aaron bc17ff567a When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-02 14:15:50 +00:00
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gatk	When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!	2009-07-02 14:15:50 +00:00
playground/gatk/walkers/indels	Fix CleanedReadInjectorTest to work with new CleanedReadInjector.	2009-07-01 15:48:06 +00:00
utils	made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.	2009-07-01 21:35:34 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00