIST.cs}man/man3/BL_VCF_INFO.3 -${PLIST.cs}man/man3/BL_VCF_INFO_AE.3 -${PLIST.cs}man/man3/BL_VCF_INFO_LEN.3 -${PLIST.cs}man/man3/BL_VCF_INFO_MAX.3 -${PLIST.cs}man/man3/BL_VCF_MULTI_SAMPLES.3 -${PLIST.cs}man/man3/BL_VCF_MULTI_SAMPLES_AE.3 -${PLIST.cs}man/man3/BL_VCF_OTHER_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_PHREDS.3 -${PLIST.cs}man/man3/BL_VCF_PHREDS_AE.3 -${PLIST.cs}man/man3/BL_VCF_PHRED_BUFF_SIZE.3 -${PLIST.cs}man/man3/BL_VCF_PHRED_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_POS.3 -${PLIST.cs}man/man3/BL_VCF_QUAL.3 -${PLIST.cs}man/man3/BL_VCF_QUAL_AE.3 -${PLIST.cs}man/man3/BL_VCF_REF.3 -${PLIST.cs}man/man3/BL_VCF_REF_AE.3 -${PLIST.cs}man/man3/BL_VCF_REF_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_SAMPLE_MAX.3 -${PLIST.cs}man/man3/BL_VCF_SET_ALT.3 -${PLIST.cs}man/man3/BL_VCF_SET_ALT_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_ALT_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_SET_ALT_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_CHROM.3 -${PLIST.cs}man/man3/BL_VCF_SET_CHROM_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_CHROM_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_FILTER.3 -${PLIST.cs}man/man3/BL_VCF_SET_FILTER_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_FILTER_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_FORMAT.3 -${PLIST.cs}man/man3/BL_VCF_SET_FORMAT_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_FORMAT_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_FORMAT_MAX.3 -${PLIST.cs}man/man3/BL_VCF_SET_ID.3 -${PLIST.cs}man/man3/BL_VCF_SET_ID_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_ID_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_INFO.3 -${PLIST.cs}man/man3/BL_VCF_SET_INFO_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_INFO_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_INFO_LEN.3 -${PLIST.cs}man/man3/BL_VCF_SET_INFO_MAX.3 -${PLIST.cs}man/man3/BL_VCF_SET_MULTI_SAMPLES.3 -${PLIST.cs}man/man3/BL_VCF_SET_MULTI_SAMPLES_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_MULTI_SAMPLES_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_OTHER_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_SET_PHREDS.3 -${PLIST.cs}man/man3/BL_VCF_SET_PHREDS_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_PHREDS_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_PHRED_BUFF_SIZE.3 -${PLIST.cs}man/man3/BL_VCF_SET_PHRED_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_SET_POS.3 -${PLIST.cs}man/man3/BL_VCF_SET_QUAL.3 -${PLIST.cs}man/man3/BL_VCF_SET_QUAL_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_QUAL_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_REF.3 -${PLIST.cs}man/man3/BL_VCF_SET_REF_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_REF_COUNT.3 -${PLIST.cs}man/man3/BL_VCF_SET_REF_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SET_SAMPLE_MAX.3 -${PLIST.cs}man/man3/BL_VCF_SET_SINGLE_SAMPLE.3 -${PLIST.cs}man/man3/BL_VCF_SET_SINGLE_SAMPLE_AE.3 -${PLIST.cs}man/man3/BL_VCF_SET_SINGLE_SAMPLE_CPY.3 -${PLIST.cs}man/man3/BL_VCF_SINGLE_SAMPLE.3 -${PLIST.cs}man/man3/BL_VCF_SINGLE_SAMPLE_AE.3 +man/man3/BL_BED_BLOCK_COUNT.3 +man/man3/BL_BED_BLOCK_SIZES.3 +man/man3/BL_BED_BLOCK_SIZES_AE.3 +man/man3/BL_BED_BLOCK_STARTS.3 +man/man3/BL_BED_BLOCK_STARTS_AE.3 +man/man3/BL_BED_CHROM.3 +man/man3/BL_BED_CHROM_AE.3 +man/man3/BL_BED_CHROM_END.3 +man/man3/BL_BED_CHROM_START.3 +man/man3/BL_BED_FIELDS.3 +man/man3/BL_BED_ITEM_RGB.3 +man/man3/BL_BED_ITEM_RGB_AE.3 +man/man3/BL_BED_NAME.3 +man/man3/BL_BED_NAME_AE.3 +man/man3/BL_BED_SCORE.3 +man/man3/BL_BED_STRAND.3 +man/man3/BL_BED_THICK_END.3 +man/man3/BL_BED_THICK_START.3 +man/man3/BL_FASTA_DESC.3 +man/man3/BL_FASTA_DESC_AE.3 +man/man3/BL_FASTA_DESC_ARRAY_SIZE.3 +man/man3/BL_FASTA_DESC_LEN.3 +man/man3/BL_FASTA_SEQ.3 +man/man3/BL_FASTA_SEQ_AE.3 +man/man3/BL_FASTA_SEQ_ARRAY_SIZE.3 +man/man3/BL_FASTA_SEQ_LEN.3 +man/man3/BL_FASTQ_DESC.3 +man/man3/BL_FASTQ_DESC_AE.3 +man/man3/BL_FASTQ_DESC_ARRAY_SIZE.3 +man/man3/BL_FASTQ_DESC_LEN.3 +man/man3/BL_FASTQ_PLUS.3 +man/man3/BL_FASTQ_PLUS_AE.3 +man/man3/BL_FASTQ_PLUS_ARRAY_SIZE.3 +man/man3/BL_FASTQ_PLUS_LEN.3 +man/man3/BL_FASTQ_QUAL.3 +man/man3/BL_FASTQ_QUAL_AE.3 +man/man3/BL_FASTQ_QUAL_ARRAY_SIZE.3 +man/man3/BL_FASTQ_QUAL_LEN.3 +man/man3/BL_FASTQ_SEQ.3 +man/man3/BL_FASTQ_SEQ_AE.3 +man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3 +man/man3/BL_FASTQ_SEQ_LEN.3 +man/man3/BL_GFF_ATTRIBUTES.3 +man/man3/BL_GFF_ATTRIBUTES_AE.3 +man/man3/BL_GFF_END.3 +man/man3/BL_GFF_FEATURE.3 +man/man3/BL_GFF_FEATURE_AE.3 +man/man3/BL_GFF_FEATURE_ID.3 +man/man3/BL_GFF_FEATURE_ID_AE.3 +man/man3/BL_GFF_GENE_NAME.3 +man/man3/BL_GFF_GENE_NAME_AE.3 +man/man3/BL_GFF_PHASE.3 +man/man3/BL_GFF_SCORE.3 +man/man3/BL_GFF_SEQUENCE.3 +man/man3/BL_GFF_SEQUENCE_AE.3 +man/man3/BL_GFF_SOURCE.3 +man/man3/BL_GFF_SOURCE_AE.3 +man/man3/BL_GFF_START.3 +man/man3/BL_GFF_STRAND.3 +man/man3/BL_OVERLAP_FEATURE1_LEN.3 +man/man3/BL_OVERLAP_FEATURE2_LEN.3 +man/man3/BL_OVERLAP_OVERLAP_END.3 +man/man3/BL_OVERLAP_OVERLAP_LEN.3 +man/man3/BL_OVERLAP_OVERLAP_START.3 +man/man3/BL_POS_LIST_ARRAY_SIZE.3 +man/man3/BL_POS_LIST_COUNT.3 +man/man3/BL_POS_LIST_POSITIONS.3 +man/man3/BL_POS_LIST_POSITIONS_AE.3 +man/man3/BL_SAM_BUFF_ALIGNMENTS.3 +man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.3 +man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3 +man/man3/BL_SAM_BUFF_BUFF_SIZE.3 +man/man3/BL_SAM_BUFF_DISCARDED_ALIGNMENTS.3 +man/man3/BL_SAM_BUFF_DISCARDED_SCORE_SUM.3 +man/man3/BL_SAM_BUFF_DISCARDED_TRAILING.3 +man/man3/BL_SAM_BUFF_INC_DISCARDED_TRAILING.3 +man/man3/BL_SAM_BUFF_INC_TOTAL_ALIGNMENTS.3 +man/man3/BL_SAM_BUFF_INC_TRAILING_ALIGNMENTS.3 +man/man3/BL_SAM_BUFF_MAPQ_HIGH.3 +man/man3/BL_SAM_BUFF_MAPQ_LOW.3 +man/man3/BL_SAM_BUFF_MAPQ_MIN.3 +man/man3/BL_SAM_BUFF_MAPQ_SUM.3 +man/man3/BL_SAM_BUFF_MAX_COUNT.3 +man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3 +man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3 +man/man3/BL_SAM_BUFF_PREVIOUS_POS.3 +man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3 +man/man3/BL_SAM_BUFF_PREVIOUS_RNAME_AE.3 +man/man3/BL_SAM_BUFF_READS_USED.3 +man/man3/BL_SAM_BUFF_TOTAL_ALIGNMENTS.3 +man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3 +man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3 +man/man3/BL_SAM_CIGAR.3 +man/man3/BL_SAM_CIGAR_AE.3 +man/man3/BL_SAM_FLAG.3 +man/man3/BL_SAM_MAPQ.3 +man/man3/BL_SAM_PNEXT.3 +man/man3/BL_SAM_POS.3 +man/man3/BL_SAM_QNAME.3 +man/man3/BL_SAM_QNAME_AE.3 +man/man3/BL_SAM_QUAL.3 +man/man3/BL_SAM_QUAL_AE.3 +man/man3/BL_SAM_QUAL_LEN.3 +man/man3/BL_SAM_RNAME.3 +man/man3/BL_SAM_RNAME_AE.3 +man/man3/BL_SAM_RNEXT.3 +man/man3/BL_SAM_RNEXT_AE.3 +man/man3/BL_SAM_SEQ.3 +man/man3/BL_SAM_SEQ_AE.3 +man/man3/BL_SAM_SEQ_LEN.3 +man/man3/BL_SAM_TLEN.3 +man/man3/BL_VCF_ALT.3 +man/man3/BL_VCF_ALT_AE.3 +man/man3/BL_VCF_ALT_COUNT.3 +man/man3/BL_VCF_CHROM.3 +man/man3/BL_VCF_CHROM_AE.3 +man/man3/BL_VCF_FILTER.3 +man/man3/BL_VCF_FILTER_AE.3 +man/man3/BL_VCF_FORMAT.3 +man/man3/BL_VCF_FORMAT_AE.3 +man/man3/BL_VCF_FORMAT_MAX.3 +man/man3/BL_VCF_ID.3 +man/man3/BL_VCF_ID_AE.3 +man/man3/BL_VCF_INFO.3 +man/man3/BL_VCF_INFO_AE.3 +man/man3/BL_VCF_INFO_LEN.3 +man/man3/BL_VCF_INFO_MAX.3 +man/man3/BL_VCF_MULTI_SAMPLES.3 +man/man3/BL_VCF_MULTI_SAMPLES_AE.3 +man/man3/BL_VCF_OTHER_COUNT.3 +man/man3/BL_VCF_PHREDS.3 +man/man3/BL_VCF_PHREDS_AE.3 +man/man3/BL_VCF_PHRED_BUFF_SIZE.3 +man/man3/BL_VCF_PHRED_COUNT.3 +man/man3/BL_VCF_POS.3 +man/man3/BL_VCF_QUAL.3 +man/man3/BL_VCF_QUAL_AE.3 +man/man3/BL_VCF_REF.3 +man/man3/BL_VCF_REF_AE.3 +man/man3/BL_VCF_REF_COUNT.3 +man/man3/BL_VCF_SAMPLE_MAX.3 +man/man3/BL_VCF_SINGLE_SAMPLE.3 +man/man3/BL_VCF_SINGLE_SAMPLE_AE.3 man/man3/biolibc.3 