Revision 8ff1cbef5fdfd753d85c90a5c5b9c57f4936cdc0 authored by Ian Ferguson on 04 April 2013, 22:41:58 UTC, committed by Scott Smith on 05 April 2013, 15:02:59 UTC
Removed default reference sequence parameters from GMT/Varscan/CopyNumberParallel, CopySegmentParallel, QuickReadcounts, Readcounts, Somatic, SomaticParallel, SomaticParallelFilter, and SomaticParallelMerge. If the reference sequence was marked as is_optional => 1 in those classes, it is now marked as is_optional => 0. Changed the reference sequence parameters to is_optional => 0 in Consensus, NormalizeCopySegments, and SomaticMt (they had recently had their default reference sequence removed). Also reformatted class definitions for all modules under GMT/Varscan (added line breaks and fixed indentation for better consistency and readability).
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.gitignore
*.kpf
*.komodoproject
Meta.sqlite3-bak
Meta.sqlite3
tags
.DS_Store
bin/perl
bin/prove
.*.swp
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