sanger-pathogens/Bio-RNASeq — pull request #19 by js21 (2014-05-09 11:11:37+00:00)
Title: Reimplementation of the total number of reads that mapped, plus deletion of several modules

BAMStats was using many modules of the VertRes codebase to calculate the total number of mapped reads from a bam file in case a correspnding .bas file was non existent.
The calculation is now done by running samtools -c -F 4 on the bam file directly in a command line terminal through Perl and capturing the output.
This should speed things up in several ways.
Several files have been discarded as they were no longer needed.