gatk-3.8

History

Eric Banks 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. * This version inherits from the original SW implementation so it can use the same matrix creation method. * A bunch of refactoring was done to the original version to clean it up a bit and to have it do the right thing for indels at the edges of the alignments. * Enum added for the overhang strategy to use; added implementation for the INDEL version of this strategy. * Lots of systematic testing added for this implementation. * NOT HOOKED UP TO HAPLOTYPE CALLER YET. Committing so that people can play around with this for now.	2013-05-13 09:36:39 -04:00
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SmithWatermanBenchmark.java	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00

Eric Banks 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.

* This version inherits from the original SW implementation so it can use the same matrix creation method.
   * A bunch of refactoring was done to the original version to clean it up a bit and to have it do the
     right thing for indels at the edges of the alignments.
     * Enum added for the overhang strategy to use; added implementation for the INDEL version of this strategy.
   * Lots of systematic testing added for this implementation.
   * NOT HOOKED UP TO HAPLOTYPE CALLER YET. Committing so that people can play around with this for now.

2013-05-13 09:36:39 -04:00

SmithWatermanBenchmark.java

New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.

2013-05-13 09:36:39 -04:00