hanna 98c268483e Fixed issues with the integration tests: ... 1) sam-jdk apparently no longer supports custom tags with type int[] values. 2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-23 23:12:22 +00:00
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annotator	Oops - forgot to check this one in.	2009-12-23 19:53:28 +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	Fixed another test	2009-12-18 05:05:03 +00:00
genotyper	2 separate changes which both affect lots of UG integration md5s, so I'm committing them together:	2009-12-23 19:03:56 +00:00
indels	Fixed issues with the integration tests:	2009-12-23 23:12:22 +00:00
recalibration	I'm making this change now (as opposed to waiting until Monday) to honor Tim's request.	2009-12-23 16:26:43 +00:00
DepthOfCoverageIntegrationTest.java	- Moved various header line printing into a single method	2009-12-04 02:15:43 +00:00
PileupWalkerIntegrationTest.java	Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.	2009-12-18 22:52:44 +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