[med-svn] [Git][med-team/subread][master] 4 commits: Annotate test-only B-D with <!nocheck>
Nilesh Patra
gitlab at salsa.debian.org
Thu Mar 11 14:00:21 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / subread
Commits:
88b58efd by Nilesh Patra at 2021-03-11T18:29:50+05:30
Annotate test-only B-D with <!nocheck>
- - - - -
589cf53e by Nilesh Patra at 2021-03-11T18:41:15+05:30
d/p/cross.patch: Fix non-cross buildability
- - - - -
f9d90bfa by Nilesh Patra at 2021-03-11T18:41:35+05:30
d/rules: Remove hardcoding on make
- - - - -
5c9b1389 by Nilesh Patra at 2021-03-11T13:51:16+00:00
Do not generate manpages during build time -- added createmanpages script which can be manually run at each release
- - - - -
20 changed files:
- debian/control
- + debian/createmanpages
- + debian/exactSNP.1
- + debian/featureCounts.1
- + debian/flattenGTF.1
- + debian/genRandomReads.1
- + debian/patches/cross.patch
- debian/patches/series
- + debian/propmapped.1
- + debian/qualityScores.1
- + debian/removeDup.1
- + debian/repair.1
- debian/rules
- + debian/subindel.1
- + debian/subjunc.1
- + debian/sublong.1
- + debian/subread-align.1
- + debian/subread-buildindex.1
- + debian/subread-fullscan.1
- + debian/subread.manpages
Changes:
=====================================
debian/control
=====================================
@@ -5,11 +5,10 @@ Uploaders: Alexandre Mestiashvili <mestia at debian.org>,
Nilesh Patra <nilesh at debian.org>
Section: science
Priority: optional
-Build-Depends: bc,
+Build-Depends: bc <!nocheck>,
debhelper-compat (= 12),
- help2man,
- python3,
- zlib1g-dev
+ python3 <!nocheck>,
+ zlib1g-dev,
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/subread
Vcs-Git: https://salsa.debian.org/med-team/subread.git
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,119 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+progpath=/usr/bin/subread-align
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/bin/subread-buildindex
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/bin/subjunc
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/bin/featureCounts
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/bin/exactSNP
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/bin/subindel
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/bin/sublong
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/subread-fullscan
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/propmapped
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/qualityScores
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/repair
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/removeDup
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/flattenGTF
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progpath=/usr/lib/subread/genRandomReads
+progname=`echo $progpath | sed "s/.*\///"`
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progpath} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/subread.manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
=====================================
debian/exactSNP.1
=====================================
@@ -0,0 +1,88 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH EXACTSNP "1" "March 2021" "exactSNP 2.0.1" "User Commands"
+.SH NAME
+exactSNP \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+Version 2.0.1
+.PP
+Usage:
+.IP
+\&./exactSNP [options] \fB\-i\fR input \fB\-g\fR reference_genome \fB\-o\fR output
+.PP
+Required arguments:
+.TP
+\fB\-i\fR <file>
+Specify name of an input file including read mapping results. The
+.IP
+[\-b if BAM] format of input file can be SAM or BAM (\fB\-b\fR needs to be specified
+.IP
+if a BAM file is provided).
+.TP
+\fB\-g\fR <file>
+Specify name of the file including all reference sequences. Only
+one single FASTA format file should be provided.
+.TP
+\fB\-o\fR <file>
+Specify name of the output file. This program outputs a VCF format
+file that includes discovered SNPs.
+.PP
+Optional arguments:
+.TP
+\fB\-a\fR <file>
+Provide a set of annotated SNPs (e.g. SNPs included in the dbSNP
+database). The supplied file should be in VCF format (gzipped file
+is accepted). Providing known SNPs to the program should improve
+its SNP calling performance. Note that the provided SNPs may or
+may not be called.
+.TP
+\fB\-b\fR
+Indicate the input file provided via \fB\-i\fR is in BAM format.
+.TP
+\fB\-Q\fR <int>
+Specify the q\-value cutoff for SNP calling at sequencing depth of
+50X. 12 by default. The corresponding p\-value cutoff is 10^(\fB\-1\fR*Q).
+Note that this program automatically adjusts the q\-value cutoff
+according to the sequencing depth at each chromosomal location.
+.HP
+\fB\-f\fR <float> Specify the minimum fraction of mis\-matched bases a SNP\-containing
+.IP
+location must have. Its value must between 0 and 1. 0 by default.
+.TP
+\fB\-n\fR <int>
+Specify the minimum number of mis\-matched bases a SNP\-containing
+location must have. 1 by default.
+.TP
+\fB\-r\fR <int>
+Specify the minimum number of mapped reads a SNP\-containing
+location must have (ie. the minimum coverage). 1 by default.
+.TP
+\fB\-x\fR <int>
+Specify the maximum depth a SNP location is allowed to have.
+1,000,000 reads by default. This option is useful for removing PCR
+artefacts.
+.TP
+\fB\-s\fR <int>
+Specify the minimum base quality scores (Phred scores) read bases
+must satisfy to be used for SNP calling. 13 by default. Read bases
+with quality scores less than 13 will be excluded from the
+analysis.
+.TP
+\fB\-t\fR <int>
+Specify the number of bases trimmed off from each end of the read.
+3 by default.
+.TP
+\fB\-T\fR <int>
+Specify the number of threads. 1 by default.
+.TP
+\fB\-v\fR
+output version of the program.
+.TP
+\fB\-C\fR <path>
+Specify the path to save the temporary files.
+.PP
+Example:
+.IP
+\&./exactSNP \fB\-i\fR my\-alignment.sam \fB\-g\fR mm10.fa \fB\-o\fR my\-SNPs.txt
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/featureCounts.1
=====================================
@@ -0,0 +1,279 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FEATURECOUNTS "1" "March 2021" "featureCounts 2.0.1" "User Commands"
+.SH NAME
+featureCounts \- toolkit for processing next-gen sequencing data
+.SH SYNOPSIS
+.B featureCounts
+[\fI\,options\/\fR] \fI\,-a <annotation_file> -o <output_file> input_file1 \/\fR[\fI\,input_file2\/\fR] ...
+.SH DESCRIPTION
+Version 2.0.1
+.PP
+## Mandatory arguments:
+.TP
+\fB\-a\fR <string>
+Name of an annotation file. GTF/GFF format by default. See
+\fB\-F\fR option for more format information. Inbuilt annotations
+(SAF format) is available in 'annotation' directory of the
+package. Gzipped file is also accepted.
