Mark DePristo 464e65ea96 Disable error correcting kmers by default in the HC ... -- The error correction algorithm can break the reference graph in some cases by error correcting us into a bad state for the reference sequence. Because we know that the error correction algorithm isn't ideal, and worse, doesn't actually seem to improve the calling itself on chr20, I've simply disabled error correction by default and allowed it to be turned on with a hidden argument. -- In the process I've changed a bit the assembly interface, moving some common arguments us into the LocalAssemblyEngine, which are turned on/off via setter methods. -- Went through the updated arguments in the HC to be @Hidden and @Advanced as appropriate -- Don't write out an errorcorrected graph when debugging and error correction isn't enabled		2013-03-26 10:05:17 -04:00
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java	Disable error correcting kmers by default in the HC	2013-03-26 10:05:17 -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