aaron 0cafd3d642 clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3614 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-22 22:42:38 +00:00
..
arguments	First pass at eliminating the old sharding system. Classes required for the original sharding system	2010-06-17 20:17:31 +00:00
contexts	Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes).	2010-06-22 18:26:37 +00:00
datasources	Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.	2010-06-21 21:42:42 +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	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +00:00
filters	Re-allowing blacklist by read group id.	2010-06-16 19:45:44 +00:00
io	Fixed UG parallelization bug. Better integration test to catch this in the future.	2010-05-25 21:03:45 +00:00
iterators	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +00:00
refdata	clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context.	2010-06-22 22:42:38 +00:00
traversals	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
walkers	-Remove Nway output option	2010-06-22 20:31:55 +00:00
CommandLineExecutable.java	Better error message when bam file / list file with wrong extension is	2010-06-03 17:52:48 +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	Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.	2010-06-18 17:37:11 +00:00
Reads.java	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +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