+.TP
+\fB\-o\fR <string>
+Name of output file including read counts. A separate file
+including summary statistics of counting results is also
+included in the output ('<string>.summary'). Both files
+are in tab delimited format.
+.TP
+input_file1 [input_file2] ...
+A list of SAM or BAM format files. They can be
+.TP
+either name or location sorted. If no files provided,
+<stdin> input is expected. Location\-sorted paired\-end reads
+are automatically sorted by read names.
+.PP
+## Optional arguments:
+# Annotation
+.TP
+\fB\-F\fR <string>
+Specify format of the provided annotation file. Acceptable
+formats include 'GTF' (or compatible GFF format) and
+\&'SAF'. 'GTF' by default. For SAF format, please refer to
+Users Guide.
+.TP
+\fB\-t\fR <string>
+Specify feature type(s) in a GTF annotation. If multiple
+types are provided, they should be separated by ',' with
+no space in between. 'exon' by default. Rows in the
+annotation with a matched feature will be extracted and
+used for read mapping.
+.TP
+\fB\-g\fR <string>
+Specify attribute type in GTF annotation. 'gene_id' by
+default. Meta\-features used for read counting will be
+extracted from annotation using the provided value.
+.TP
+\fB\-\-extraAttributes\fR
+Extract extra attribute types from the provided GTF
+annotation and include them in the counting output. These
+attribute types will not be used to group features. If
+more than one attribute type is provided they should be
+separated by comma.
+.TP
+\fB\-A\fR <string>
+Provide a chromosome name alias file to match chr names in
+annotation with those in the reads. This should be a twocolumn comma\-delimited text file. Its first column should
+include chr names in the annotation and its second column
+should include chr names in the reads. Chr names are case
+sensitive. No column header should be included in the
+file.
+.PP
+# Level of summarization
+.TP
+\fB\-f\fR
+Perform read counting at feature level (eg. counting
+reads for exons rather than genes).
+.PP
+# Overlap between reads and features
+.TP
+\fB\-O\fR
+Assign reads to all their overlapping meta\-features (or
+features if \fB\-f\fR is specified).
+.TP
+\fB\-\-minOverlap\fR <int>
+Minimum number of overlapping bases in a read that is
+required for read assignment. 1 by default. Number of
+overlapping bases is counted from both reads if paired
+end. If a negative value is provided, then a gap of up
+to specified size will be allowed between read and the
+feature that the read is assigned to.
+.TP
+\fB\-\-fracOverlap\fR <float> Minimum fraction of overlapping bases in a read that is
+required for read assignment. Value should be within range
+[0,1]. 0 by default. Number of overlapping bases is
+counted from both reads if paired end. Both this option
+and '\-\-minOverlap' option need to be satisfied for read
+assignment.
+.TP
+\fB\-\-fracOverlapFeature\fR <float> Minimum fraction of overlapping bases in a
+feature that is required for read assignment. Value
+should be within range [0,1]. 0 by default.
+.TP
+\fB\-\-largestOverlap\fR
+Assign reads to a meta\-feature/feature that has the
+largest number of overlapping bases.
+.TP
+\fB\-\-nonOverlap\fR <int>
+Maximum number of non\-overlapping bases in a read (or a
+read pair) that is allowed when being assigned to a
+feature. No limit is set by default.
+.TP
+\fB\-\-nonOverlapFeature\fR <int> Maximum number of non\-overlapping bases in a feature
+that is allowed in read assignment. No limit is set by
+default.
+.TP
+\fB\-\-readExtension5\fR <int> Reads are extended upstream by <int> bases from their
+5' end.
+.TP
+\fB\-\-readExtension3\fR <int> Reads are extended upstream by <int> bases from their
+3' end.
+.TP
+\fB\-\-read2pos\fR <5:3>
+Reduce reads to their 5' most base or 3' most base. Read
+counting is then performed based on the single base the
+read is reduced to.
+.PP
+# Multi\-mapping reads
+.TP
+\fB\-M\fR
+Multi\-mapping reads will also be counted. For a multimapping read, all its reported alignments will be
+counted. The 'NH' tag in BAM/SAM input is used to detect
+multi\-mapping reads.
+.PP
+# Fractional counting
+.TP
+\fB\-\-fraction\fR
+Assign fractional counts to features. This option must
+be used together with '\-M' or '\-O' or both. When '\-M' is
+specified, each reported alignment from a multi\-mapping
+read (identified via 'NH' tag) will carry a fractional
+count of 1/x, instead of 1 (one), where x is the total
+number of alignments reported for the same read. When '\-O'
+is specified, each overlapping feature will receive a
+fractional count of 1/y, where y is the total number of
+features overlapping with the read. When both '\-M' and
+\&'\-O' are specified, each alignment will carry a fractional
+count of 1/(x*y).
+.PP
+# Read filtering
+.TP
+\fB\-Q\fR <int>
+The minimum mapping quality score a read must satisfy in
+order to be counted. For paired\-end reads, at least one
+end should satisfy this criteria. 0 by default.
+.TP
+\fB\-\-splitOnly\fR
+Count split alignments only (ie. alignments with CIGAR
+string containing 'N'). An example of split alignments is
+exon\-spanning reads in RNA\-seq data.
+.TP
+\fB\-\-nonSplitOnly\fR
+If specified, only non\-split alignments (CIGAR strings do
+not contain letter 'N') will be counted. All the other
+alignments will be ignored.
+.TP
+\fB\-\-primary\fR
+Count primary alignments only. Primary alignments are
+identified using bit 0x100 in SAM/BAM FLAG field.
+.TP
+\fB\-\-ignoreDup\fR
+Ignore duplicate reads in read counting. Duplicate reads
+are identified using bit Ox400 in BAM/SAM FLAG field. The
+whole read pair is ignored if one of the reads is a
+duplicate read for paired end data.
+.PP
+# Strandness
+.TP
+\fB\-s\fR <int or string>
+Perform strand\-specific read counting. A single integer
+value (applied to all input files) or a string of commaseparated values (applied to each corresponding input
+file) should be provided. Possible values include:
+0 (unstranded), 1 (stranded) and 2 (reversely stranded).
+Default value is 0 (ie. unstranded read counting carried
+out for all input files).
+.PP
+# Exon\-exon junctions
+.TP
+\fB\-J\fR
+Count number of reads supporting each exon\-exon junction.
