Mark DePristo 2472828e1c HC bug fixes: no longer create reference graphs with cycles ... -- Though not intended, it was possible to create reference graphs with cycles in the case where you started the graph with a homopolymer of length > the kmer. The previous test would fail to catch this case. Now its not possible -- Lots of code cleanup and refactoring in this push. Split the monolithic createGraphFromSequences into simple calls to addReferenceKmersToGraph and addReadKmersToGraph which themselves share lower level functions like addKmerPairFromSeqToGraph. -- Fix performance problem with reduced reads and the HC, where we were calling add kmer pair for each count in the reduced read, instead of just calling it once with a multiplicity of count. -- Refactor addKmersToGraph() to use things like addOrUpdateEdge, now the code is very clear		2013-03-26 10:12:24 -04:00
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java	HC bug fixes: no longer create reference graphs with cycles	2013-03-26 10:12:24 -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