delangel 5eef15cfdf a) Bad bug fix to CombineVariants: when indels were being merged, the reference base provided was wrong - ref.getBases()[0] was being used, but this returns bease at start of window. Instead, the reference at current locus should be used. ... b) Cosmetic change to Beagle annotation description. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3861 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-23 15:13:47 +00:00
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annotator	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
concordance	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3775 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-13 00:56:12 +00:00
coverage	GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line	2010-06-02 22:26:32 +00:00
fasta	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +00:00
filters	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
genotyper	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
indels	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too.	2010-07-19 22:13:18 +00:00
sequenom	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +00:00
varianteval	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
variantrecalibration	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
variantutils	a) Bad bug fix to CombineVariants: when indels were being merged, the reference base provided was wrong - ref.getBases()[0] was being used, but this returns bease at start of window. Instead, the reference at current locus should be used.	2010-07-23 15:13:47 +00:00
PileupWalkerIntegrationTest.java	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +00:00
PrintReadsWalkerUnitTest.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
VariantsToVCFIntegrationTest.java	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00