+Junctions were identified from those exon\-spanning reads
+in the input (containing 'N' in CIGAR string). Counting
+results are saved to a file named '<output_file>.jcounts'
+.TP
+\fB\-G\fR <string>
+Provide the name of a FASTA\-format file that contains the
+reference sequences used in read mapping that produced the
+provided SAM/BAM files. This optional argument can be used
+with '\-J' option to improve read counting for junctions.
+.PP
+# Parameters specific to paired end reads
+.TP
+\fB\-p\fR
+If specified, fragments (or templates) will be counted
+instead of reads. This option is only applicable for
+paired\-end reads; single\-end reads are always counted as
+reads.
+.TP
+\fB\-B\fR
+Only count read pairs that have both ends aligned.
+.TP
+\fB\-P\fR
+Check validity of paired\-end distance when counting read
+pairs. Use \fB\-d\fR and \fB\-D\fR to set thresholds.
+.TP
+\fB\-d\fR <int>
+Minimum fragment/template length, 50 by default.
+.TP
+\fB\-D\fR <int>
+Maximum fragment/template length, 600 by default.
+.TP
+\fB\-C\fR
+Do not count read pairs that have their two ends mapping
+to different chromosomes or mapping to same chromosome
+but on different strands.
+.TP
+\fB\-\-donotsort\fR
+Do not sort reads in BAM/SAM input. Note that reads from
+the same pair are required to be located next to each
+other in the input.
+.PP
+# Number of CPU threads
+.TP
+\fB\-T\fR <int>
+Number of the threads. 1 by default.
+.PP
+# Read groups
+.TP
+\fB\-\-byReadGroup\fR
+Assign reads by read group. "RG" tag is required to be
+present in the input BAM/SAM files.
+.PP
+# Long reads
+.TP
+\fB\-L\fR
+Count long reads such as Nanopore and PacBio reads. Long
+read counting can only run in one thread and only reads
+(not read\-pairs) can be counted. There is no limitation on
+the number of 'M' operations allowed in a CIGAR string in
+long read counting.
+.PP
+# Assignment results for each read
+.TP
+\fB\-R\fR <format>
+Output detailed assignment results for each read or readpair. Results are saved to a file that is in one of the
+following formats: CORE, SAM and BAM. See Users Guide for
+more info about these formats.
+.TP
+\fB\-\-Rpath\fR <string>
+Specify a directory to save the detailed assignment
+results. If unspecified, the directory where counting
+results are saved is used.
+.PP
+# Miscellaneous
+.TP
+\fB\-\-tmpDir\fR <string>
+Directory under which intermediate files are saved (later
+removed). By default, intermediate files will be saved to
+the directory specified in '\-o' argument.
+.TP
+\fB\-\-maxMOp\fR <int>
+Maximum number of 'M' operations allowed in a CIGAR
+string. 10 by default. Both 'X' and '=' are treated as 'M'
+and adjacent 'M' operations are merged in the CIGAR
+string.
+.TP
+\fB\-\-verbose\fR
+Output verbose information for debugging, such as unmatched chromosome/contig names.
+.TP
+\fB\-v\fR
+Output version of the program.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/flattenGTF.1
=====================================
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FLATTENGTF "1" "March 2021" "flattenGTF 2.0.1" "User Commands"
+.SH NAME
+flattenGTF \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+flattenGTF Version 2.0.1
+.IP
+Flatten features included in a GTF annotation and save the modified annotation
+to a SAF format file.
+.SS "Usage:"
+.IP
+\&./flattenGTF [options] \fB\-a\fR <input_file> \fB\-o\fR <output_file>
+.PP
+## Mandatory arguments:
+.TP
+\fB\-a\fR <file>
+Name of an annotation file in GTF/GFF format.
+.TP
+\fB\-o\fR <file>
+Name of output file.
+.PP
+## Optional arguments:
+.TP
+\fB\-t\fR <string>
+Specify feature type in a GTF annotation. 'exon' by default.
+Features with the specified feature type are extracted from the
+annotation for processing.
+.TP
+\fB\-g\fR <string>
+Specify attribute type in GTF annotation. 'gene_id' by default.
+This attribute type is used to group features into metafeatures.
+.TP
+\fB\-C\fR
+Merging overlapping exons into multiple non\-overlapping exons but
+all the edges are kept.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/genRandomReads.1
=====================================
@@ -0,0 +1,84 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH GENRANDOMREADS "1" "March 2021" "genRandomReads 2.0.1" "User Commands"
+.SH NAME
+genRandomReads \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+Error: a transcript file must be provide!
+Error: the output prefix must be provide!
+Error: the wanted expression levels must be provided!
+Warning: no read number is specified. Generating one million reads.
+.PP
+Usage:
+.IP
+For scanning a FASTA/gz file:
+.IP
+\fI\,/usr/lib/subread/genRandomReads\/\fP \fB\-\-summarizeFasta\fR \e
+.HP
+\fB\-\-transcriptFasta\fR <file> \fB\-\-outputPrefix\fR <string> [\-\-simpleTranscriptId]
+.IP
+For generating read/pairs:
+.IP
+\fI\,/usr/lib/subread/genRandomReads\/\fP \fB\-\-transcriptFasta\fR <file>\e
+.HP
+\fB\-\-outputPrefix\fR <string> \fB\-\-expressionLevels\fR <file> [other options]
+.TP
+\fB\-\-summarizeFasta\fR
+Only output the transcript names and lengths.
+.TP
+\fB\-\-transcriptFasta\fR <file>
+The transcript database in FASTA/gz format.
+.TP
+\fB\-\-outputPrefix\fR <string>
+The prefix of the output files.
+.TP
+\fB\-\-totalReads\fR
+<int> Total read/pairs in output.
+.TP
+\fB\-\-expressionLevels\fR <file>
+Two column table delimited by <TAB>, giving the
+wanted TPM values. Columns: TranscriptID and TPM
+.TP
+\fB\-\-readLen\fR <int>
+The length of the output reads. 100 by default.
+.TP
+\fB\-\-totalReads\fR <int>
+Total read/pairs in the output.
+.TP
+\fB\-\-randSeed\fR <int64>
+Seed to generate random numbers. UNIXTIME is used
+as the random seed by default.
+.TP
+\fB\-\-qualityRefFile\fR <file>
+A textual file containing Phred+33 quanlity strings
+for simulating sequencing errors. The quality
+strings have to have the same length as the output
+reads. No sequencing errors are simulated when this
+option is omitted.
+.TP
+\fB\-\-floorStrategy\fR
+How to deal with round\-up errors. 'FLOOR': generate
+less than wanted reads; 'RANDOM': randomly assign
+margin reads to transcripts; 'ITERATIVE': find the
+best M value to have ~N reads.
