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gatk-3.8/java/test/org/broadinstitute/sting
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chartl 88cb93cc3c Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass. 
Homopolymer Run now does the "right" thing (e.g. single bases are represented as HRun = 0 rather than HRun = 1) for indels. AlleleBalance now does something close enough to correct.

Added a convenience method to VariantContext that will return the indel length (or lengths if a site is not biallelic).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3409 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-05-21 13:02:01 +00:00
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alignment Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath. 2010-04-01 17:17:16 +00:00
commandline The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
gatk Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass. 2010-05-21 13:02:01 +00:00
playground Make VA annotate dbsnp again 2010-05-11 14:06:53 +00:00
utils Genotyper now is using bytes not chars. Passes all tests. 2010-05-20 21:02:44 +00:00
BaseTest.java Walkers and integration tests that calculate and compare callable bases 2010-05-07 21:33:47 +00:00
WalkerTest.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00