Guillermo del Angel d4e7655d14 Added ability to call multiallelic indels, if -multiallelic is included in UG arguments. Simple idea: we genotype all alleles with count >= minIndelCnt. ... To support this, refactored code that computes consensus alleles. To ease merging of mulitple alt alleles, we create a single vc for each alt alleles and then use VariantContextUtils.simpleMerge to carry out merging, which takes care of handling all corner conditions already. In order to use this, interface to GenotypeLikelihoodsCalculationModel changed to pass in a GenomeLocParser object (why are these objects to hard to handle??). More testing is required and feature turned off my default.		2012-01-06 11:24:38 -05:00
..
arguments	First draft of a test script for I/O performance with the new asynchronous I/O processing.	2011-11-30 13:13:16 -05:00
contexts	Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.	2011-11-05 23:54:28 -04:00
datasources	Found the bug in the engine: RodLocusView was using the wrong seek method so that it would only move to the first locus of a shard (and with multi-locus shards, this meant that we never processed RODs from the other positions). In fact, because the seek(Shard) method is extremely misleading and now no longer used, I think it's safer to delete it and make everyone use the much more transparent seek(GenomeLoc). Note that I have not re-enabled my improvements to the intervals accumulation of ReferenceDataSource because that inefficiency is still present downstream in RodLocusView; need to discuss those changes with Matt.	2011-12-26 14:45:19 -05:00
examples	@Hidden for DocumentationTest and GATKDocsExample	2011-09-23 09:03:37 -04:00
executive	Initial commit of the Active Region Traversal. Not ready to be used by anyone yet.	2012-01-04 17:03:21 -05:00
filters	It wouldn't harm integrationtests if we had our logic right... :-)	2011-11-10 14:03:22 -05:00
io	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00
iterators	Bugfix/Rewrite: Algorithm to determine adaptor boundaries	2011-12-20 17:48:39 -05:00
phonehome	Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.	2011-10-27 13:58:19 -04:00
refdata	Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.	2011-11-28 14:18:28 -05:00
report	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
resourcemanagement	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
samples	Corrected bug causing getChildrenWithParents() to not take the last family member into consideration.	2011-12-09 14:51:34 +01:00
traversals	Initial commit of the Active Region Traversal. Not ready to be used by anyone yet.	2012-01-04 17:03:21 -05:00
walkers	Added ability to call multiallelic indels, if -multiallelic is included in UG arguments. Simple idea: we genotype all alleles with count >= minIndelCnt.	2012-01-06 11:24:38 -05:00
CommandLineExecutable.java	Removed -B support. Now explodes with error if -B provided.	2011-08-16 16:13:47 -04:00
CommandLineGATK.java	Check for null comment	2011-11-23 10:47:21 -05:00
DownsampleType.java	…
DownsamplingMethod.java	…
GenomeAnalysisEngine.java	Initial commit of the Active Region Traversal. Not ready to be used by anyone yet.	2012-01-04 17:03:21 -05:00
ReadMetrics.java	Counts of records failing filters are displayed sorted	2011-10-06 18:42:26 -07:00
ReadProperties.java	Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.	2011-12-06 10:10:38 -05:00
WalkerManager.java	Removed support for RMD in @Requires and @Allows	2011-08-03 15:36:55 -04:00
package-info.java	…