Mark DePristo 5226b24a11 HaplotypeCaller instructure cleanup and unit testing ... -- UnitTest for isRootOfDiamond along with key bugfix detected while testing -- Fix up the equals methods in BaseEdge. Now called hasSameSourceAndTarget and seqEquals. A much more meaningful naming -- Generalize graphEquals to use seqEquals, so it works equally well with Debruijn and SeqGraphs -- Add BaseVertex method called seqEquals that returns true if two BaseVertex objects have the same sequence -- Reorganize SeqGraph mergeNodes into a single master function that does zipping, branch merging, and zipping again, rather than having this done in the DeBruijnAssembler itself -- Massive expansion of the SeqGraph unit tests. We now really test out the zipping and branch merging code. -- Near final cleanup of the current codebase -- DeBruijnVertex cleanup and optimizations. Since kmer graphs don't allow sequences longer than the kmer size, the suffix is always a byte, not a byte[]. Optimize the code to make use of this constraint		2013-03-20 22:54:37 -04:00
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java	HaplotypeCaller instructure cleanup and unit testing	2013-03-20 22:54:37 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00