ebanks bf451873ff 1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction ... 2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week). 3. Added integration tests for joint estimation model git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-13 18:02:18 +00:00
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concordance	Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...)	2009-11-10 02:41:37 +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	VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output	2009-11-10 13:24:58 +00:00
genotyper	1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction	2009-11-13 18:02:18 +00:00
indels	Another case of reordering of read groups blowing up checksums.	2009-11-13 00:07:35 +00:00
recalibration	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +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