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
..
alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	A 'fat shard' finder. Cranks through the indices of a BAM file or list of	2011-05-10 12:56:47 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	Removing broken imports (boo)	2011-04-26 18:55:25 +00:00
playground/gatk/walkers	Moving VQSR v2 to core.	2011-05-03 20:20:06 +00:00
utils	A 'fat shard' finder. Cranks through the indices of a BAM file or list of	2011-05-10 12:56:47 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00