This is the command maskAlignedReads that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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)
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