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Made number of samples to put variant site in M2 pon adjustable #4566

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merged 2 commits into from
Mar 23, 2018
Merged

Made number of samples to put variant site in M2 pon adjustable #4566

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1390b5e
made number of samples required to put variant site in M2 pon an adju…
davidbenjamin Mar 23, 2018
7077e80
whoops
davidbenjamin Mar 23, 2018
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18 changes: 14 additions & 4 deletions .../java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormals.java
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,10 @@ public class CreateSomaticPanelOfNormals extends CommandLineProgram {
public static final String INPUT_VCFS_LIST_LONG_NAME = "vcfs";
public static final String INPUT_VCFS_LIST_SHORT_NAME = "vcfs";

public static final String MIN_SAMPLE_COUNT_LONG_NAME = "min-sample-count";

public static final int DEFAULT_MIN_SAMPLE_COUNT = 2;

public static final String DUPLICATE_SAMPLE_STRATEGY_LONG_NAME = "duplicate-sample-strategy";

public enum DuplicateSampleStrategy {
Expand All @@ -114,6 +118,14 @@ public enum DuplicateSampleStrategy {
doc="VCFs for samples to include. May be specified either one at a time, or as one or more .args file containing multiple VCFs, one per line.", optional = false)
private Set<File> vcfs = new LinkedHashSet<>(0);

/**
* The VCFs can be input as either one or more .args file(s) containing one VCF per line, or VCFs can be
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I think this comment block got copied and pasted from above

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Whoops!

* specified explicitly on the command line.
*/
@Argument(fullName = MIN_SAMPLE_COUNT_LONG_NAME,
doc="Number of samples containing a variant site required to include it in the panel of normals.", optional = true)
private int minSampleCount = DEFAULT_MIN_SAMPLE_COUNT;

/**
* How to handle duplicate samples: THROW_ERROR to fail, CHOOSE_FIRST to use the first vcf with each sample name, ALLOW_ALL to use all samples regardless of duplicate sample names."
*/
Expand Down Expand Up @@ -178,10 +190,8 @@ public Object doWork() {
return "SUCCESS";
}

//TODO: this is the old Mutect behavior that just looks for multiple hits
//TODO: we should refine this
private static void processVariantsAtSamePosition(final List<VariantContext> variants, final VariantContextWriter writer) {
if (variants.size() > 1){
private void processVariantsAtSamePosition(final List<VariantContext> variants, final VariantContextWriter writer) {
if (variants.size() >= minSampleCount){
final VariantContext mergedVc = AssemblyBasedCallerUtils.makeMergedVariantContext(variants);
final VariantContext outputVc = new VariantContextBuilder()
.source(mergedVc.getSource())
Expand Down