NAME

       arden-filter - filter a SAM file based on the analysis with ARDEN

SYNOPSIS

       arden-filter [INPUT SAM] [OUTPUTFILE] [OPTIONS]...

DESCRIPTION

       Script  to  filter  and  a  SAM  file based on the analysis with ARDEN. It is necessary to
       specify the desired cutoffs for RQS,GAPS and MM.  Type: python filter -e  1  for  printing
       some examples.

OPTIONS

       Required Arguments:

       OUTPUTFILE
              Outputfilename

       INPUT  Single SAM file to filter.

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

       -r RQS, --rqs=RQS
              Threshold for minimum read quality score.. [default: 0]

       -m MM, --mismatches=MM
              Threshold for maximum number of mismatches in an alignment [default: 3]

       -g GAPS, --gaps=GAPS
              Threshold for maximum number of gaps in an alignment.  [default: 3]

       -e PEXAMPLES, --examples=PEXAMPLES
              set to 1 if you want to print examples