.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BAM2FASTX "1" "May 2016" "bam2fastx 2.1.1+dfsg" "User Commands"
.SH NAME
bam2fastx \- tophat component converting bam directly into fastx
.SH DESCRIPTION
.SS "bam2fastx v2.1.1 () usage:"
.IP
bam2fastx [\-\-fasta|\-a] [\-C|\-\-color] [\-P|\-\-paired] [\-N]
[\-A|\-\-all|\-M|\-\-mapped\-only] [\-Q] [\-\-sam|\-s|\-t] [\-o <outfname>] <in.bam>
.PP
By default, bam2fastx only converts the unmapped reads from the input file,
.IP
discarding those unmapped reads flagged as QC failed.
The input BAM/SAM file MUST be sorted by read name (\fB\-n\fR option for samtools
sort). If the input file name is "\-", stdin will be used instead.
.SH OPTIONS
.TP
\fB\-A\fR,\-\-all
convert all reads (mapped and unmapped)
(but discarding those flagged as QC failed, unless \fB\-Q\fR)
.TP
\fB\-P\fR
paired reads are expected and converted into two output
files (see <outfname> comments below)
.TP
\fB\-Q\fR
convert unmapped reads even when flagged as QC failed
.TP
\fB\-M\fR,\-\-maped\-only
convert only mapped reads
.TP
\fB\-N\fR
for \fB\-P\fR, append  \fI\,/1\/\fP and \fI\,/2\/\fP suffixes to read names
.TP
\fB\-O\fR
ignore the original quality values (OQ tag) and write the
current quality values (default is to use OQ data if found)
.TP
\fB\-C\fR,\-\-color
reads are in ABI SOLiD color format
.TP
\fB\-s\fR,\-t,\-\-sam
input is a SAM text file (default: BAM input expected)
.TP
\fB\-a\fR,\-\-fasta
output FASTA records, not FASTQ (discard quality values)
.TP
\fB\-o\fR <outfname>
output file name or template (see below)
.IP
<outfname> serves as a name template when \fB\-P\fR option is provided, as suffixes
\&.1 and .2 will be automatically inserted before the file extension in
<outfname>, such that two file names will be created.
If <outfname> ends in .gz or .bz2 then bam2fastx will write the
output compressed by gzip or bzip2 respectively.
.IP
Example of converting all paired reads from a BAM file to FASTQ format:
.IP
bam2fastx \fB\-PANQ\fR \fB\-o\fR sample.fq.gz sample.sortedbyname.bam
.IP
In this example the output will be written in two files:
.IP
sample.1.fq.gz and sample.2.fq.gz