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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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ebanks 42aff1d2c3 Annotator in general should be able to annotate monomorphic or tri-allelic sites. 
It's up to the individual annotations to decide whether they want to annotate or not.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-11 19:52:18 +00:00
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annotator Annotator in general should be able to annotate monomorphic or tri-allelic sites. 2010-01-11 19:52:18 +00:00
concordance Check for division by 0 in annotations 2010-01-07 19:27:15 +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 Annotator in general should be able to annotate monomorphic or tri-allelic sites. 2010-01-11 19:52:18 +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 Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10). 2010-01-11 14:28:52 +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