.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH PARSEALIGNMENT "1" "September 2019" "parseAlignment 0.7.5+dfsg" "User Commands"
.SH NAME
parseAlignment \- pre\-compute probabilities of (observed) reads alignments
.SH SYNOPSIS
.B parseAlignment
\fI\,-o <outFileName> -s <trSeqFileName>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,alignment 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\-\-excludeSingletons\fR
.IP
Exclude single mate alignments for paired\-end reads. (default: Off)
.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.
.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\-\-mateNamesDiffer\fR
.IP
Mates from paired\-end reads have different names. (default: Off)
.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 speedup mostly when using non\-uniform read distribution model (i.e. no \fB\-\-uniform\fR flag). (default: 4)
.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\-\-show1warning\fR
.IP
Show first alignments that are considered wrong (TID unknown, TID mismatch, wrong strand). (default: Off)
.HP
\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
.IP
File to save transcript information extracted from [BS]AM file and reference.
.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)