man/man3/bl_bed_check_order.3 man/man3/bl_bed_gff_cmp.3 @@ -436,6 +260,8 @@ man/man3/bl_gff_set_strand.3 man/man3/bl_gff_skip_header.3 man/man3/bl_gff_to_bed.3 man/man3/bl_gff_write.3 +man/man3/bl_next_start_codon.3 +man/man3/bl_next_stop_codon.3 man/man3/bl_overlap_print.3 man/man3/bl_overlap_set_all.3 man/man3/bl_overlap_set_feature1_len.3 @@ -555,6 +381,6 @@ man/man3/bl_vcf_set_sample_max.3 man/man3/bl_vcf_set_single_sample.3 man/man3/bl_vcf_set_single_sample_ae.3 man/man3/bl_vcf_set_single_sample_cpy.3 -man/man3/bl_vcf_skip_header.3 +man/man3/bl_vcf_skip_meta_data.3 man/man3/bl_vcf_write_ss_call.3 man/man3/bl_vcf_write_static_fields.3 Index: pkgsrc/biology/biolibc/buildlink3.mk diff -u pkgsrc/biology/biolibc/buildlink3.mk:1.6 pkgsrc/biology/biolibc/buildlink3.mk:1.7 --- pkgsrc/biology/biolibc/buildlink3.mk:1.6 Sat Sep 18 00:42:39 2021 +++ pkgsrc/biology/biolibc/buildlink3.mk Tue Dec 14 18:58:57 2021 @@ -1,12 +1,14 @@ -# $NetBSD: buildlink3.mk,v 1.6 2021/09/18 00:42:39 bacon Exp $ +# $NetBSD: buildlink3.mk,v 1.7 2021/12/14 18:58:57 bacon Exp $ BUILDLINK_TREE+= biolibc .if !defined(BIOLIBC_BUILDLINK3_MK) BIOLIBC_BUILDLINK3_MK:= -BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.0 +BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.1 BUILDLINK_PKGSRCDIR.biolibc?= ../../biology/biolibc + +.include "../../devel/libxtend/buildlink3.mk" .endif # BIOLIBC_BUILDLINK3_MK BUILDLINK_TREE+= -biolibc Index: pkgsrc/biology/biolibc/distinfo diff -u pkgsrc/biology/biolibc/distinfo:1.8 pkgsrc/biology/biolibc/distinfo:1.9 --- pkgsrc/biology/biolibc/distinfo:1.8 Tue Oct 26 10:03:37 2021 +++ pkgsrc/biology/biolibc/distinfo Tue Dec 14 18:58:57 2021 @@ -1,5 +1,5 @@ -$NetBSD: distinfo,v 1.8 2021/10/26 10:03:37 nia Exp $ +$NetBSD: distinfo,v 1.9 2021/12/14 18:58:57 bacon Exp $ -BLAKE2s (biolibc-0.2.0.11-65b3b132c813bb04b3a9886d08f51af8137a60e6.tar.gz) = 3c67ef7f9ff2c4a190e7a604560bdc26ac2e8050bdc283025226654222911048 -SHA512 (biolibc-0.2.0.11-65b3b132c813bb04b3a9886d08f51af8137a60e6.tar.gz) = 2c63ceecc1a7ff1509ffe6791fdb42d1051e02bbf14cabb99f387289df9457629f8e4cc168d51527881c0cea2ad731c0250c3e320ed35bd2750cb9d2dcb1ade5 -Size (biolibc-0.2.0.11-65b3b132c813bb04b3a9886d08f51af8137a60e6.tar.gz) = 119372 bytes +BLAKE2s (biolibc-0.2.1.tar.gz) = e81198c3ae3185592c58cdd72b046db0bce898845bf4f850a46a35c2cadb09b6 +SHA512 (biolibc-0.2.1.tar.gz) = 0743199591e6f3b8ea9986bbddcba972538925787aa01463236d9c7ec809860eb2ee5174bbc8f00d04e33d1802f7ff87f0d4fb010a21cb3a2eb6bb1978cb2647 +Size (biolibc-0.2.1.tar.gz) = 104282 bytes --_----------=_163950833782330--