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
..
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	A fix for Marian Thieme's NPE in the new sharding system.	2011-04-21 19:47:14 +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	Two embarassing bug fixes:	2011-05-05 17:08:34 +00:00
CommandLineExecutableUnitTest.java	Fix for bug GSA-441: BAM file list with blank lines gives a confusing error	2011-04-01 15:04:35 +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