+.TP
+\fB\-\-pairedEnd\fR
+Generate paired\-end reads.
+.HP
+\fB\-\-insertionLenMean\fR <float>,\-\-insertionLenSigma <float>,\-\-insertionLenMin <int>,
+.TP
+\fB\-\-insertionLenMax\fR <int>
+Parameters of a truncated normal distribution for
+deciding insertion lengths of paired\-end reads.
+Default values: mean=160, sigma=30, min=110, max=400
+.TP
+\fB\-\-simpleTranscriptId\fR
+Truncate transcript names to the first '|' or space.
+.TP
+\fB\-\-truthInReadNames\fR
+Encode the true locations of reads in read names.
+.TP
+\fB\-\-noActualReads\fR
+Do not actually generate reads in fastq.gz files.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/patches/cross.patch
=====================================
@@ -0,0 +1,122 @@
+Description: Make build cross buildable -- fix compilation flags
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-03-11
+--- a/src/Makefile.Linux
++++ b/src/Makefile.Linux
+@@ -1,7 +1,5 @@
+ #MACOS = -D MACOS
+
+-
+-CC_EXEC = gcc
+ OPT_LEVEL = 3
+
+ include makefile.version
+@@ -9,7 +7,7 @@
+
+ CCFLAGS += -O${OPT_LEVEL} -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
+ LDFLAGS += ${STATIC_MAKE} -pthread -lz -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
+-CC = ${CC_EXEC} ${CCFLAGS} ${CFLAGS} ${CPPFLAGS} -fmessage-length=0 -ggdb
++CFLAGS += ${CCFLAGS} -fmessage-length=0 -ggdb
+
+
+ ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc
+@@ -38,55 +36,55 @@
+ cd longread-one && $(MAKE)
+
+ genRandomReads: gen_rand_reads.c ${ALL_OBJECTS}
+- ${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ flattenGTF: flattenAnnotations.c ${ALL_OBJECTS}
+- ${CC} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ detectionCall: detection-calls.c ${ALL_OBJECTS}
+- ${CC} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ repair: read-repair.c ${ALL_OBJECTS}
+- ${CC} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ txUnique: tx-unique.c tx-unique.h ${ALL_OBJECTS}
+- ${CC} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ globalReassembly: global-reassembly.c ${ALL_OBJECTS}
+- ${CC} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ propmapped: propmapped.c ${ALL_OBJECTS}
+- ${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ exactSNP: SNPCalling.c SNPCalling.h ${ALL_OBJECTS}
+- ${CC} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS}
+- ${CC} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS}
+- ${CC} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ subindel: SUBindel.c core.h subread.h ${ALL_OBJECTS}
+- ${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ featureCounts: readSummary.c subread.h ${ALL_OBJECTS}
+- ${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ subread-align: core-interface-aligner.c ${ALL_OBJECTS}
+- ${CC} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ subjunc: core-interface-subjunc.c ${ALL_OBJECTS}
+- ${CC} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ subtools: subtools.c ${ALL_OBJECTS}
+- ${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ qualityScores: qualityScores.c ${ALL_OBJECTS}
+- ${CC} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ subread-fullscan: fullscan.c ${ALL_OBJECTS}
+- ${CC} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} ${CFLAGS} ${CPPFLAGS} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ clean:
+ rm -f core featureCounts exactSNP removeDup subread-buildindex ${ALL_OBJECTS}
+--- a/src/longread-one/Makefile
++++ b/src/longread-one/Makefile
+@@ -1,4 +1,3 @@
+-CC_EXEC = gcc
+ OPT_LEVEL = 3
+
+ include ../makefile.version
+@@ -6,7 +5,7 @@
+
+ CCFLAGS += -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
+ LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+-CC = ${CC_EXEC} ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -fmessage-length=0 -ggdb
++CFLAGS += ${CCFLAGS} -fmessage-length=0 -ggdb
+
+ ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable
+ ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
+@@ -20,8 +19,8 @@
+ rm -f *.o LRM
+
+ LRM: longread-mapping.c ${ALL_OBJECTS}
+- ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} $(CFLAGS) $(CPPFLAGS) -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ $(ALL_OBJECTS): $(ALL_C) $(ALL_H)
+- $(CC) -o $@ -c $(subst .o,.c,$@)
++ $(CC) $(CFLAGS) $(CPPFLAGS) -o $@ -c $(subst .o,.c,$@)
+
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ fix_ftbfs_kfreebsd.patch
arch_specific_flags.patch
2to3.patch
gcc10.patch
+cross.patch
=====================================
debian/propmapped.1
=====================================
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH PROPMAPPED "1" "March 2021" "propmapped 2.0.1" "User Commands"
+.SH NAME
+propmapped \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+propMapped v2.0.1
+.IP
+Calculate the proportion of mapped reads/fragments.
+.PP
+Usage:
+.IP
+\&./prommapped [options] \fB\-i\fR <file>
+.PP
+Required arguments:
+.TP
+\fB\-i\fR <string>
+An input file containing read mapping results. Both SAM or BAM
+formats are supported.
+.PP
+Optional arguments:
+.TP
+\fB\-o\fR <string>
+Name of output file including mapping statistics.
+.TP
+\fB\-f\fR
+If specified, fragments (read pairs) will be counted instead of
+individual reads. This option is only applicable for paired\-end
+reads.
+.TP
+\fB\-p\fR
+If specified, only properly paired reads will be counted. This
+option is only applicable for paired\-end reads.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/qualityScores.1
=====================================
@@ -0,0 +1,49 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH QUALITYSCORES "1" "March 2021" "qualityScores 2.0.1" "User Commands"
+.SH NAME
+qualityScores \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+qualityScore Version 2.0.1
+.IP
+Retrieve Phred score for read bases
+.PP
+Usage:
+.IP
+\&./qualityScores [options] \fB\-i\fR <input_file> \fB\-o\fR <output_file>
+.PP
+Required arguments:
+.TP
+\fB\-i\fR <string>
+Name of input file including read data. The default format is
+Fastq.
+.TP
+\fB\-o\fR <string>
+Name of output file that is a text file including Phred scores
+for each read base.
+.PP
+Optional arguments:
+.HP
+\fB\-\-gzFASTQinput\fR Input file is in gzipped Fastq format.
+.TP
+\fB\-\-BAMinput\fR
+Input file is in BAM format.
