.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH MASKALIGNEDREADS.PY "1" "December 2015" "maskAlignedReads.py 0.2.0" "User Commands"
.SH NAME
maskAlignedReads.py \- Mask aligned reads in regions file
.SH DESCRIPTION
usage: maskAlignedReads.py [\-h] [\-v] [\-l LOGFILE] [\-d] [\-i]
.IP
inCmpFile inRgnFofn outRgnFofn
.PP
Use in.cmp.h5 to mask corresponing regions of files in in.rgn.h5, write output
to a new rgn.fofn.
.SS "positional arguments:"
.TP
inCmpFile
An input cmp.h5 file.
.TP
inRgnFofn
A fofn of input region table files.
.TP
outRgnFofn
A fofn of output region table files.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-v\fR, \fB\-\-version\fR
show program's version number and exit
.TP
\fB\-l\fR LOGFILE, \fB\-\-logFile\fR LOGFILE
Specify a file to log to. Defaults to stderr.
(default: None)
.TP
\fB\-d\fR, \fB\-\-debug\fR
Increases verbosity of logging (default: False)
.TP
\fB\-i\fR, \fB\-\-info\fR
Display informative log entries (default: False)