chartl b68d6e06b7 Rollback of the previous "fix" and implementation of the real fix. ... We totally *do* want to annotate the call if called by another walker. Totally boneheaded misenterpretation of what the code was doing -- Eric, please forgive me for being an idiot. Instead, change the StingException to what it really should be -- an IllegalStateException, which is not coincidentally already handled by the calling function. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2067 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 06:09:24 +00:00
..
alignment	Finally reinstate the iterator-style interface. Get rid of some scaffolding code.	2009-11-16 02:34:19 +00:00
gatk	Rollback of the previous "fix" and implementation of the real fix.	2009-11-18 06:09:24 +00:00
playground	Working with byte arrays is faster than working with Strings so the Covariates now take in byte arrays. None of the Covariates themselves used the reference base so I removed it. DinucCovariate now returns a Dinuc object which implements Comparable instead of returning a String because it was too slow. CountCovariates now uses a read filter to filter out unmapped reads and allows the user to specify -cov all which will use all of the available covariates, of which there are 7 now. If no covariates are specified it defaults to ReadGroup and QualityScore, the two required covariates. Initial code in place to leave SOLID bases alone if they have bad color space quality. TableRecalibration uses @Requires to tell the GATK to not give the reference bases since they weren't being used for anything.	2009-11-17 21:50:52 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read.	2009-11-17 17:20:13 +00:00