pkgsrc-Changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
CVS commit: pkgsrc/biology/biolibc
Module Name: pkgsrc
Committed By: bacon
Date: Sat Aug 28 18:34:37 UTC 2021
Modified Files:
pkgsrc/biology/biolibc: Makefile PLIST buildlink3.mk distinfo
Added Files:
pkgsrc/biology/biolibc/files: plist-mods.sh
Log Message:
biology/biolibc: Update to 0.2.0
Major API overhaul
New classes for FASTA and FASTQ
Generate accessor and mutator functions for all classes
Generate man pages for all functions and macros
Export delimiter-separated-value class to libxtend
To generate a diff of this commit:
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/biolibc/Makefile \
pkgsrc/biology/biolibc/PLIST pkgsrc/biology/biolibc/buildlink3.mk \
pkgsrc/biology/biolibc/distinfo
cvs rdiff -u -r0 -r1.1 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.
Modified files:
Index: pkgsrc/biology/biolibc/Makefile
diff -u pkgsrc/biology/biolibc/Makefile:1.3 pkgsrc/biology/biolibc/Makefile:1.4
--- pkgsrc/biology/biolibc/Makefile:1.3 Tue Jun 15 13:47:46 2021
+++ pkgsrc/biology/biolibc/Makefile Sat Aug 28 18:34:37 2021
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.3 2021/06/15 13:47:46 bacon Exp $
+# $NetBSD: Makefile,v 1.4 2021/08/28 18:34:37 bacon Exp $
-DISTNAME= biolibc-0.1.3.2
+DISTNAME= biolibc-0.2.0
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG= 69d937861329b1842778d98091e65b3c3c624add
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://github.com/auerlab/biolibc
@@ -17,9 +16,11 @@ BUILD_TARGET= apple
INSTALL_TARGET= apple-install
.else
INSTALL_TARGET= install-strip
+PLIST.cs= yes
.endif
-MAKE_ENV+= DYLIB_PATH=${PREFIX}/lib
+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:1.3 pkgsrc/biology/biolibc/PLIST:1.4
--- pkgsrc/biology/biolibc/PLIST:1.3 Tue Jun 15 13:47:46 2021
+++ pkgsrc/biology/biolibc/PLIST Sat Aug 28 18:34:37 2021
@@ -1,9 +1,13 @@
-@comment $NetBSD: PLIST,v 1.3 2021/06/15 13:47:46 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2021/08/28 18:34:37 bacon Exp $
include/biolibc/bed.h
include/biolibc/biolibc.h
-include/biolibc/dsv.h
+include/biolibc/biostring.h
+include/biolibc/fasta.h
+include/biolibc/fastq.h
+include/biolibc/fastx.h
include/biolibc/gff.h
-include/biolibc/plist.h
+include/biolibc/overlap.h
+include/biolibc/pos-list.h
include/biolibc/sam-buff.h
include/biolibc/sam.h
include/biolibc/vcf.h
@@ -11,19 +15,546 @@ lib/libbiolibc.a
lib/libbiolibc.so
lib/libbiolibc.so.2
lib/libbiolibc.so.2.0
-man/man3/bed_check_order.3
-man/man3/bed_gff_cmp.3
-man/man3/bed_read_feature.3
-man/man3/bed_set_chromosome.3
-man/man3/bed_set_end_pos.3
-man/man3/bed_set_fields.3
-man/man3/bed_set_name.3
-man/man3/bed_set_rgb_str.3
-man/man3/bed_set_score.3
-man/man3/bed_set_start_pos.3
-man/man3/bed_set_strand.3
-man/man3/bed_set_thick_end_pos.3
-man/man3/bed_set_thick_start_pos.3
-man/man3/bed_skip_header.3
-man/man3/bed_write_feature.3
+${PLIST.cs}man/man3/BL_BED_BLOCK_COUNT.3
+${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
+${PLIST.cs}man/man3/BL_POS_LIST_POSITIONS_AE.3
+${PLIST.cs}man/man3/BL_POS_LIST_SET_ARRAY_SIZE.3
+${PLIST.cs}man/man3/BL_POS_LIST_SET_COUNT.3
