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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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ebanks b668d32cf1 Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2494 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-03 21:31:04 +00:00
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annotator moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
concordance Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful. 2009-12-29 17:30:47 +00:00
fasta moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
filters moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
genotyper Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. 2010-01-03 21:31:04 +00:00
indels moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
recalibration Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now. 2009-12-29 21:01:32 +00:00
DepthOfCoverageIntegrationTest.java moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
PileupWalkerIntegrationTest.java Now that we changed how deletions are represented, got to update MD5... 2009-12-30 22:00:58 +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