aaron b3fd145161 fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no ... features in that contig. Thanks to Mark for finding this. I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3865 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-23 18:39:55 +00:00
..
arguments	The first step in integrating Jim's tree based index scheme:	2010-07-19 04:49:27 +00:00
contexts	Improvements to variant combine. Now calculates AC/AN/AF correctly by calling into the VariantAnnotator engine. Automatically removes annotations that are inconsistent across incoming VCs (in simpleMerge). TODO bug fix for Guillermo/Eric.	2010-07-23 13:33:11 +00:00
datasources	Repackaged datasource-specific command-line tools into their own package. Added a tag renamer tool.	2010-07-22 19:50:34 +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	More improvements to exception handling during multithreaded runs based on	2010-07-22 22:13:01 +00:00
filters	Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.	2010-07-19 19:10:29 +00:00
io	1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.	2010-07-20 06:16:45 +00:00
iterators	FindBugs fixes throughout the code base	2010-07-18 16:29:59 +00:00
refdata	fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no	2010-07-23 18:39:55 +00:00
traversals	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
walkers	VariantEval can now see the EvaluationContext group objects, so they can decide if/when to print interesting sites. GenotypeConcordance has a hard-coded option to print FNs that is on the way to being generally useful. VCFWriter now uses the US locale for formatting floating point numbers; I believe this fixes a long-standing annoyance. Italian guys will check on this.	2010-07-23 17:16:50 +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	FindBugs fixes throughout the code base	2010-07-18 16:29:59 +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