+.TP
+\fB\-\-SAMinput\fR
+Input file is in SAM format.
+.TP
+\fB\-\-first\-end\fR
+Use only first reads in paired\-end data. Only applicable for
+paired\-end BAM/SAM input.
+.TP
+\fB\-\-second\-end\fR
+Use only second reads in paired\-end data. Only applicable for
+paired\-end BAM/SAM input.
+.HP
+\fB\-\-counted\-reads\fR <int> Total number of reads to be extracted from the input
+.IP
+file. 10,000 by default.
+.HP
+\fB\-\-phred\-offset\fR <33|64> refer to subread aligner.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/removeDup.1
=====================================
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH REMOVEDUP "1" "March 2021" "removeDup 2.0.1" "User Commands"
+.SH NAME
+removeDup \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+removeDup Version 2.0.1
+.IP
+Remove duplicated reads.
+.SS "Usage:"
+.IP
+\&./removeDup [options] \fB\-i\fR <input_file> \fB\-o\fR <output_file>
+.PP
+Required arguments:
+.HP
+\fB\-i\fR <string> Name of input file in SAM/BAM format.
+.HP
+\fB\-o\fR <string> Name of output SAM file including filtered reads. The format is
+.IP
+BAM unless '\-S' is specified.
+.PP
+Optional arguments:
+.TP
+\fB\-S\fR
+Generate the SAM format output.
+.TP
+\fB\-r\fR <int>
+Specify the duplication cutoff. All the reads mapped to a location
+are removed from the output if the number of reads mapped to this
+location is equal or higher than the cutoff. 10 by default.
+.HP
+\fB\-t\fR <string> A directory storing temporary files generated by the program.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/repair.1
=====================================
@@ -0,0 +1,47 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH REPAIR "1" "March 2021" "repair 2.0.1" "User Commands"
+.SH NAME
+repair \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+repair Version 2.0.1
+.IP
+Find reads that are from the same pair in the input and then place them next
+.PP
+to each other in the output. A dummy read is added for each singleton read
+that does not have a pair. The output file is compatible with featureCounts
+program.
+.PP
+Usage:
+.IP
+\&./repair [options] \fB\-i\fR <input_file> \fB\-o\fR <output_file>
+.PP
+Required arguments:
+.TP
+\fB\-i\fR <string>
+Name of input file. BAM format by default.
+.TP
+\fB\-o\fR <string>
+Name of output file. The output file is in BAM format.
+.PP
+Optional arguments:
+.TP
+\fB\-S\fR
+The input file is in SAM format.
+.TP
+\fB\-c\fR
+Compress the output BAM file. This will reduce the size of BAM
+file, but will increase the time of retrieving reads from BAM
+file.
+.TP
+\fB\-T\fR <int>
+Number of CPU threads. 8 by default.
+.TP
+\fB\-d\fR
+Do not add dummy reads for singleton reads.
+.TP
+\fB\-t\fR
+Do not include sequences and quality scores of reads in the
+output file.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/rules
=====================================
@@ -2,11 +2,6 @@
export DH_VERBOSE=1
-pkg := subread
-mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
-bindir := $(CURDIR)/bin
-utildir := $(CURDIR)/bin/utilities
-
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/architecture.mk
ifeq ($(origin CC),default)
@@ -21,86 +16,26 @@ ifeq ($(DEB_HOST_ARCH_OS), kfreebsd)
endif
%:
- dh $@
-
-override_dh_clean:
- cd src; make -f Makefile.Linux clean
- dh_clean
+ dh $@ --buildsystem=makefile
override_dh_auto_clean:
dh_auto_clean
rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz
rm -rf bin src/longread-one/make.version
find . -name "*.o" -delete
+ dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux
override_dh_auto_build:
- cd src; make -f Makefile.Linux
- dh_auto_build -- CC=$(CC)
+ dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=$(CC) ; \
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
debian/tests/subread-tests $(CURDIR)
endif
-HELP2MAN = help2man --no-info --help-option="''" --no-discard-stderr
-
override_dh_auto_install:
#fix for gzip-file-is-not-multi-arch-same-safe
find $(CURDIR) -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "$${name%.*}"' \;
-
- mkdir -p $(mandir)
- $(HELP2MAN) --name='an accurate and efficient aligner for mapping both genomic \
-DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
- $(bindir)/subread-align | debian/filter.pl > $(mandir)/subread-align.1;
-
- $(HELP2MAN) --name='builds an base-space or color-space index using the reference sequences' \
- $(bindir)/subread-buildindex | debian/filter.pl > $(mandir)/subread-buildindex.1;
-
- $(HELP2MAN) --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
- $(bindir)/subjunc | debian/filter.pl > $(mandir)/subjunc.1;
-
- $(HELP2MAN) --name='a highly efficient and accurate read summarization program' \
- $(bindir)/featureCounts | debian/filter.pl > $(mandir)/featureCounts.1;
-
- $(HELP2MAN) --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
- $(bindir)/exactSNP | debian/filter.pl > $(mandir)/exactSNP.1;
-
- $(HELP2MAN) --name='detect short and long indels' \
- $(bindir)/subindel | debian/filter.pl > $(mandir)/subindel.1;
-
- $(HELP2MAN) --name='long-read aligner that is designed based on seed-and-vote' \
- $(bindir)/sublong| debian/filter.pl > $(mandir)/sublong.1;
-
- $(HELP2MAN) --name='scans the entire genome and reports all matches of a specified sequence' \
- $(utildir)/subread-fullscan | debian/filter.pl > $(mandir)/subread-fullscan.1;
-
-# $(HELP2MAN) --name='counting the coverage of mapped reads at each location on the entire reference genome' \
-# $(utildir)/coverageCount | debian/filter.pl > $(mandir)/coverageCount.1;
-
-# $(HELP2MAN) --name='detectionCall' \
-# $(utildir)/detectionCall | debian/filter.pl > $(mandir)/detectionCall.1;
-
- $(HELP2MAN) --name='calculate the proportion of mapped reads/fragments' \
- $(utildir)/propmapped | debian/filter.pl > $(mandir)/propmapped.1;
-
- $(HELP2MAN) --name='retrieve Phred score for read bases' \
- $(utildir)/qualityScores| debian/filter.pl > $(mandir)/qualityScores.1;
-
- $(HELP2MAN) --name='Find reads that are from the same pair in the input and then place them next \
-to each other in the output. A dummy read is added for each singleton read that does not have a pair. \
-The output file is compatible with featureCounts program' \
- $(utildir)/repair| debian/filter.pl > $(mandir)/repair.1;
-
- $(HELP2MAN) --name='Remove duplicated reads' \
- $(utildir)/removeDup| debian/filter.pl > $(mandir)/removeDup.1;
-
- $(HELP2MAN) --name='Flatten features included in a GTF annotation and save the modified annotation \
-to a SAF format file.' \
- $(utildir)/flattenGTF| debian/filter.pl > $(mandir)/flattenGTF.1;
-
- $(HELP2MAN) --name='helper tool from subread suite' \
- $(utildir)/genRandomReads| debian/filter.pl > $(mandir)/genRandomReads.1;
-
dh_auto_install
override_dh_installexamples-indep:
=====================================
debian/subindel.1
=====================================
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SUBINDEL "1" "March 2021" "subindel 2.0.1" "User Commands"
+.SH NAME
+subindel \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+SubIndel: detect short and long indels
+.SS "Usage:"
+.IP
+subindel \fB\-i\fR <SAM file> \fB\-g\fR <subread index> \fB\-o\fR <output VCF> {\-d <expected fragment distance>} {\-I <max indel length>} {\-\-paired\-end}
+.SS "Example:"
+.IP
+subindel \fB\-i\fR my_paired_end_reads.SAM \fB\-g\fR my_index \fB\-o\fR my_result \fB\-d\fR 300 \fB\-I\fR 200 \fB\-\-paired\-end\fR
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/subjunc.1
=====================================
@@ -0,0 +1,210 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SUBJUNC "1" "March 2021" "subjunc 2.0.1" "User Commands"
+.SH NAME
+subjunc \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+Version 2.0.1
+.PP
+Usage:
+.IP
+\&./subjunc [options] \fB\-i\fR <index_name> \fB\-r\fR <input> \fB\-o\fR <output>
+.PP
+## Mandatory arguments:
+.TP
+\fB\-i\fR <index>
+Base name of the index.
