ebanks bb312814a2 UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter). ... Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-16 17:28:09 +00:00
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annotator	UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).	2009-12-16 17:28:09 +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	UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).	2009-12-16 17:28:09 +00:00
indels	Another case of reordering of read groups blowing up checksums.	2009-11-13 00:07:35 +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