delangel 7d7ce6cf00 Two embarassing bug fixes: ... a) Forgot to convert from phred to log-prob when computing gap penalties from recal table. b) Forgot to uncomment code to correctly deal with hard-clipped bases in a read. But because of this, had to do a short term workaround to at least temporarily return class from hardClipAdaptorSequence to GATKSAMRecord. Otherwise, I get exceptions when casting because somehow some reads in HiSeq get to be SAMRecord (which GATKSAMRecord inherits from) but some reads get to be BAMRecords (which can't be cast into GATKSAMRecord), not sure why. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5771 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-05 17:08:34 +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	Two embarassing bug fixes:	2011-05-05 17:08:34 +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	Fixed O(N^2) operation when scattering interval files.	2011-05-05 03:32:35 +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