maskAlignedReads.py1
Mask aligned reads in regions file
Part of maskAlignedReads(1).
Overview
usage: maskAlignedReads [-h] [-v] [-l LOGFILE] [-d] [-i]
-
inCmpFile inRgnFofn outRgnFofn
Use in.cmp.h5 to mask corresponding 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)
History
- Debian 10 (Buster): the text shown here
- Debian 9 (Stretch)
--debug since Debian 10 (Buster);
--help since Debian 10 (Buster);
--info since Debian 10 (Buster);
--logFile since Debian 10 (Buster);
--version since Debian 10 (Buster);
-d since Debian 10 (Buster);
-h since Debian 10 (Buster);
-i since Debian 10 (Buster);
-l since Debian 10 (Buster);
-v since Debian 10 (Buster).