Mark DePristo c9f5b53efa Bugfix for HC can fail to assemble the correct reference sequence in some cases ... -- Ultimately this was caused by overly aggressive merging of CommonSuffixMerger. In the case where you have this graph: ACT [ref source] -> C G -> ACT -> C we would merge into G -> ACT -> C which would linearlize into GACTC Causing us to add bases to the reference source node that couldn't be recovered. The solution was to ensure that CommonSuffixMerger only operates when all nodes to be merged aren't source nodes themselves. -- Added a convenient argument to the haplotype caller (captureAssemblyFailureBAM) that will write out the exact reads to a BAM file that went into a failed assembly run (going to a file called AssemblyFailure.BAM). This can be used to rerun the haplotype caller to produce the exact error, which can be hard in regions of deep coverage where the downsampler state determines the exact reads going into assembly and therefore makes running with a sub-interval not reproduce the error -- Did some misc. cleanup of code while debugging -- [delivers #50917729]		2013-06-03 16:16:39 -04:00
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java	Bugfix for HC can fail to assemble the correct reference sequence in some cases	2013-06-03 16:16:39 -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