ebanks 36d493e645 All standard annotations now inherit from StandardVariantAnnotation. Users can specify whether they want all annotations, just the standard annotations, or specific annotations. When calling in from another walker, the default is just the standard ones. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2134 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 03:55:12 +00:00
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annotator	New annotation: ResidualQuality	2009-11-23 20:04:01 +00:00
concordance	Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord.	2009-11-19 18:17:47 +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	-Added VariantFiltration integration tests	2009-11-24 02:36:27 +00:00
genotyper	All standard annotations now inherit from StandardVariantAnnotation. Users can specify whether they want all annotations, just the standard annotations, or specific annotations. When calling in from another walker, the default is just the standard ones.	2009-11-24 03:55:12 +00:00
indels	Another case of reordering of read groups blowing up checksums.	2009-11-13 00:07:35 +00:00
recalibration	Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order	2009-11-23 19:51:36 +00:00
DepthOfCoverageIntegrationTest.java	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +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