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Merge pull request #162 from broadinstitute/md_path_sw_update 

Slight update to Path SW parameters.
This commit is contained in:
Ryan Poplin 2013-04-12 10:38:26 -07:00
parent 4ef6e0deb1 0e627bce93
commit e5b9b6041c
2 changed files with 3 additions and 2 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
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@ -86,7 +86,7 @@ public class Path<T extends BaseVertex> {
// used in the bubble state machine to apply Smith-Waterman to the bubble sequence
// these values were chosen via optimization against the NA12878 knowledge base
public static final Parameters NEW_SW_PARAMETERS = new Parameters(20.0, -20.0, -26.0, -0.1);
public static final Parameters NEW_SW_PARAMETERS = new Parameters(10, -20.0, -26.0, -0.1);
private static final byte[] STARTING_SW_ANCHOR_BYTES = "XXXXXXXXX".getBytes();

3
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
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@ -445,6 +445,7 @@ public class KBestPathsUnitTest extends BaseTest {
Arrays.asList("", "C", "1I"),
Arrays.asList("AAA", "CGT", "3D3I"),
Arrays.asList("TAT", "CAC", "3M"),
Arrays.asList("GCTG", "GTCG", "4M"),
Arrays.asList("AAAAA", "", "5D"),
Arrays.asList("", "AAAAA", "5I"),
Arrays.asList("AAAAACC", "CCGGGGGG", "5D2M6I")
@ -460,7 +461,7 @@ public class KBestPathsUnitTest extends BaseTest {
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "SystematicRefAltSWTestData", enabled = true)
@Test(dataProvider = "SystematicRefAltSWTestData", enabled = !DEBUG)
public void testRefAltSW(final String prefix, final String end, final String refMid, final String altMid, final String midCigar) {
// Construct the assembly graph
SeqGraph graph = new SeqGraph();