+${PLIST.cs}man/man3/BL_POS_LIST_SET_POSITIONS.3
+${PLIST.cs}man/man3/BL_POS_LIST_SET_POSITIONS_AE.3
+${PLIST.cs}man/man3/BL_POS_LIST_SET_POSITIONS_CPY.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_BUFF_SIZE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_DISCARDED_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_DISCARDED_SCORE_SUM.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_DISCARDED_TRAILING.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_INC_DISCARDED_TRAILING.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_INC_TOTAL_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_INC_TRAILING_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MAPQ_HIGH.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MAPQ_LOW.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MAPQ_MIN.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MAPQ_SUM.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MAX_COUNT.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_PREVIOUS_POS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_PREVIOUS_RNAME_AE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_READS_USED.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_ALIGNMENTS_AE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_ALIGNMENTS_CPY.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_BUFFERED_COUNT.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_BUFF_SIZE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_DISCARDED_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_DISCARDED_SCORE_SUM.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_DISCARDED_TRAILING.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MAPQ_HIGH.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MAPQ_LOW.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MAPQ_MIN.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MAPQ_SUM.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MAX_COUNT.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MAX_DISCARDED_SCORE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_MIN_DISCARDED_SCORE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_PREVIOUS_POS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME_AE.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME_CPY.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_READS_USED.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_TOTAL_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_TRAILING_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_SET_UNMAPPED_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_TOTAL_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3
+${PLIST.cs}man/man3/BL_SAM_CIGAR.3
+${PLIST.cs}man/man3/BL_SAM_CIGAR_AE.3
+${PLIST.cs}man/man3/BL_SAM_FLAG.3
+${PLIST.cs}man/man3/BL_SAM_MAPQ.3
+${PLIST.cs}man/man3/BL_SAM_PNEXT.3
+${PLIST.cs}man/man3/BL_SAM_POS.3
+${PLIST.cs}man/man3/BL_SAM_QNAME.3
+${PLIST.cs}man/man3/BL_SAM_QNAME_AE.3
+${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/biolibc.3
+man/man3/bl_bed_check_order.3
+man/man3/bl_bed_gff_cmp.3
+man/man3/bl_bed_read.3
+man/man3/bl_bed_set_block_count.3
+man/man3/bl_bed_set_block_sizes.3
