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)