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)
