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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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rpoplin 0a6bd5a270 CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2498 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-04 20:52:15 +00:00
..
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 -Misc improvements to VCF code 2010-01-04 02:28:47 +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 CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used. 2010-01-04 20:52:15 +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