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[pkgsrc/trunk]: pkgsrc/biology/biolibc biology/biolibc: Update to 0.2.0
details: https://anonhg.NetBSD.org/pkgsrc/rev/d3f118c87f2b
branches: trunk
changeset: 457544:d3f118c87f2b
user: bacon <bacon%pkgsrc.org@localhost>
date: Sat Aug 28 18:34:37 2021 +0000
description:
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
diffstat:
biology/biolibc/Makefile | 9 +-
biology/biolibc/PLIST | 567 ++++++++++++++++++++++++++++++++++-
biology/biolibc/buildlink3.mk | 4 +-
biology/biolibc/distinfo | 10 +-
biology/biolibc/files/plist-mods.sh | 4 +
5 files changed, 565 insertions(+), 29 deletions(-)
diffs (truncated from 650 to 300 lines):
diff -r 631116dcc550 -r d3f118c87f2b biology/biolibc/Makefile
--- a/biology/biolibc/Makefile Sat Aug 28 18:34:09 2021 +0000
+++ b/biology/biolibc/Makefile Sat Aug 28 18:34:37 2021 +0000
@@ -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= ${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG= 69d937861329b1842778d98091e65b3c3c624add
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://github.com/auerlab/biolibc
@@ -17,9 +16,11 @@
INSTALL_TARGET= apple-install
.else
INSTALL_TARGET= install-strip
+PLIST.cs= yes
.endif
-MAKE_ENV+= DYLIB_PATH=${PREFIX}/lib
+MAKE_ENV+= DYLIB_PATH=${PREFIX}/lib MANDIR=${PREFIX}/${PKGMANDIR}
+PLIST_VARS= cs
pre-build:
cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend
diff -r 631116dcc550 -r d3f118c87f2b biology/biolibc/PLIST
--- a/biology/biolibc/PLIST Sat Aug 28 18:34:09 2021 +0000
+++ b/biology/biolibc/PLIST Sat Aug 28 18:34:37 2021 +0000
@@ -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.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
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