README

Written by Kevin Weitemier, copyright(c) 2011-2013

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version. A copy of this license is distributed with this software and is
available at <http://www.gnu.org/licenses/>.

Purpose: Calculates the proportion of reads at a position
    that differ from the majority.

Syntax: polymorphic_read_counter_bwaPileup.pl [filename]

[filename] must be a file in samtools mpileup format.

Output is tab-delimited file with:

Name, pileup position, reference base, proportion of non-consensus reads, number of reads, consensus base, differing bases (may be blank), their qual scores (may be blank), all bases, all qual scores.


Version history:
    version 0.0, 17 Feb 2011
    version 0.01 23 Feb 2011 -      made it slightly faster, maybe?
    version 1.00b 03 Mar 2011 -     Added ability to handle lines where the consensus differs from the reference.
    version 1.01b 09 Mar 2011 -     Fixed a bug when the sequence line contains only Ns.
    version 2.00b 11 Apr 2011 -     Reduced memory use, added output fields, fixed bug related to ^$.
    version 3.00b 14 Apr 2011 -     Added section displaying the differing reads and their qual scores.
    version 3.01b 15 Apr 2011 -     Explicitly undefined variables, which maybe helps memory usage.
    version 3.02b 18 Apr 2011 -     Prints a shortened but otherwise unmodified reads line.
    version 3.03b 29 Oct 2013 -     Modified to work with mpileup output