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Change default blocking and NON-REF LOD params for M2 GVCF mode #5615

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merged 2 commits into from
Jan 29, 2019
Merged

Change default blocking and NON-REF LOD params for M2 GVCF mode #5615

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996a8b3
Change default blocking and NON-REF LOD params for M2 GVCF mode
ldgauthier Jan 28, 2019
1f7d895
Oops -- change tests to match
ldgauthier Jan 28, 2019
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4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -251,12 +251,12 @@ public double getInitialLod() {
"(must be specified in increasing order)", optional = true)
public List<Double> GVCFGQBands = new ArrayList<>(70);
{
for (double i = -4.0; i <= 1; i = i + 0.5) {
for (double i = -2.5; i <= 1; i = i + 0.5) {
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Could you use GVCFGQBands = Arrays.asList(MathUtils.createEvenlySpacedPoints(-2.5, 1, 8))?

GVCFGQBands.add(i);
}
}

@Advanced
@Argument(fullName = "minimum-allele-fraction", shortName = "min-AF", doc = "Lower bound of variant allele fractions to consider when calculating variant LOD", optional = true)
public double minAF = 0.01;
public double minAF = 0.00;
}
5 changes: 3 additions & 2 deletions src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java
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Expand Up @@ -676,7 +676,8 @@ public void testMitochondrialRefConf() throws Exception {
"-O", standardVcf.getAbsolutePath(),
"-ERC", "GVCF",
"-LODB", "-2.0",
"-LODB", "0.0");
"-LODB", "0.0",
"-min-AF", "0.01");
runCommandLine(args);

//check ref conf-specific headers are output
Expand Down Expand Up @@ -718,7 +719,7 @@ public void testMitochondrialRefConf() throws Exception {
"-ERC", "GVCF",
"-LODB", "-2.0",
"-LODB", "0.0",
"-min-AF", "0.0");
"-min-AF", "0.00");
runCommandLine(args3);
final Pair<VCFHeader, List<VariantContext>> result_noThreshold = VariantContextTestUtils.readEntireVCFIntoMemory(unthresholded.getAbsolutePath());

Expand Down