+man/man3/bl_bed_set_block_sizes_ae.3
+man/man3/bl_bed_set_block_sizes_cpy.3
+man/man3/bl_bed_set_block_starts.3
+man/man3/bl_bed_set_block_starts_ae.3
+man/man3/bl_bed_set_block_starts_cpy.3
+man/man3/bl_bed_set_chrom_ae.3
+man/man3/bl_bed_set_chrom_cpy.3
+man/man3/bl_bed_set_chrom_end.3
+man/man3/bl_bed_set_chrom_start.3
+man/man3/bl_bed_set_fields.3
+man/man3/bl_bed_set_item_rgb_ae.3
+man/man3/bl_bed_set_item_rgb_cpy.3
+man/man3/bl_bed_set_name_ae.3
+man/man3/bl_bed_set_name_cpy.3
+man/man3/bl_bed_set_score.3
+man/man3/bl_bed_set_strand.3
+man/man3/bl_bed_set_thick_end.3
+man/man3/bl_bed_set_thick_start.3
+man/man3/bl_bed_skip_header.3
+man/man3/bl_bed_write.3
+man/man3/bl_chrom_name_cmp.3
+man/man3/bl_fasta_free.3
+man/man3/bl_fasta_init.3
+man/man3/bl_fasta_read.3
+man/man3/bl_fasta_set_desc.3
+man/man3/bl_fasta_set_desc_ae.3
+man/man3/bl_fasta_set_desc_array_size.3
+man/man3/bl_fasta_set_desc_cpy.3
+man/man3/bl_fasta_set_desc_len.3
+man/man3/bl_fasta_set_seq.3
+man/man3/bl_fasta_set_seq_ae.3
+man/man3/bl_fasta_set_seq_array_size.3
+man/man3/bl_fasta_set_seq_cpy.3
+man/man3/bl_fasta_set_seq_len.3
+man/man3/bl_fasta_write.3
+man/man3/bl_fastq_free.3
+man/man3/bl_fastq_init.3
+man/man3/bl_fastq_read.3
+man/man3/bl_fastq_set_desc.3
+man/man3/bl_fastq_set_desc_ae.3
+man/man3/bl_fastq_set_desc_array_size.3
+man/man3/bl_fastq_set_desc_cpy.3
+man/man3/bl_fastq_set_desc_len.3
+man/man3/bl_fastq_set_plus.3
+man/man3/bl_fastq_set_plus_ae.3
+man/man3/bl_fastq_set_plus_array_size.3
+man/man3/bl_fastq_set_plus_cpy.3
+man/man3/bl_fastq_set_plus_len.3
+man/man3/bl_fastq_set_qual.3
+man/man3/bl_fastq_set_qual_ae.3
+man/man3/bl_fastq_set_qual_array_size.3
+man/man3/bl_fastq_set_qual_cpy.3
+man/man3/bl_fastq_set_qual_len.3
+man/man3/bl_fastq_set_seq.3
+man/man3/bl_fastq_set_seq_ae.3
+man/man3/bl_fastq_set_seq_array_size.3
+man/man3/bl_fastq_set_seq_cpy.3
+man/man3/bl_fastq_set_seq_len.3
+man/man3/bl_fastq_write.3
+man/man3/bl_fastx_desc.3
+man/man3/bl_fastx_desc_len.3
+man/man3/bl_fastx_free.3
+man/man3/bl_fastx_init.3
+man/man3/bl_fastx_plus.3
+man/man3/bl_fastx_plus_len.3
+man/man3/bl_fastx_qual.3
+man/man3/bl_fastx_qual_len.3
+man/man3/bl_fastx_read.3
+man/man3/bl_fastx_seq.3
+man/man3/bl_fastx_seq_len.3
+man/man3/bl_fastx_write.3
+man/man3/bl_gff_read.3
+man/man3/bl_gff_set_attributes.3
+man/man3/bl_gff_set_attributes_ae.3
+man/man3/bl_gff_set_attributes_cpy.3
+man/man3/bl_gff_set_end.3
+man/man3/bl_gff_set_feature_ae.3
+man/man3/bl_gff_set_feature_cpy.3
+man/man3/bl_gff_set_feature_id.3
+man/man3/bl_gff_set_feature_id_ae.3
+man/man3/bl_gff_set_feature_id_cpy.3
+man/man3/bl_gff_set_gene_name.3
+man/man3/bl_gff_set_gene_name_ae.3
+man/man3/bl_gff_set_gene_name_cpy.3
+man/man3/bl_gff_set_phase.3
+man/man3/bl_gff_set_score.3
+man/man3/bl_gff_set_sequence_ae.3
+man/man3/bl_gff_set_sequence_cpy.3
+man/man3/bl_gff_set_source_ae.3
+man/man3/bl_gff_set_source_cpy.3
+man/man3/bl_gff_set_start.3
+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_overlap_print.3
+man/man3/bl_overlap_set_all.3
+man/man3/bl_overlap_set_feature1_len.3
+man/man3/bl_overlap_set_feature2_len.3
