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ArgumentsBuilder in Mutect2 pipeline tool tests #6219

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Oct 17, 2019
Merged

ArgumentsBuilder in Mutect2 pipeline tool tests #6219

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36 changes: 18 additions & 18 deletions ...stitute/hellbender/tools/walkers/contamination/CalculateContaminationIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import org.apache.commons.math3.random.RandomGenerator;
import org.apache.commons.math3.random.RandomGeneratorFactory;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
Expand Down Expand Up @@ -87,11 +88,11 @@ public void testArtificialData(final boolean includeHomAlts) {
final File contaminationTable = createTempFile("contamination", ".table");
final File segmentationsTable = createTempFile("segments", ".table");

final String[] args = {
"-I", psTable.getAbsolutePath(),
"-O", contaminationTable.getAbsolutePath(),
"-" + CalculateContamination.TUMOR_SEGMENTATION_SHORT_NAME, segmentationsTable.getAbsolutePath()
};
final ArgumentsBuilder args = new ArgumentsBuilder()
.addInput(psTable)
.addOutput(contaminationTable)
.addFileArgument(CalculateContamination.TUMOR_SEGMENTATION_SHORT_NAME, segmentationsTable);

runCommandLine(args);

final double calculatedContamination = ContaminationRecord.readFromFile(contaminationTable).get(0).getContamination();
Expand All @@ -111,10 +112,10 @@ public void testSpikeIn(final File pileupSummary, final double spikeIn, final do
final File contaminationTable = createTempFile("contamination", ".table");
final double contamination = spikeIn + baselineContamination;

final String[] args = {
"-I", pileupSummary.getAbsolutePath(),
"-O", contaminationTable.getAbsolutePath(),
};
final ArgumentsBuilder args = new ArgumentsBuilder()
.addInput(pileupSummary)
.addOutput(contaminationTable);

runCommandLine(args);

final double calculatedContamination = ContaminationRecord.readFromFile(contaminationTable).get(0).getContamination();
Expand All @@ -141,12 +142,11 @@ public void testMatchedNormal() {
final double contamination = 0.08 + baselineContamination;
final File contaminationTable = createTempFile("contamination", ".table");

final ArgumentsBuilder args = new ArgumentsBuilder()
.addInput(contaminated)
.addFileArgument(CalculateContamination.MATCHED_NORMAL_SHORT_NAME, normal)
.addOutput(contaminationTable);

final String[] args = {
"-I", contaminated.getAbsolutePath(),
"-" + CalculateContamination.MATCHED_NORMAL_SHORT_NAME, normal.getAbsolutePath(),
"-O", contaminationTable.getAbsolutePath(),
};
runCommandLine(args);

final double calculatedContamination = ContaminationRecord.readFromFile(contaminationTable).get(0).getContamination();
Expand All @@ -158,10 +158,10 @@ public void testSmallGenePanelWithNoHomAlts() {
final File inputPileups = new File(CONTAMINATION_TEST_DATA_DIRECTORY, "small_gene_panel.pileups");
final File contaminationTable = createTempFile("contamination", ".table");

final String[] args = {
"-I", inputPileups.getAbsolutePath(),
"-O", contaminationTable.getAbsolutePath(),
};
final ArgumentsBuilder args = new ArgumentsBuilder()
.addInput(inputPileups)
.addOutput(contaminationTable);

runCommandLine(args);

final double calculatedContamination = ContaminationRecord.readFromFile(contaminationTable).get(0).getContamination();
Expand Down
29 changes: 16 additions & 13 deletions ...adinstitute/hellbender/tools/walkers/contamination/GetPileupSummariesIntegrationTest.java
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Expand Up @@ -3,6 +3,7 @@
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.testng.Assert;
import org.testng.annotations.Test;

