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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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asivache 1373fee278 Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change. 
VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument. 

SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-04-21 18:19:03 +00:00
..
arguments The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
contexts Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday 2010-04-20 17:38:09 +00:00
datasources The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
examples Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes 2010-02-05 21:47:54 +00:00
executive The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
filters The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
io Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change. 2010-04-21 18:19:03 +00:00
iterators In the new sharding system, if no read group is present, hallucinate one. Added 2010-03-07 23:01:34 +00:00
refdata Continuing to stamp out the non-ASCII copyright virus. 2010-04-21 14:50:45 +00:00
traversals Fare thee well, oh LocusWindowTraversal. 2010-03-29 13:17:26 +00:00
walkers Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change. 2010-04-21 18:19:03 +00:00
CommandLineExecutable.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
CommandLineGATK.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
GATKErrorReport.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
GenomeAnalysisEngine.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
Reads.java changes to intelligently log overflowing locus pile-ups. 2010-01-20 08:09:48 +00:00
WalkerManager.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
package-info.java Put a major.minor version into the GATK Javadoc for reading. Also, 2010-01-15 21:48:30 +00:00