+man/man3/bl_overlap_set_overlap_end.3
+man/man3/bl_overlap_set_overlap_len.3
+man/man3/bl_overlap_set_overlap_start.3
+man/man3/bl_pos_list_add_position.3
+man/man3/bl_pos_list_allocate.3
+man/man3/bl_pos_list_free.3
+man/man3/bl_pos_list_from_csv.3
+man/man3/bl_pos_list_set_array_size.3
+man/man3/bl_pos_list_set_count.3
+man/man3/bl_pos_list_set_positions.3
+man/man3/bl_pos_list_set_positions_ae.3
+man/man3/bl_pos_list_set_positions_cpy.3
+man/man3/bl_pos_list_sort.3
+man/man3/bl_sam_buff_add_alignment.3
+man/man3/bl_sam_buff_alignment_ok.3
+man/man3/bl_sam_buff_check_order.3
+man/man3/bl_sam_buff_free_alignment.3
+man/man3/bl_sam_buff_init.3
+man/man3/bl_sam_buff_out_of_order.3
+man/man3/bl_sam_buff_set_alignments.3
+man/man3/bl_sam_buff_set_alignments_ae.3
+man/man3/bl_sam_buff_set_alignments_cpy.3
+man/man3/bl_sam_buff_set_buff_size.3
+man/man3/bl_sam_buff_set_buffered_count.3
+man/man3/bl_sam_buff_set_discarded_alignments.3
+man/man3/bl_sam_buff_set_discarded_score_sum.3
+man/man3/bl_sam_buff_set_discarded_trailing.3
+man/man3/bl_sam_buff_set_mapq_high.3
+man/man3/bl_sam_buff_set_mapq_low.3
+man/man3/bl_sam_buff_set_mapq_min.3
+man/man3/bl_sam_buff_set_mapq_sum.3
+man/man3/bl_sam_buff_set_max_count.3
+man/man3/bl_sam_buff_set_max_discarded_score.3
+man/man3/bl_sam_buff_set_min_discarded_score.3
+man/man3/bl_sam_buff_set_previous_pos.3
+man/man3/bl_sam_buff_set_previous_rname_ae.3
+man/man3/bl_sam_buff_set_previous_rname_cpy.3
+man/man3/bl_sam_buff_set_reads_used.3
+man/man3/bl_sam_buff_set_total_alignments.3
+man/man3/bl_sam_buff_set_trailing_alignments.3
+man/man3/bl_sam_buff_set_unmapped_alignments.3
+man/man3/bl_sam_buff_shift.3
+man/man3/bl_sam_copy.3
+man/man3/bl_sam_free.3
+man/man3/bl_sam_init.3
+man/man3/bl_sam_read.3
+man/man3/bl_sam_set_cigar_ae.3
+man/man3/bl_sam_set_cigar_cpy.3
+man/man3/bl_sam_set_flag.3
+man/man3/bl_sam_set_mapq.3
+man/man3/bl_sam_set_pnext.3
+man/man3/bl_sam_set_pos.3
+man/man3/bl_sam_set_qname_ae.3
+man/man3/bl_sam_set_qname_cpy.3
+man/man3/bl_sam_set_qual.3
+man/man3/bl_sam_set_qual_ae.3
+man/man3/bl_sam_set_qual_cpy.3
+man/man3/bl_sam_set_qual_len.3
+man/man3/bl_sam_set_rname_ae.3
+man/man3/bl_sam_set_rname_cpy.3
+man/man3/bl_sam_set_rnext_ae.3
+man/man3/bl_sam_set_rnext_cpy.3
+man/man3/bl_sam_set_seq.3
+man/man3/bl_sam_set_seq_ae.3
+man/man3/bl_sam_set_seq_cpy.3
+man/man3/bl_sam_set_seq_len.3
+man/man3/bl_sam_set_tlen.3
+man/man3/bl_sam_write.3
+man/man3/bl_vcf_call_downstream_of_alignment.3
+man/man3/bl_vcf_call_in_alignment.3
+man/man3/bl_vcf_call_out_of_order.3
+man/man3/bl_vcf_free.3
+man/man3/bl_vcf_get_sample_ids.3
+man/man3/bl_vcf_init.3
+man/man3/bl_vcf_parse_field_spec.3
+man/man3/bl_vcf_read_ss_call.3
+man/man3/bl_vcf_read_static_fields.3
+man/man3/bl_vcf_sample_alloc.3
+man/man3/bl_vcf_set_alt_ae.3
+man/man3/bl_vcf_set_alt_count.3
+man/man3/bl_vcf_set_alt_cpy.3
+man/man3/bl_vcf_set_chrom_ae.3
+man/man3/bl_vcf_set_chrom_cpy.3
+man/man3/bl_vcf_set_filter_ae.3
+man/man3/bl_vcf_set_filter_cpy.3
+man/man3/bl_vcf_set_format.3
+man/man3/bl_vcf_set_format_ae.3
+man/man3/bl_vcf_set_format_cpy.3
+man/man3/bl_vcf_set_format_max.3
+man/man3/bl_vcf_set_id_ae.3