Expand All @@ -18,13 +19,14 @@ public class GetPileupSummariesIntegrationTest extends CommandLineProgramTest {
@Test
public void test() {
final File output = createTempFile("output", ".table");
final String[] args = {
"-I", NA12878.getAbsolutePath(),
"-V", thousandGenomes,
"-L", thousandGenomes,
"-O", output.getAbsolutePath(),
"-" + GetPileupSummaries.MAX_SITE_AF_SHORT_NAME, "0.9"
};

final ArgumentsBuilder args = new ArgumentsBuilder()
.addInput(NA12878)
.addVCF(new File(thousandGenomes))
.addIntervalFile(new File(thousandGenomes))
.addOutput(output)
.addNumericArgument(GetPileupSummaries.MAX_SITE_AF_SHORT_NAME, 0.9);

runCommandLine(args);

final ImmutablePair<String, List<PileupSummary>> sampleAndResult = PileupSummary.readFromFile(output);
Expand Down Expand Up @@ -67,12 +69,13 @@ public void test() {
public void testNoAFFieldInHeader() {
final File vcfWithoutAF = new File(publicTestDir, "empty.vcf");
final File output = createTempFile("output", ".table");
final String[] args = {
"-I", NA12878.getAbsolutePath(),
"-V", vcfWithoutAF.getAbsolutePath(),
"-L", vcfWithoutAF.getAbsolutePath(),
"-O", output.getAbsolutePath(),
};

final ArgumentsBuilder args = new ArgumentsBuilder()
.addInput(NA12878)
.addVCF(vcfWithoutAF)
.addIntervalFile(vcfWithoutAF)
.addOutput(output);

runCommandLine(args);
}

Expand Down
9 changes: 6 additions & 3 deletions ...a/org/broadinstitute/hellbender/tools/walkers/mutect/MergeMutectStatsIntegrationTest.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.broadinstitute.hellbender.tools.walkers.mutect;

import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.testng.Assert;
import org.testng.annotations.Test;

Expand All @@ -24,9 +25,11 @@ public void simpleTest() {
MutectStats.writeToFile(stats1, statsFile1);
MutectStats.writeToFile(stats2, statsFile2);

final List<String> args = Arrays.asList("--" + Mutect2.MUTECT_STATS_SHORT_NAME, statsFile1.getAbsolutePath(),
"--" + Mutect2.MUTECT_STATS_SHORT_NAME, statsFile2.getAbsolutePath(),
"-O", merged.getAbsolutePath());
final ArgumentsBuilder args = new ArgumentsBuilder()
.addFileArgument(Mutect2.MUTECT_STATS_SHORT_NAME, statsFile1)
.addFileArgument(Mutect2.MUTECT_STATS_SHORT_NAME, statsFile2)
.addOutput(merged);

runCommandLine(args);

final List<MutectStats> mergedStats = MutectStats.readFromFile(merged);
Expand Down
115 changes: 56 additions & 59 deletions ...te/hellbender/tools/walkers/readorientation/LearnReadOrientationModelIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,11 @@
import org.broadinstitute.hellbender.engine.FeatureDataSource;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.broadinstitute.hellbender.tools.walkers.SplitIntervals;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls;
import org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2;
import org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
import org.testng.Assert;
Expand Down Expand Up @@ -47,30 +49,29 @@ public void testOnRealBam(final int scatterCount) throws IOException {

// Step 1: SplitIntervals
final File intervalDir = createTempDir("intervals");
runCommandLine(
Arrays.asList(
"-R", b37_reference_20_21,
"-L", intervalList,
"-O", intervalDir.getAbsolutePath(),
"-" + SplitIntervals.SCATTER_COUNT_SHORT_NAME, Integer.toString(scatterCount)),
SplitIntervals.class.getSimpleName());

final ArgumentsBuilder splitIntervalsArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addIntervalFile(new File(intervalList))
.addOutput(intervalDir)
.addNumericArgument(SplitIntervals.SCATTER_COUNT_SHORT_NAME, scatterCount);

runCommandLine(splitIntervalsArgs, SplitIntervals.class.getSimpleName());

