aaron fc91e3e30e equals signs can be important ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@870 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-01 16:56:21 +00:00
..
dataSources	enabled underlying filtering of zero mapping quality reads, vastly improves system performance	2009-05-29 14:51:08 +00:00
executive	Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.	2009-06-01 15:34:38 +00:00
iterators	equals signs can be important	2009-06-01 16:56:21 +00:00
refdata	synchronizing, no real changes	2009-05-29 21:56:14 +00:00
traversals	Fix bug in unit tests created by new filter in TraversalEngine.	2009-06-01 15:50:44 +00:00
walkers	Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.	2009-05-26 15:58:21 +00:00
CommandLineGATK.java	Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception.	2009-05-20 19:17:16 +00:00
GATKArgumentCollection.java	enabled underlying filtering of zero mapping quality reads, vastly improves system performance	2009-05-29 14:51:08 +00:00
GenomeAnalysisEngine.java	enabled underlying filtering of zero mapping quality reads, vastly improves system performance	2009-05-29 14:51:08 +00:00
LocusContext.java	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
OutputTracker.java	Lazy creation of output streams. Only create output streams when absolutely necessary.	2009-05-26 21:56:57 +00:00
Reads.java	enabled underlying filtering of zero mapping quality reads, vastly improves system performance	2009-05-29 14:51:08 +00:00
WalkerManager.java	Farewell, functionalj. You promised much, but you could not deliver.	2009-05-28 01:35:49 +00:00