[med-svn] r15702 - in trunk/packages/bitseq/trunk/debian: . mans

Wed Jan 1 19:10:55 UTC 2014

Author: tille
Date: 2014-01-01 19:10:55 +0000 (Wed, 01 Jan 2014)
New Revision: 15702

Added:
   trunk/packages/bitseq/trunk/debian/manpages
   trunk/packages/bitseq/trunk/debian/mans/
   trunk/packages/bitseq/trunk/debian/mans/getVariance.1
   trunk/packages/bitseq/trunk/debian/mans/getWithinGeneExpression.1
   trunk/packages/bitseq/trunk/debian/mans/parseAlignment.1
   trunk/packages/bitseq/trunk/debian/mans/transposeLargeFile.1
Log:
Start writing some help2man based manpages


Added: trunk/packages/bitseq/trunk/debian/manpages
===================================================================

--- trunk/packages/bitseq/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/manpages	2014-01-01 19:10:55 UTC (rev 15702)
@@ -0,0 +1 @@
+debian/mans/*.1

Added: trunk/packages/bitseq/trunk/debian/mans/getVariance.1
===================================================================
--- trunk/packages/bitseq/trunk/debian/mans/getVariance.1	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/mans/getVariance.1	2014-01-01 19:10:55 UTC (rev 15702)
@@ -0,0 +1,35 @@
+.TH GETVARIANCE "1" "January 2014" "getVariance 0.7.0" "User Commands"
+.SH NAME
+getVariance \- estimates variance of MCMC samples
+.SH SYNOPSIS
+.B getVariance
+\fI-o <outFileName>  \fR[\fIOPTIONS\fR] [\fIsampleFiles\fR]
+.SH DESCRIPTION
+Estimates variance of MCMC samples from 1 or multiple replicates.
+.IP
+[sample Files] should contain transposed MCMC samples from replicates.
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-l\fR ,   \fB\-\-log\fR
+.IP
+Use logged values. (default: Off)
+.HP
+\fB\-\-norm=\fR<normalization>
+.IP
+Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).
+.HP
+\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
+.IP
+Name of the output file.
+.HP
+\fB\-t\fR <type> ,   \fB\-\-type=\fR<type>
+.IP
+Type of variance, possible values: [sample,sqDif] for sample variance or squared difference. (default: sample)
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)

Added: trunk/packages/bitseq/trunk/debian/mans/getWithinGeneExpression.1
===================================================================
--- trunk/packages/bitseq/trunk/debian/mans/getWithinGeneExpression.1	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/mans/getWithinGeneExpression.1	2014-01-01 19:10:55 UTC (rev 15702)
@@ -0,0 +1,57 @@
+.TH GETWITHINGENEEXPRESSION "1" "January 2014" "getWithinGeneExpression 0.7.0" "User Commands"
+.SH NAME
+getWithinGeneExpression \- compute relative expression of transcripts within genes
+.SH SYNOPSIS
+.B getWithinGeneExpression
+\fI-t <trInfoFileName>  \fR[\fIOPTIONS\fR] [\fIsamplesFile\fR]
+.SH DESCRIPTION
+Computes relative expression of transcripts within genes.
+.IP
+[samplesFile] should contain transposed MCMC expression samples.
+program can produce means and variance and write them into [sumFile]
+or individual MCMC samples which are written into [outFile].
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-a\fR ,   \fB\-\-adjustByLength\fR
+.IP
+Adjust expression by transcripts length. (default: Off)
+.HP
+\fB\-G\fR <geneListFile> ,   \fB\-\-geneList=\fR<geneListFile>
+.IP
+Name of the file containing list of gene names (one for each transcript).
+.HP
+\fB\-\-groupByGene\fR
+.IP
+Group transcripts by genes (this can change the default order of output. (default: Off)
+.HP
+\fB\-l\fR ,   \fB\-\-log\fR
+.IP
+Use logged values. (default: Off)
+.HP
+\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
+.IP
+Name of the output file.
+.HP
+\fB\-s\fR <sumFileName> ,   \fB\-\-sumFile=\fR<sumFileName>
+.IP
+Name of summarization file where true mean, true variance and relative mean and relative variance are saved.
+.HP
+\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
+.IP
+Name of the transcript file.
+.HP
+\fB\-T\fR <trMapFile> ,   \fB\-\-trMap=\fR<trMapFile>
+.IP
+Name of the file containing transcript to gene mapping.
+.HP
+\fB\-\-updateTrFile\fR
+.IP
+Update trInfoFile if new gene names were provided (with trMapFile or geneListFile). (default: Off)
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)

