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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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chartl 9d2a485532 Update to AminoAcidTransition eval module 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3783 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-13 17:12:03 +00:00
..
arguments The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this 2010-07-01 22:28:55 +00:00
contexts 1. Updated tests and added integration test for liftover code. 2010-07-12 17:58:18 +00:00
datasources eagerDecode is now false. 2010-07-07 22:51:48 +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 Fix for sharding ref walkers via monolithic sharding. Introduces the potential bug (for 2010-07-06 04:34:38 +00:00
filters Various code improvements based on FindBugs 2010-07-09 15:04:48 +00:00
io Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor. 2010-06-30 18:37:58 +00:00
iterators The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this 2010-07-01 22:28:55 +00:00
refdata Updating to VCF 4.0 2010-07-12 20:18:30 +00:00
traversals A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup. 2010-06-20 04:42:26 +00:00
walkers Update to AminoAcidTransition eval module 2010-07-13 17:12:03 +00:00
CommandLineExecutable.java merging now very close to working. Bug todo in writer and vcf infrastructure. Can almost create merged snp and indel files 2010-07-02 20:09:25 +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
DownsampleType.java We're unable to make the naive deduper more worldly, so we're killing it instead. 2010-06-18 13:54:27 +00:00
DownsamplingMethod.java We're unable to make the naive deduper more worldly, so we're killing it instead. 2010-06-18 13:54:27 +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 Interval support for ref walkers while streaming. 2010-07-07 03:14:59 +00:00
Reads.java The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this 2010-07-01 22:28:55 +00:00
WalkerManager.java Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of: 2010-05-28 14:52:44 +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