hanna f275be6968 A 'fat shard' finder. Cranks through the indices of a BAM file or list of ... BAM files looking for outliers (outliers right now are defined naively as shards whose sizes are more than 5 stddevs away from the mean). Runs in 13 minutes per chromosome on 707 low pass whole genome BAMs -- not great, but much faster than running UG on the same region to discover anomalies. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5782 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-10 12:56:47 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
refdata	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
report	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00
traversals	Fix requested by Lee Lichtenstein: first check to see whether it's time for	2011-04-20 03:22:48 +00:00
walkers	Fix for IndelRealigner memory problem. Now the Constrained mate fixing writer is told whether a read has been modified and, if it wasn't, can dump it when the cache needs to get flushed at places with tons of coverage.	2011-05-06 19:34:41 +00:00
GenomeAnalysisEngineUnitTest.java	Fix for bug GSA-449: Intervals that are not in GATK format are not validated	2011-04-27 18:12:10 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00