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

5 files changed, 158 insertions, 337 deletions

diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index 7af041ba9d1..8bcd4e70169 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -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
diff --git a/biology/biolibc/PLIST b/biology/biolibc/PLIST
index 682370abd08..9848b7b7923 100644
--- a/biology/biolibc/PLIST
+++ b/biology/biolibc/PLIST
@@ -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
-${PLIST.cs}man/man3/BL_POS_LIST_POSITIONS_AE.3
-${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/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
diff --git a/biology/biolibc/buildlink3.mk b/biology/biolibc/buildlink3.mk
index 71ea4118d9d..b5a67990f3e 100644
--- a/biology/biolibc/buildlink3.mk
+++ b/biology/biolibc/buildlink3.mk
@@ -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
diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo
index 8b53087429c..f93e11d5f94 100644
--- a/biology/biolibc/distinfo
+++ b/biology/biolibc/distinfo
@@ -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
diff --git a/biology/biolibc/files/plist-mods.sh b/biology/biolibc/files/plist-mods.sh
deleted file mode 100755
index 2e012e59009..00000000000
--- a/biology/biolibc/files/plist-mods.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh -e
-
-# Plugin for local changes to PLIST folling make print-PLIST
-sed -i'' -e 's|^man/man3/BL_|${PLIST.cs}&|' PLIST.new