ebanks 772f558ae0 Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code. ... Small change for Ryan to get hard-clipped reads working for the recalibrator. PLEASE DO NOT RELEASE THIS WEEK. I still have some more testing to do and need Mark to run WG jobs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-25 20:04:33 +00:00
..
alignment	BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.	2010-05-20 14:05:13 +00:00
analyzecovariates	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.	2010-05-25 20:04:33 +00:00
oneoffprojects	A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads,	2010-05-23 21:49:54 +00:00
playground	Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator	2010-05-24 14:38:54 +00:00
utils	Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.	2010-05-25 20:04:33 +00:00