---
name: "maskAlignedReads"
section: "1"
platform: "linux"
package: "pbalign"
version: "0.3.2-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/maskAlignedReads"
---

# maskAlignedReads(1)

Mask aligned reads in regions file

## NAME

maskAlignedReads - Mask aligned reads in regions file

## DESCRIPTION

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)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.