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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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depristo e21376219d Updates to CombineVariants for Tim. -setKey can be null. Integrationtests for -setKey foo and -setKey null. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3870 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-23 22:35:52 +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 Updates to CombineVariants for Tim. -setKey can be null. Integrationtests for -setKey foo and -setKey null. 2010-07-23 22:35:52 +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