Khalid Shakir b8b7f28aa9 Revving Picard to pick up new SamFileHeaderMerger. ... Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut(). In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124. - Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs. - Updated md5s to match new expectations after looking at TLEN diff engine output.		2012-05-02 16:47:28 -04:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	PED support for Inbreeding Coefficient annotation	2012-04-25 12:56:47 -04:00
beagle	Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)	2012-01-23 08:25:34 -05:00
bqsr	disabling all BQSR unit tests	2012-04-30 14:39:55 -04:00
coverage	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00
diagnostics	GATKReport v1.0	2012-03-12 23:09:19 -04:00
diffengine	Fixing MD5's (new GATKReport header was missing from old md5's)	2012-03-19 15:28:45 -04:00
fasta	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
filters	Again, fixing the add call when we really mean replace	2011-11-21 19:15:56 -05:00
genotyper	As promised in the release notes for 1.6, I am removing the old deprecated genotyping framework revolving around the misordering of alleles and have moved the fixed version in its place in preparation for release 1.7 (or 2.0?).	2012-05-01 16:18:24 -04:00
indels	Revving Picard to pick up new SamFileHeaderMerger.	2012-05-02 16:47:28 -04:00
phasing	Added respectPhaseInInput flag to RBP and integration tests	2012-03-22 17:40:21 -04:00
qc	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
recalibration	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
validation	Added integration test for ValidationSiteSelector, correct MD5's	2012-03-26 16:39:55 -04:00
varianteval	AC strat now checks if evals will be merged before throwing an error on multiple eval files.	2012-04-19 16:08:55 -04:00
variantrecalibration	Removed experimental feature (aka hack) that was meant for 1000G consensus but remained in VQSR data manager - QD was being scaled by indel length. There's no evidence any more that QD is length-dependent, neither in CEU trio data nor in latest 1000G P2 calls	2012-04-20 10:58:34 -04:00
variantutils	Add header lines for AC,AF, and AN tags	2012-05-02 15:33:34 -04:00
BAQIntegrationTest.java	merge master	2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java	Updating MD5s for updated BAM with read groups	2011-10-06 12:15:48 -07:00
FlagStatIntegrationTest.java	Adding integration test for Flag Stat	2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
PrintReadsUnitTest.java	Better location for the downsampling of reads in PrintReads	2012-01-14 14:06:09 -05:00