+.TP
+\fB\-r\fR <string>
+Name of an input read file. If paired\-end, this should be
+the first read file (typically containing "R1"in the file
+name) and the second should be provided via "\-R".
+Acceptable formats include gzipped FASTQ, FASTQ, gzipped
+FASTA and FASTA.
+These formats are identified automatically.
+.PP
+## Optional arguments:
+# input reads and output
+.TP
+\fB\-o\fR <string>
+Name of an output file. By default, the output is in BAM
+format. Omitting this option makes the output be written to
+STDOUT.
+.TP
+\fB\-R\fR <string>
+Name of the second read file in paired\-end data (typically
+containing "R2" the file name).
+.TP
+\fB\-\-SAMinput\fR
+Input reads are in SAM format.
+.TP
+\fB\-\-BAMinput\fR
+Input reads are in BAM format.
+.TP
+\fB\-\-SAMoutput\fR
+Save mapping results in SAM format.
+.PP
+# Phred offset
+.TP
+\fB\-P\fR <3:6>
+Offset value added to the Phred quality score of each read
+base. '3' for phred+33 and '6' for phred+64. '3' by default.
+.PP
+# thresholds for mapping
+.TP
+\fB\-n\fR <int>
+Number of selected subreads, 14 by default.
+.TP
+\fB\-m\fR <int>
+Consensus threshold for reporting a hit (minimal number of
+subreads that map in consensus) . If paired\-end, this gives
+the consensus threshold for the anchor read (anchor read
+receives more votes than the other read in the same pair).
+1 by default.
+.TP
+\fB\-p\fR <int>
+Consensus threshold for the non\- anchor read in a pair. 1 by
+default.
+.TP
+\fB\-M\fR <int>
+Maximum number of mis\-matched bases allowed in each reported
+alignment. 3 by default. Mis\-matched bases found in softclipped bases are not counted.
+.PP
+# unique mapping and multi\-mapping
+.TP
+\fB\-\-multiMapping\fR
+Report multi\-mapping reads in addition to uniquely mapped
+reads. Use "\-B" to set the maximum number of equally\-best
+alignments to be reported.
+.TP
+\fB\-B\fR <int>
+Maximum number of equally\-best alignments to be reported for
+a multi\-mapping read. Equally\-best alignments have the same
+number of mis\-matched bases. 1 by default.
+.PP
+# indel detection
+.TP
+\fB\-I\fR <int>
+Maximum length (in bp) of indels that can be detected. 5 by
+default. Indels of up to 200bp long can be detected.
+.TP
+\fB\-\-complexIndels\fR
+Detect multiple short indels that are in close proximity
+(they can be as close as 1bp apart from each other).
+.PP
+# read trimming
+.TP
+\fB\-\-trim5\fR <int>
+Trim off <int> number of bases from 5' end of each read. 0
+by default.
+.TP
+\fB\-\-trim3\fR <int>
+Trim off <int> number of bases from 3' end of each read. 0
+by default.
+.PP
+# distance and orientation of paired end reads
+.TP
+\fB\-d\fR <int>
+Minimum fragment/insert length, 50bp by default.
+.TP
+\fB\-D\fR <int>
+Maximum fragment/insert length, 600bp by default.
+.TP
+\fB\-S\fR <ff:fr:rf>
+Orientation of first and second reads, 'fr' by default (
+forward/reverse).
+.PP
+# number of CPU threads
+.TP
+\fB\-T\fR <int>
+Number of CPU threads used, 1 by default.
+.PP
+# read group
+.TP
+\fB\-\-rg\-id\fR <string>
+Add read group ID to the output.
+.TP
+\fB\-\-rg\fR <string>
+Add <tag:value> to the read group (RG) header in the output.
+.PP
+# read order
+.TP
+\fB\-\-keepReadOrder\fR
+Keep order of reads in BAM output the same as that in the
+input file. Reads from the same pair are always placed next
+to each other no matter this option is specified or not.
+.TP
+\fB\-\-sortReadsByCoordinates\fR Output location\-sorted reads. This option is
+applicable for BAM output only. A BAI index file is also
+generated for each BAM file so the BAM files can be directly
+loaded into a genome browser.
+.PP
+# color space reads
+.TP
+\fB\-b\fR
+Convert color\-space read bases to base\-space read bases in
+the mapping output. Note that read mapping is performed at
+color\-space.
+.PP
+# dynamic programming
+.TP
+\fB\-\-DPGapOpen\fR <int> Penalty for gap opening in short indel detection. \fB\-1\fR by
+default.
+.TP
+\fB\-\-DPGapExt\fR <int>
+Penalty for gap extension in short indel detection. 0 by
+default.
