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SelectVariants use a GATKPathSpecifier for output #5870

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merged 1 commit into from
Apr 9, 2019
Merged

SelectVariants use a GATKPathSpecifier for output #5870

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4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
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Original file line number Diff line number Diff line change
Expand Up @@ -776,7 +776,7 @@ public final SAMFileGATKReadWriter createSAMWriter(final Path outputPath, final

/**
* Creates a VariantContextWriter whose outputFile type is determined by
* the outPathName's extension, using the best available sequence dictionary for
* the vcfOutput's extension, using the best available sequence dictionary for
* this tool, and default index, leniency and md5 generation settings.
*
* Deprecated, use {@link #createVCFWriter(Path)} instead.
Expand All @@ -790,7 +790,7 @@ public VariantContextWriter createVCFWriter(final File outFile) {

/**
* Creates a VariantContextWriter whose outputFile type is determined by
* outPath's extension, using the best available sequence dictionary for
* vcfOutput's extension, using the best available sequence dictionary for
* this tool, and default index, leniency and md5 generation settings.
*
* @param outPath output Path for this writer. May not be null.
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6 changes: 3 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants.java
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Expand Up @@ -18,8 +18,8 @@
import org.broadinstitute.barclay.argparser.Hidden;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.engine.GATKPathSpecifier;
import org.broadinstitute.hellbender.engine.filters.*;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import picard.cmdline.programgroups.VariantManipulationProgramGroup;
import org.broadinstitute.hellbender.engine.FeatureInput;
import org.broadinstitute.hellbender.engine.FeatureContext;
Expand Down Expand Up @@ -137,7 +137,7 @@ public final class SelectVariants extends VariantWalker {
@Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
doc="Path to which variants should be written")
public String outPathName = null;
public GATKPathSpecifier vcfOutput = null;

/**
* This argument can be specified multiple times in order to provide multiple sample names, or to specify
Expand Down Expand Up @@ -525,7 +525,7 @@ public void onTraversalStart() {
}
}

final Path outPath = IOUtils.getPath(outPathName);
final Path outPath = vcfOutput.toPath();
vcfWriter = createVCFWriter(outPath);
vcfWriter.writeHeader(new VCFHeader(actualLines, samples));
}
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