/ polymorphic_read_counter_bwaPileup Publicforked from kweitemier/polymorphic_read_counter_bwaPileup
This branch is 1 commit behind kweitemier:master.
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