NAME

       maskAlignedReads.py - Mask aligned reads in regions file

DESCRIPTION

       usage: maskAlignedReads.py [-h] [-v] [-l LOGFILE] [-d] [-i]

              inCmpFile inRgnFofn outRgnFofn

       Use  in.cmp.h5  to  mask corresponing regions of files in in.rgn.h5, write output to a new
       rgn.fofn.

   positional arguments:
       inCmpFile
              An input cmp.h5 file.

       inRgnFofn
              A fofn of input region table files.

       outRgnFofn
              A fofn of output region table files.

   optional arguments:
       -h, --help
              show this help message and exit

       -v, --version
              show program's version number and exit

       -l LOGFILE, --logFile LOGFILE
              Specify a file to log to. Defaults to stderr.  (default: None)

       -d, --debug
              Increases verbosity of logging (default: False)

       -i, --info
              Display informative log entries (default: False)