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Merge pull request #184 from broadinstitute/rp_revert_sw_params 

After debate reverting SW parameter changes temporarily while we explore...
This commit is contained in:
Mark DePristo 2013-04-23 12:32:13 -07:00
parent cb2a8f83de cb4ec3437a
commit 90fc249c8d
3 changed files with 4 additions and 4 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(10, -20.0, -26.0, -0.1);
public static final Parameters NEW_SW_PARAMETERS = new Parameters(20.0, -15.0, -26.0, -1.1);
private static final byte[] STARTING_SW_ANCHOR_BYTES = "XXXXXXXXX".getBytes();

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cac0d88fa4471c7a0ac96533a9a6354b"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("eb5772b825120a0b8710e5add485d73a"));
executeTest("HCTestStructuralIndels: ", spec);
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
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@ -425,7 +425,7 @@ public class KBestPathsUnitTest extends BaseTest {
logger.warn("AltPath : " + altPath + " cigar " + altPath.calculateCigar());
Assert.assertEquals(refPath.calculateCigar().toString(), "51M");
Assert.assertEquals(altPath.calculateCigar().toString(), "3M14D2M20I32M");
Assert.assertEquals(altPath.calculateCigar().toString(), "3M6I48M");
}
// -----------------------------------------------------------------
@ -443,7 +443,7 @@ public class KBestPathsUnitTest extends BaseTest {
Arrays.asList("G", "C", "1M"),
Arrays.asList("G", "", "1D"),
Arrays.asList("", "C", "1I"),
Arrays.asList("AAA", "CGT", "3D3I"),
Arrays.asList("AAA", "CGT", "3M"),
Arrays.asList("TAT", "CAC", "3M"),
Arrays.asList("GCTG", "GTCG", "4M"),
Arrays.asList("AAAAA", "", "5D"),