// Step 2: CollectF1R2Counts
final File[] intervals = intervalDir.listFiles();
final List<File> extractedDirs = IntStream.range(0, intervals.length).mapToObj(i -> createTempDir("extracted_" + i)).collect(Collectors.toList());
final List<File> scatteredTarGzs = IntStream.range(0, intervals.length).mapToObj(i -> new File(scatteredDir, "scatter_" + i + ".tar.gz")).collect(Collectors.toList());
for (int i = 0; i < intervals.length; i++){

runCommandLine(Arrays.asList(
"-R", b37_reference_20_21,
"-I", hapmapBamSnippet,
"-L", intervals[i].getAbsolutePath(),
"-O", scatteredTarGzs.get(i).getAbsolutePath()),
CollectF1R2Counts.class.getSimpleName());
final ArgumentsBuilder collectF1R2CountsArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addInput(new File(hapmapBamSnippet))
.addIntervalFile(intervals[i])
.addOutput(scatteredTarGzs.get(i));

runCommandLine(collectF1R2CountsArgs, CollectF1R2Counts.class.getSimpleName());
IOUtils.extractTarGz(scatteredTarGzs.get(i).toPath(), extractedDirs.get(i).toPath());

final int iFinal = i;
final File refHist = F1R2CountsCollector.getRefHistogramsFromExtractedTar(extractedDirs.get(i)).get(0);

// Ensure that we print every bin, even when the count is 0
Expand All @@ -80,9 +81,9 @@ public void testOnRealBam(final int scatterCount) throws IOException {

// Step 3: LearnReadOrientationModel
final File priorTarGz = createTempFile("prior", ".tar.gz");
final ArgumentsBuilder args = new ArgumentsBuilder();
args.addArgument(StandardArgumentDefinitions.OUTPUT_LONG_NAME, priorTarGz.getAbsolutePath());
IntStream.range(0, intervals.length).forEach(n -> args.addArgument(StandardArgumentDefinitions.INPUT_LONG_NAME, scatteredTarGzs.get(n).getAbsolutePath()));
final ArgumentsBuilder args = new ArgumentsBuilder()
.addOutput(priorTarGz);
IntStream.range(0, intervals.length).forEach(n -> args.addInput(scatteredTarGzs.get(n)));

runCommandLine(args.getArgsList(), LearnReadOrientationModel.class.getSimpleName());

Expand All @@ -97,22 +98,20 @@ public void testOnRealBam(final int scatterCount) throws IOException {
final File filteredVcf = GATKBaseTest.createTempFile("filtered", ".vcf");
final File bamout = GATKBaseTest.createTempFile("SM-CEMAH", ".bam");

new Main().instanceMain(makeCommandLineArgs(
Arrays.asList(
"-I", hapmapBamSnippet,
"-R", b37_reference_20_21,
"-O", unfilteredVcf.getAbsolutePath(),
"-bamout", bamout.getAbsolutePath()),
Mutect2.class.getSimpleName()));
final ArgumentsBuilder mutect2Args = new ArgumentsBuilder()
.addReference(b37Reference)
.addInput(new File(hapmapBamSnippet))
.addOutput(unfilteredVcf)
.addFileArgument(AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_LONG_NAME, bamout);
runCommandLine(mutect2Args, Mutect2.class.getSimpleName());

new Main().instanceMain(makeCommandLineArgs(
Arrays.asList(
"-V", unfilteredVcf.getAbsolutePath(),
"-R", b37_reference_20_21,
"--" + M2FiltersArgumentCollection.ARTIFACT_PRIOR_TABLE_NAME, priorTarGz.getAbsolutePath(),
"-O", filteredVcf.getAbsolutePath()),
FilterMutectCalls.class.getSimpleName()));
final ArgumentsBuilder filterArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addVCF(unfilteredVcf)
.addFileArgument(M2FiltersArgumentCollection.ARTIFACT_PRIOR_TABLE_NAME, priorTarGz)
.addOutput(filteredVcf);

runCommandLine(filterArgs, FilterMutectCalls.class.getSimpleName());

// These artifacts have been verified manually
// The pair is of type (Position, Expected Source of Prior Probability)
Expand Down Expand Up @@ -152,7 +151,7 @@ public void testTwoSamples() throws Exception {
.addArgument(StandardArgumentDefinitions.INPUT_LONG_NAME, countsTarGz.getAbsolutePath())
.addArgument(StandardArgumentDefinitions.OUTPUT_LONG_NAME, priorsTarGz.getAbsolutePath());

runCommandLine(args.getArgsList(), LearnReadOrientationModel.class.getSimpleName());
runCommandLine(args, LearnReadOrientationModel.class.getSimpleName());

