maskAlignedReads.py(1) 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)