ebanks b3f561710f Optimizations: ... 1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having). 2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler) UG now runs in half the time for JOINT_ESTIMATE model. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 16:27:39 +00:00
..
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	Optimizations:	2009-11-24 16:27:39 +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