+.TP
+\fB\-\-DPMismatch\fR <int> Penalty for mismatches in short indel detection. 0 by
+default.
+.TP
+\fB\-\-DPMatch\fR <int>
+Score for matched bases in short indel detection. 2 by
+default.
+.PP
+# detect all junctions including gene fusions
+.TP
+\fB\-\-allJunctions\fR
+Detect exon\-exon junctions (both canonical and non\-canonical
+junctions) and structural variants in RNA\-seq data. Refer to
+Users Guide for reporting of junctions and fusions.
+.PP
+# gene annotation
+.TP
+\fB\-a\fR
+Name of an annotation file (gzipped file is accepted).
+GTF/GFF format by default. See \fB\-F\fR option for more format
+information.
+.TP
+\fB\-F\fR
+Specify format of the provided annotation file. Acceptable
+formats include 'GTF' (or compatible GFF format) and
+\&'SAF'. 'GTF' by default. For SAF format, please refer to
+Users Guide.
+.TP
+\fB\-A\fR
+Provide a chromosome name alias file to match chr names in
+annotation with those in the reads. This should be a twocolumn comma\-delimited text file. Its first column should
+include chr names in the annotation and its second column
+should include chr names in the index. Chr names are case
+sensitive. No column header should be included in the
+file.
+.TP
+\fB\-\-gtfFeature\fR <string>
+Specify feature type in GTF annotation. 'exon'
+by default. Features used for read counting will be
+extracted from annotation using the provided value.
+.TP
+\fB\-\-gtfAttr\fR <string>
+Specify attribute type in GTF annotation. 'gene_id'
+by default. Meta\-features used for read counting will be
+extracted from annotation using the provided value.
+.PP
+# others
+.TP
+\fB\-v\fR
+Output version of the program.
+.PP
+Refer to Users Manual for detailed description to the arguments.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/sublong.1
=====================================
@@ -0,0 +1,49 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SUBLONG "1" "March 2021" "sublong 2.0.1" "User Commands"
+.SH NAME
+sublong \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+Please specify the input, output files and the index.
+.PP
+Sublong v2.0.1
+.PP
+Usage:
+.PP
+\&./sublong [options] \fB\-i\fR <index_name> \fB\-r\fR <input> \fB\-o\fR <output>
+.PP
+## Mandatory arguments:
+.TP
+\fB\-i\fR <string>
+Base name of the index. The index must be built as a full index
+and has only one block.
+.TP
+\fB\-r\fR <string>
+Name of an input read file. Acceptable formats include gzipped
+FASTQ and FASTQ (automatically identified).
+.TP
+\fB\-o\fR <string>
+Name of an output file in BAM format.
+.PP
+## Optional arguments:
+# input reads and output
+.TP
+\fB\-\-SAMoutput\fR
+Save mapping results in SAM format.
+.PP
+# number of CPU threads
+.TP
+\fB\-T\fR <int>
+Number of CPU threads used. 1 by default.
+.PP
+# others
+.TP
+\fB\-v\fR
+Output version of the program.
+.TP
+\fB\-X\fR
+Turn on the RNA\-seq mode.
+.PP
+Refer to Users Manual for detailed description to the arguments.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/subread-align.1
=====================================
@@ -0,0 +1,215 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SUBREAD-ALIGN "1" "March 2021" "subread-align 2.0.1" "User Commands"
+.SH NAME
+subread-align \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+Version 2.0.1
+.PP
+Usage:
+.PP
+\&./subread\-align [options] \fB\-i\fR <index_name> \fB\-r\fR <input> \fB\-t\fR <type> \fB\-o\fR <output>
+.PP
+## Mandatory arguments:
+.TP
+\fB\-i\fR <string>
+Base name of the index.
+.TP
+\fB\-r\fR <string>
+Name of an input read file. If paired\-end, this should be
+the first read file (typically containing "R1"in the file
+name) and the second should be provided via "\-R".
+Acceptable formats include gzipped FASTQ, FASTQ, gzipped
+FASTA and FASTA.
+These formats are identified automatically.
+.TP
+\fB\-t\fR <int>
+Type of input sequencing data. Its values include
+0: RNA\-seq data
+1: genomic DNA\-seq data.
+.PP
+## Optional arguments:
+# input reads and output
+.TP
+\fB\-o\fR <string>
+Name of an output file. By default, the output is in BAM
+format. Omitting this option makes the output be written to
+STDOUT.
+.TP
+\fB\-R\fR <string>
+Name of the second read file in paired\-end data (typically
+containing "R2" the file name).
+.TP
+\fB\-\-SAMinput\fR
+Input reads are in SAM format.
+.TP
+\fB\-\-BAMinput\fR
+Input reads are in BAM format.
+.TP
+\fB\-\-SAMoutput\fR
+Save mapping results in SAM format.
+.PP
+# Phred offset
+.TP
+\fB\-P\fR <3:6>
+Offset value added to the Phred quality score of each read
+base. '3' for phred+33 and '6' for phred+64. '3' by default.
+.PP
+# thresholds for mapping
+.TP
+\fB\-n\fR <int>
+Number of selected subreads, 10 by default.
+.TP
+\fB\-m\fR <int>
+Consensus threshold for reporting a hit (minimal number of
+subreads that map in consensus) . If paired\-end, this gives
+the consensus threshold for the anchor read (anchor read
+receives more votes than the other read in the same pair).
+3 by default
+.TP
+\fB\-p\fR <int>
+Consensus threshold for the non\- anchor read in a pair. 1 by
+default.
+.TP
+\fB\-M\fR <int>
+Maximum number of mis\-matched bases allowed in each reported
+alignment. 3 by default. Mis\-matched bases found in softclipped bases are not counted.
+.PP
+# unique mapping and multi\-mapping
+.TP
+\fB\-\-multiMapping\fR
+Report multi\-mapping reads in addition to uniquely mapped
+reads. Use "\-B" to set the maximum number of equally\-best
+alignments to be reported.
+.TP
+\fB\-B\fR <int>
+Maximum number of equally\-best alignments to be reported for
+a multi\-mapping read. Equally\-best alignments have the same
+number of mis\-matched bases. 1 by default.
+.PP
+# indel detection
+.TP
+\fB\-I\fR <int>
+Maximum length (in bp) of indels that can be detected. 5 by
+default. Indels of up to 200bp long can be detected.
+.TP
+\fB\-\-complexIndels\fR
+Detect multiple short indels that are in close proximity
+(they can be as close as 1bp apart from each other).
