switchStrand.py

common.ngseq.switchStrand.py

This stand-alone script reads a bam file and switches the strand alignment of each read in the file. The reads in the bam file have the sequence of the read stored appropriate to the 5’-3’ forwards strand of the reference DNA regardless of whether the read maps to the forward or reverse strand. This is good, because it means that all this script has to do to reverse the strandedness information is change the flags saying whether a read maps on the forward or reverse strand.

module_version:1.1 created_on:2013-07-08

Command-line Arguments

usage:

switchStrand.py :param: <input bam file> :param: <output bam file> -l|--log <file> [--tmpdir] [-v|--verbose] [--version] [--help]

Required Parameters

para:

<input bam file>

The input bam file

param:

<output bam file>

he output bam file

--logfile|-l

The name (inc. path) of the log file from the wrapper.

Optional Parameter

--help|-h

Print a basic description of the tool and its options to STDOUT.

--version

Show program’s version number and exit.

--verbose|-v

Turn on verbose logging (recommended).

Output

A bam file with the new read sequences and strand assignments.