Mark DePristo 33720b83eb No longer merge overlapping fragments from HaplotypeCaller ... -- Merging overlapping fragments turns out to be a bad idea. In the case where you can safely merge the reads you only gain a small about of overlapping kmers, so the potential gains are relatively small. That's in contrast to the very large danger of merging reads inappropriately, such as when the reads only overlap in a repetitive region, and you artificially construct reads that look like the reference but actually may carry a larger true insertion w.r.t. the reference. Because this problem isn't limited to repetitive sequeuence, but in principle could occur in any sequence, it's just not safe to do this merging. Best to leave haplotype construction to the assembly graph.		2013-06-13 15:05:32 -04:00
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java	No longer merge overlapping fragments from HaplotypeCaller	2013-06-13 15:05:32 -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