ebanks c75ec67f84 When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2392 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-17 19:01:08 +00:00
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annotator	When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs.	2009-12-17 19:01:08 +00:00
concordance	I want to move over to hpprojects tonight, so I'm checking in various changes all in one go:	2009-12-13 02:52:18 +00:00
fasta	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00
filters	VariantFiltration now details the filters it has used in the header of the VCF it produces.	2009-12-09 15:36:15 +00:00
genotyper	Joint Estimate is now the default calculation model.	2009-12-16 19:41:02 +00:00
indels	fixing md5 sum; new version of IndelIntervalWalker does the right thing...	2009-12-17 01:04:13 +00:00
recalibration	CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads.	2009-12-14 21:52:30 +00:00
DepthOfCoverageIntegrationTest.java	- Moved various header line printing into a single method	2009-12-04 02:15:43 +00:00
PileupWalkerIntegrationTest.java	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview	2009-12-02 15:41:35 +00:00
PrintReadsWalkerTest.java	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).	2009-10-02 19:35:35 +00:00