+.PP
+# read trimming
+.TP
+\fB\-\-trim5\fR <int>
+Trim off <int> number of bases from 5' end of each read. 0
+by default.
+.TP
+\fB\-\-trim3\fR <int>
+Trim off <int> number of bases from 3' end of each read. 0
+by default.
+.PP
+# distance and orientation of paired end reads
+.TP
+\fB\-d\fR <int>
+Minimum fragment/insert length, 50bp by default.
+.TP
+\fB\-D\fR <int>
+Maximum fragment/insert length, 600bp by default.
+.TP
+\fB\-S\fR <ff:fr:rf>
+Orientation of first and second reads, 'fr' by default (
+forward/reverse).
+.PP
+# number of CPU threads
+.TP
+\fB\-T\fR <int>
+Number of CPU threads used, 1 by default.
+.PP
+# read group
+.TP
+\fB\-\-rg\-id\fR <string>
+Add read group ID to the output.
+.TP
+\fB\-\-rg\fR <string>
+Add <tag:value> to the read group (RG) header in the output.
+.PP
+# read order
+.TP
+\fB\-\-keepReadOrder\fR
+Keep order of reads in BAM output the same as that in the
+input file. Reads from the same pair are always placed next
+to each other no matter this option is specified or not.
+.TP
+\fB\-\-sortReadsByCoordinates\fR Output location\-sorted reads. This option is
+applicable for BAM output only. A BAI index file is also
+generated for each BAM file so the BAM files can be directly
+loaded into a genome browser.
+.PP
+# color space reads
+.TP
+\fB\-b\fR
+Convert color\-space read bases to base\-space read bases in
+the mapping output. Note that read mapping is performed at
+color\-space.
+.PP
+# dynamic programming
+.TP
+\fB\-\-DPGapOpen\fR <int> Penalty for gap opening in short indel detection. \fB\-1\fR by
+default.
+.TP
+\fB\-\-DPGapExt\fR <int>
+Penalty for gap extension in short indel detection. 0 by
+default.
+.TP
+\fB\-\-DPMismatch\fR <int> Penalty for mismatches in short indel detection. 0 by
+default.
+.TP
+\fB\-\-DPMatch\fR <int>
+Score for matched bases in short indel detection. 2 by
+default.
+.PP
+# detect structural variants
+.TP
+\fB\-\-sv\fR
+Detect structural variants (eg. long indel, inversion,
+duplication and translocation) and report breakpoints. Refer
+to Users Guide for breakpoint reporting.
+.PP
+# gene annotation
+.TP
+\fB\-a\fR
+Name of an annotation file (gzipped file is accepted).
+GTF/GFF format by default. See \fB\-F\fR option for more format
+information.
+.TP
+\fB\-F\fR
+Specify format of the provided annotation file. Acceptable
+formats include 'GTF' (or compatible GFF format) and
+\&'SAF'. 'GTF' by default. For SAF format, please refer to
+Users Guide.
+.TP
+\fB\-A\fR
+Provide a chromosome name alias file to match chr names in
+annotation with those in the reads. This should be a twocolumn comma\-delimited text file. Its first column should
+include chr names in the annotation and its second column
+should include chr names in the index. Chr names are case
+sensitive. No column header should be included in the
+file.
+.TP
+\fB\-\-gtfFeature\fR <string>
+Specify feature type in GTF annotation. 'exon'
+by default. Features used for read counting will be
+extracted from annotation using the provided value.
+.TP
+\fB\-\-gtfAttr\fR <string>
+Specify attribute type in GTF annotation. 'gene_id'
+by default. Meta\-features used for read counting will be
+extracted from annotation using the provided value.
+.PP
+# others
+.TP
+\fB\-v\fR
+Output version of the program.
+.PP
+Refer to Users Manual for detailed description to the arguments.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/subread-buildindex.1
=====================================
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SUBREAD-BUILDINDEX "1" "March 2021" "subread-buildindex 2.0.1" "User Commands"
+.SH NAME
+subread-buildindex \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+Version 2.0.1
+.PP
+Usage:
+.IP
+\&./subread\-buildindex [options] \fB\-o\fR <basename> {FASTA[.gz] file1}\e
+.IP
+[FASTA[.gz] file2] ...
+.PP
+Required arguments:
+.TP
+\fB\-o\fR <basename>
+base name of the index to be created
+.PP
+Optional arguments:
+.TP
+\fB\-F\fR
+build a full index for the reference genome. 16bp subreads
+will be extracted from every position of the reference
+genome. Size of the index is typically 3 times the size of
+index built from using the default setting.
+.TP
+\fB\-B\fR
+create one block of index. The built index will not be split
+into multiple pieces. This makes the largest amount of
+memory be requested when running alignments, but it enables
+the maximum mapping speed to be achieved. This option
+overrides \fB\-M\fR when it is provided as well.
+.TP
+\fB\-M\fR <int>
+size of requested memory(RAM) in megabytes, 8000 by default.
+.TP
+\fB\-f\fR <int>
+specify the threshold for removing uninformative subreads
+(highly repetitive 16mers in the reference). 100 by default.
+.TP
+\fB\-c\fR
+build a color\-space index.
+.TP
+\fB\-v\fR
+output version of the program.
+.PP
+For more information about these arguments, please refer to the User Manual.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/subread-fullscan.1
=====================================
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SUBREAD-FULLSCAN "1" "March 2021" "subread-fullscan 2.0.1" "User Commands"
+.SH NAME
+subread-fullscan \- toolkit for processing next-gen sequencing data
+.SH DESCRIPTION
+subread\-fullscan Version 2.0.1
+.IP
+This program scans the entire genome to find all high\-similarity locations to
+.PP
+a specified read.
+.PP
+Usage:
+.IP
+\&./subread\-fullscan [options] \fB\-i\fR <index_name> <read_string>
+.PP
+Required arguments:
+.TP
+\fB\-i\fR <string>
+Base name of the index.
+.TP
+read_string
+The read bases.
+.PP
+Optional arguments:
+.TP
+\fB\-m\fR <float>
+The minimum fraction of matched bases in the read, 0.8 by default
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/subread.manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/subread/-/compare/a683588f618e59a120dacd404bc2d8fee66075c9...5c9b138901d065a45134ccf5e458b49084107f8e
--
View it on GitLab: https://salsa.debian.org/med-team/subread/-/compare/a683588f618e59a120dacd404bc2d8fee66075c9...5c9b138901d065a45134ccf5e458b49084107f8e
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