final File extractedPriorsDir = createTempDir("extracted");
IOUtils.extractTarGz(priorsTarGz.toPath(), extractedPriorsDir.toPath());
Expand All @@ -168,24 +167,23 @@ public void testFewSites() throws IOException {
final File extractedDir = createTempDir("extracted");
final File scatteredTarGz = createTempFile("counts", ".tar.gz");

final ArgumentsBuilder collectF1R2Args = new ArgumentsBuilder()
.addReference(b37Reference)
.addInput(new File(hapmapBamSnippet))
.addInterval(new SimpleInterval("20:10000-10001"))
.addOutput(scatteredTarGz);

runCommandLine(Arrays.asList(
"-R", b37_reference_20_21,
"-I", hapmapBamSnippet,
"-L", "20:10000-10001",
"-O", scatteredTarGz.getAbsolutePath()),
CollectF1R2Counts.class.getSimpleName());
runCommandLine(collectF1R2Args, CollectF1R2Counts.class.getSimpleName());

IOUtils.extractTarGz(scatteredTarGz.toPath(), extractedDir.toPath());


// Step 2: LearnReadOrientationModel
final File priorTarGz = createTempFile("prior", ".tar.gz");
final ArgumentsBuilder args = new ArgumentsBuilder()
.addArgument(StandardArgumentDefinitions.OUTPUT_LONG_NAME, priorTarGz.getAbsolutePath())
.addArgument(StandardArgumentDefinitions.INPUT_LONG_NAME, scatteredTarGz.getAbsolutePath());
.addInput(scatteredTarGz)
.addOutput(priorTarGz);

runCommandLine(args.getArgsList(), LearnReadOrientationModel.class.getSimpleName());
runCommandLine(args, LearnReadOrientationModel.class.getSimpleName());

final File extractedPriorDir = createTempDir("extracted_priors");
IOUtils.extractTarGz(priorTarGz.toPath(), extractedPriorDir.toPath());
Expand All @@ -197,22 +195,21 @@ public void testFewSites() throws IOException {
final File filteredVcf = GATKBaseTest.createTempFile("filtered", ".vcf");
final File bamout = GATKBaseTest.createTempFile("SM-CEMAH", ".bam");

new Main().instanceMain(makeCommandLineArgs(
Arrays.asList(
"-I", hapmapBamSnippet,
"-R", b37_reference_20_21,
"-L", "20:24000000-26000000",
"-O", unfilteredVcf.getAbsolutePath(),
"-bamout", bamout.getAbsolutePath()),
Mutect2.class.getSimpleName()));

new Main().instanceMain(makeCommandLineArgs(
Arrays.asList(
"-V", unfilteredVcf.getAbsolutePath(),
"-R", b37_reference_20_21,
"--" + M2FiltersArgumentCollection.ARTIFACT_PRIOR_TABLE_NAME, priorTarGz.getAbsolutePath(),
"-O", filteredVcf.getAbsolutePath()),
FilterMutectCalls.class.getSimpleName()));

final ArgumentsBuilder mutect2Args = new ArgumentsBuilder()
.addReference(b37Reference)
.addInput(new File(hapmapBamSnippet))
.addInterval(new SimpleInterval("20:24000000-26000000"))
.addFileArgument(AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_LONG_NAME, bamout)
.addOutput(unfilteredVcf);
runCommandLine(mutect2Args, Mutect2.class.getSimpleName());

final ArgumentsBuilder filterArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addVCF(unfilteredVcf)
.addFileArgument(M2FiltersArgumentCollection.ARTIFACT_PRIOR_TABLE_NAME, priorTarGz)
.addOutput(filteredVcf);

runCommandLine(filterArgs, FilterMutectCalls.class.getSimpleName());
}
}
4 changes: 4 additions & 0 deletions src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java
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Expand Up @@ -162,6 +162,10 @@ public ArgumentsBuilder addInterval(Locatable interval){
return this;
}

public ArgumentsBuilder addIntervalFile(final File interval){
return addFileArgument("L", interval);
}

public ArgumentsBuilder addMask(final File mask){
return addFileArgument(IntervalArgumentCollection.EXCLUDE_INTERVALS_LONG_NAME, mask);
}
Expand Down