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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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aaron 72e030a670 require that snps be biallelic before we pass them to the TiTv calculation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-05-06 22:33:00 +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 DbSNP moved over to tribble 2010-05-03 06:02:35 +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 VCF moved over to tribble. 2010-05-05 17:28:48 +00:00
iterators Checking in the reference implementation of the downsampler for back comparison. 2010-04-30 15:41:13 +00:00
refdata turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory. 2010-05-06 16:36:58 +00:00
traversals Fare thee well, oh LocusWindowTraversal. 2010-03-29 13:17:26 +00:00
walkers require that snps be biallelic before we pass them to the TiTv calculation. 2010-05-06 22:33:00 +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 DbSNP moved over to tribble 2010-05-03 06:02:35 +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