NAME

       bam2fastx - converts bam directly into fastx

SYNOPSIS

       bam2fastx [--fasta|-a|--fastq|-q] [--color] [-Q] [--sam|-s|-t]

DESCRIPTION

              [-M|--mapped-only|-A|--all] [-o <outfile>] [-P|--paired] [-N] <in.bam>

       Note: By default, reads flagged as not passing quality controls are

              discarded; the -Q option can be used to ignore the QC flag.

       Use the -N option if the /1 and /2 suffixes should be appended to

              read names according to the SAM flags

       Use the -O option to ignore the OQ tag, if present, when writing quality values