Provided by: tophat_2.1.1+dfsg1-1_amd64 
NAME
bam2fastx - tophat component converting bam directly into fastx
DESCRIPTION
bam2fastx v2.1.1 () usage:
bam2fastx [--fasta|-a] [-C|--color] [-P|--paired] [-N] [-A|--all|-M|--mapped-only] [-Q]
[--sam|-s|-t] [-o <outfname>] <in.bam>
By default, bam2fastx only converts the unmapped reads from the input file,
discarding those unmapped reads flagged as QC failed. The input BAM/SAM file MUST be sorted by
read name (-n option for samtools sort). If the input file name is "-", stdin will be used
instead.
OPTIONS
-A,--all
convert all reads (mapped and unmapped) (but discarding those flagged as QC failed, unless -Q)
-P paired reads are expected and converted into two output files (see <outfname> comments below)
-Q convert unmapped reads even when flagged as QC failed
-M,--maped-only
convert only mapped reads
-N for -P, append /1 and /2 suffixes to read names
-O ignore the original quality values (OQ tag) and write the current quality values (default is to
use OQ data if found)
-C,--color
reads are in ABI SOLiD color format
-s,-t,--sam
input is a SAM text file (default: BAM input expected)
-a,--fasta
output FASTA records, not FASTQ (discard quality values)
-o <outfname>
output file name or template (see below)
<outfname> serves as a name template when -P 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.
Example of converting all paired reads from a BAM file to FASTQ format:
bam2fastx -PANQ -o sample.fq.gz sample.sortedbyname.bam
In this example the output will be written in two files:
sample.1.fq.gz and sample.2.fq.gz