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Adding arg to VariantFiltration to write your own description in Header #8831

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merged 4 commits into from
May 15, 2024
Merged

Adding arg to VariantFiltration to write your own description in Header #8831

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8d0a416
adding arg to variant filtration to write your own description in VCF…
meganshand May 14, 2024
d8750e0
doc
meganshand May 14, 2024
032418b
arg check
meganshand May 14, 2024
4babf10
better arg name
meganshand May 15, 2024
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16 changes: 15 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,7 @@ public final class VariantFiltration extends VariantWalker {
public static final String CLUSTER_WINDOW_SIZE_LONG_NAME = "cluster-window-size";
public static final String MASK_EXTENSION_LONG_NAME = "mask-extension";
public static final String MASK_NAME_LONG_NAME = "mask-name";
public static final String MASK_DESCRIPTION_LONG_NAME = "mask-desc";
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I might spell out mask-description for this argument name, since the other mask arguments don't have abbreviations

public static final String FILTER_NOT_IN_MASK_LONG_NAME = "filter-not-in-mask";
public static final String MISSING_VAL_LONG_NAME = "missing-values-evaluate-as-failing";
public static final String INVERT_LONG_NAME = "invert-filter-expression";
Expand Down Expand Up @@ -238,6 +239,14 @@ public final class VariantFiltration extends VariantWalker {
@Argument(fullName=ALLELE_SPECIFIC_LONG_NAME, optional=true, doc="Set mask at the allele level. This option is not compatible with clustering.")
public boolean applyForAllele = false;

/**
* If a mask interval list is provided, then set the description of the filter in the VCF header to this String.
* Note that if spaces are needed, then the entire description should be enclosed in quotes. Also note that if
* --filter-not-in-mask is used, the description should be adapted to reflect the reverse logic.
*/
@Argument(fullName=MASK_DESCRIPTION_LONG_NAME, optional=true, doc="Description to add to the FILTER field in VCF header for the mask filter.")
public String maskDescription;

// JEXL expressions for the filters
private List<JexlVCMatchExp> filterExps;
private List<JexlVCMatchExp> genotypeFilterExps;
Expand Down Expand Up @@ -305,7 +314,9 @@ private void initializeVcfWriter() {
}

if ( mask != null ) {
if (filterRecordsNotInMask) {
if (maskDescription != null) {
hInfo.add(new VCFFilterHeaderLine(maskName, maskDescription));
} else if (filterRecordsNotInMask) {
hInfo.add(new VCFFilterHeaderLine(maskName, "Doesn't overlap a user-input mask"));
} else {
hInfo.add(new VCFFilterHeaderLine(maskName, "Overlaps a user-input mask"));
Expand All @@ -331,6 +342,9 @@ public void onTraversalStart() {
if (filterRecordsNotInMask && mask == null) {
throw new CommandLineException.BadArgumentValue(FILTER_NOT_IN_MASK_LONG_NAME, "argument not allowed if mask argument is not provided");
}
if (maskDescription != null && mask == null) {
throw new CommandLineException.BadArgumentValue(MASK_DESCRIPTION_LONG_NAME, "argument not allowed if mask argument is not provided");
}
filterExps = VariantContextUtils.initializeMatchExps(filterNames, filterExpressions);
genotypeFilterExps = VariantContextUtils.initializeMatchExps(genotypeFilterNames, genotypeFilterExpressions);
howToTreatMissingValues = failMissingValues ? JexlMissingValueTreatment.TREAT_AS_MATCH : JexlMissingValueTreatment.TREAT_AS_MISMATCH;
Expand Down
18 changes: 18 additions & 0 deletions ...org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltrationIntegrationTest.java
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@@ -1,12 +1,14 @@
package org.broadinstitute.hellbender.tools.walkers.filters;

import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.engine.FeatureDataSource;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
Expand Down Expand Up @@ -91,6 +93,22 @@ public void testMaskReversed() throws IOException {
spec.executeTest("testMaskReversed", this);
}

@Test
public void testMaskDescription() throws IOException {
final File output = createTempFile("testHeader", ".vcf");

final ArgumentsBuilder args = new ArgumentsBuilder();
args.add("V", getTestFile("vcfexample2.vcf"))
.add("mask-name", "foo")
.add("mask-desc", "description")
.add("mask:BED", getToolTestDataDir() + "goodMask.bed");
args.addOutput(output);

runCommandLine(args);
VCFHeader header = VariantContextTestUtils.getVCFHeader(output.getAbsolutePath());
header.getFilterLines().stream().filter(f -> f.getID().equals("foo")).forEach(f -> Assert.assertEquals(f.getDescription(), "description"));
}

@Test
public void testIllegalFilterName() throws IOException {
final IntegrationTestSpec spec = new IntegrationTestSpec(
Expand Down
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