Added: trunk/packages/bitseq/trunk/debian/mans/parseAlignment.1
===================================================================
--- trunk/packages/bitseq/trunk/debian/mans/parseAlignment.1	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/mans/parseAlignment.1	2014-01-01 19:10:55 UTC (rev 15702)
@@ -0,0 +1,87 @@
+.TH PARSEALIGNMENT "1" "January 2014" "parseAlignment 0.7.0" "User Commands"
+.SH NAME
+parseAlignment \- pre\-compute probabilities of (observed) reads' alignments
+.SH SYNOPSIS
+.B parseAlignment
+\fI\-o <outFileName> \-s <trSeqFileName> \-\-trSeqHeader <trSeqHeader>  \fR[\fIOPTIONS\fR] [\fIalignment file\fR]
+.SH DESCRIPTION
+Pre\-computes probabilities of (observed) reads' alignments.
+.IP
+[alignment file] should be in either SAM or BAM format.
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-\-distributionFile=\fR<distributionFileName>
+.IP
+Name of file to which read\-distribution should be saved.
+.HP
+\fB\-e\fR <expFileName> ,   \fB\-\-expressionFile=\fR<expFileName>
+.IP
+Transcript relative expression estimates \fB\-\-\-\fR for better non\-uniform read distribution estimation.
+.HP
+\fB\-\-failed=\fR<failed>
+.IP
+File name where to save names of reads that failed to align as pair.
+.HP
+\fB\-f\fR <format> ,   \fB\-\-format=\fR<format>
+.IP
+Input format: either SAM, BAM.
+.HP
+\fB\-\-lenMu=\fR<lenMu>
+.IP
+Set mean of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))
+.HP
+\fB\-\-lenSigma=\fR<lenSigma>
+.IP
+Set sigma^2 (or variance) of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))
+.HP
+\fB\-l\fR <maxAlignments> ,   \fB\-\-limitA=\fR<maxAlignments>
+.IP
+Limit maximum number of alignments per read. (Reads with more alignments are skipped.)
+.HP
+\fB\-\-noiseMismatches=\fR<numNoiseMismatches>
+.IP
+Number of mismatches to be considered as noise. (default: 6)
+.HP
+\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
+.IP
+Name of the output file.
+.HP
+\fB\-P\fR <procN> ,   \fB\-\-procN=\fR<procN>
+.IP
+Maximum number of threads to be used. This provides parallelization only when computing non\-uniform read distribution (i.e. runs without \fB\-\-uniform\fR flag). (default: 3)
+.HP
+\fB\-N\fR <readsN> ,   \fB\-\-readsN=\fR<readsN>
+.IP
+Total number of reads. This is not necessary if [SB]AM contains also reads with no valid alignments.
+.HP
+\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
+.IP
+If transcript(reference sequence) information is contained within SAM file, program will write this information into <trInfoFile>, otherwise it will look for this information in <trInfoFile>.
+.HP
+\fB\-s\fR <trSeqFileName> ,   \fB\-\-trSeqFile=\fR<trSeqFileName>
+.IP
+Transcript sequence in FASTA format \fB\-\-\-\fR for non\-uniform read distribution estimation.
+.HP
+\fB\-\-trSeqHeader=\fR<trSeqHeader>
+.IP
+Transcript sequence header format enables gene name extraction (standard/gencode). (default: standard)
+.HP
+\fB\-\-uniform\fR
+.IP
+Use uniform read distribution. (default: Off)
+.HP
+\fB\-\-unstranded\fR
+.IP
+Paired read are not strand specific. (default: Off)
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)
+.HP
+\fB\-V\fR ,   \fB\-\-veryVerbose\fR
+.IP
+Very verbose output. (default: Off)

Added: trunk/packages/bitseq/trunk/debian/mans/transposeLargeFile.1
===================================================================
--- trunk/packages/bitseq/trunk/debian/mans/transposeLargeFile.1	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/mans/transposeLargeFile.1	2014-01-01 19:10:55 UTC (rev 15702)
@@ -0,0 +1,21 @@
+.TH TRANSPOSELARGEFILE "1" "January 2014" "transposeLargeFile 0.7.0" "User Commands"
+.SH NAME
+transposeLargeFile \- helper for bitseq to transpose files lines and columns
+.SH SYNOPSIS
+.B transposeLargeFile
+\fI-o <outFileName>  \fR[\fIOPTIONS\fR] [\fIinput files\fR]
+.SH DESCRIPTION
+Transposes [input files] into [outFileName] so that there are M lines with N columns each.
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
+.IP
+Name of the output file.
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)


