asivache 835f1067d8 added isHom() and isHet() queries to the Genotype interface (with the obvious meaning) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-16 18:41:39 +00:00
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AllelicVariant.java	Added isReference() to AllelicVariant and updated rodDbSNP accordingly	2009-04-07 14:49:20 +00:00
Genotype.java	added isHom() and isHet() queries to the Genotype interface (with the obvious meaning)	2009-04-16 18:41:39 +00:00
HapMapAlleleFrequenciesROD.java	rod's now have names. Use getName() to access it. Next step is better interface to accessing rods	2009-04-03 16:41:33 +00:00
RefMetaDataTracker.java	New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java	2009-04-09 22:04:59 +00:00
ReferenceOrderedData.java	New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java	2009-04-09 22:04:59 +00:00
ReferenceOrderedDatum.java	rod's now have names. Use getName() to access it. Next step is better interface to accessing rods	2009-04-03 16:41:33 +00:00
rodDbSNP.java	Added isReference() to AllelicVariant and updated rodDbSNP accordingly	2009-04-07 14:49:20 +00:00
rodGFF.java	rod's now have names. Use getName() to access it. Next step is better interface to accessing rods	2009-04-03 16:41:33 +00:00
rodSAMPileup.java	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.	2009-04-14 22:13:10 +00:00