+man/man3/bl_vcf_set_id_cpy.3
+man/man3/bl_vcf_set_info.3
+man/man3/bl_vcf_set_info_ae.3
+man/man3/bl_vcf_set_info_cpy.3
+man/man3/bl_vcf_set_info_len.3
+man/man3/bl_vcf_set_info_max.3
+man/man3/bl_vcf_set_multi_samples.3
+man/man3/bl_vcf_set_multi_samples_ae.3
+man/man3/bl_vcf_set_multi_samples_cpy.3
+man/man3/bl_vcf_set_other_count.3
+man/man3/bl_vcf_set_phred_buff_size.3
+man/man3/bl_vcf_set_phred_count.3
+man/man3/bl_vcf_set_phreds.3
+man/man3/bl_vcf_set_phreds_ae.3
+man/man3/bl_vcf_set_phreds_cpy.3
+man/man3/bl_vcf_set_pos.3
+man/man3/bl_vcf_set_qual_ae.3
+man/man3/bl_vcf_set_qual_cpy.3
+man/man3/bl_vcf_set_ref_ae.3
+man/man3/bl_vcf_set_ref_count.3
+man/man3/bl_vcf_set_ref_cpy.3
+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_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:1.3 pkgsrc/biology/biolibc/buildlink3.mk:1.4
--- pkgsrc/biology/biolibc/buildlink3.mk:1.3 Tue Jun 15 13:47:46 2021
+++ pkgsrc/biology/biolibc/buildlink3.mk Sat Aug 28 18:34:37 2021
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.3 2021/06/15 13:47:46 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.4 2021/08/28 18:34:37 bacon Exp $
BUILDLINK_TREE+= biolibc
.if !defined(BIOLIBC_BUILDLINK3_MK)
BIOLIBC_BUILDLINK3_MK:=
-BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.1.3
+BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.0
BUILDLINK_PKGSRCDIR.biolibc?= ../../biology/biolibc
.endif # BIOLIBC_BUILDLINK3_MK
Index: pkgsrc/biology/biolibc/distinfo
diff -u pkgsrc/biology/biolibc/distinfo:1.3 pkgsrc/biology/biolibc/distinfo:1.4
--- pkgsrc/biology/biolibc/distinfo:1.3 Tue Jun 15 13:47:46 2021
+++ pkgsrc/biology/biolibc/distinfo Sat Aug 28 18:34:37 2021
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.3 2021/06/15 13:47:46 bacon Exp $
+$NetBSD: distinfo,v 1.4 2021/08/28 18:34:37 bacon Exp $
-SHA1 (biolibc-0.1.3.2-69d937861329b1842778d98091e65b3c3c624add.tar.gz) = 0e6b006e282e2a75089d7ac3f220cb506804fcb6
-RMD160 (biolibc-0.1.3.2-69d937861329b1842778d98091e65b3c3c624add.tar.gz) = e758cabbf0969b1f3493709a77cf87454c9967f5
-SHA512 (biolibc-0.1.3.2-69d937861329b1842778d98091e65b3c3c624add.tar.gz) =
d71b70c1a293e992e84e999bed646ffcf0dc6f693a3213816519204b6cb3c7fc91eaa2b0531bc0bbd74f9f43fd4845efefb52f3ba673a7d763a9debc43b9c7ba
-Size (biolibc-0.1.3.2-69d937861329b1842778d98091e65b3c3c624add.tar.gz) = 30047 bytes
+SHA1 (biolibc-0.2.0.tar.gz) = 53aac7456c96bd938bde246ffe02abe1ea147c23
+RMD160 (biolibc-0.2.0.tar.gz) = bc8791766839b27ffb7c79591af7e6b376e77497
+SHA512 (biolibc-0.2.0.tar.gz) = b44fabc32a63385d64e143490ea3cd18dc75fc8e6d2995a44cc20b2fe5434656ea8f3c7c7a1eac9be7a0d7f208b2216c2e3089dee2d7b390cf737220518d3630
+Size (biolibc-0.2.0.tar.gz) = 117553 bytes
Added files:
Index: pkgsrc/biology/biolibc/files/plist-mods.sh
diff -u /dev/null pkgsrc/biology/biolibc/files/plist-mods.sh:1.1
--- /dev/null Sat Aug 28 18:34:37 2021
+++ pkgsrc/biology/biolibc/files/plist-mods.sh Sat Aug 28 18:34:37 2021
@@ -0,0 +1,4 @@
+#!/bin/sh -e
+
+# Plugin for local changes to PLIST folling make print-PLIST
+sed -i'' -e 's|^man/man3/BL_|${PLIST.cs}&|' PLIST.new
Home |
Main Index |
Thread Index |
Old Index