Mark DePristo 66910b036c Added new and improved suffix and node merging algorithms ... -- These new algorithms are more powerful than the restricted diamond merging algoriths, in that they can merge nodes with multiple incoming and outgoing edges. Together the splitter + merger algorithms will correctly merge many more cases than the original headless and tailless diamond merger. -- Refactored haplotype caller infrastructure into graphs package, code cleanup -- Cleanup new merging / splitting algorithms, with proper docs and unit tests -- Fix bug in zipping of linear chains. Because the multiplicity can be 0, protect ourselves with a max function call -- Fix BaseEdge.max unit test -- Add docs and some more unit tests -- Move error correct from DeBruijnGraph to DeBruijnAssembler -- Replaced uses of System.out.println with logger.info -- Don't make multiplicity == 0 nodes look like they should be pruned -- Fix toString of Path		2013-03-27 15:31:18 -04:00
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java	Added new and improved suffix and node merging algorithms	2013-03-27 15:31:18 -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