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