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Contig stratification should defer to user-defined intervals #7238

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merged 6 commits into from
May 3, 2021
Merged

Contig stratification should defer to user-defined intervals #7238

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c805743
Contig stratification should defer to user-defined intervals
bbimber Apr 30, 2021
7874be6
Add test case
bbimber Apr 30, 2021
75e470a
Code review
bbimber May 3, 2021
7ca616d
Split apart code to make intent clearer
bbimber May 3, 2021
f228a3d
Restore original test style with static files for expected output
bbimber May 3, 2021
61cd15b
No need to create ArrayList
bbimber May 3, 2021
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4 changes: 4 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEvalEngine.java
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Expand Up @@ -485,6 +485,10 @@ public long getnProcessedLoci() {
return traversalIntervals.stream().mapToLong(SimpleInterval::size).sum();
}

public List<SimpleInterval> getTraversalIntervals() {
return Collections.unmodifiableList(traversalIntervals);
}

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This transformation seems pretty specific to the contig strat class, so I think it would make more sense to keep it there, and instead expose an intervals getter on VariantEvalEngine.

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ok

private boolean compHasMatchingEval(final VariantContext comp, final Collection<VariantContext> evals) {
// find all of the matching comps
for ( final VariantContext eval : evals ) {
Expand Down
21 changes: 14 additions & 7 deletions .../java/org/broadinstitute/hellbender/tools/walkers/varianteval/stratifications/Contig.java
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@@ -1,30 +1,37 @@
package org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications;

import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine;
import org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext;
import org.broadinstitute.hellbender.utils.SimpleInterval;

import java.util.*;

/**
* Stratifies the evaluation by each contig in the reference sequence
* Stratifies the evaluation by each contig in the reference sequence. Note: if the user supplies custom intervals, it will defer to these rather than the full sequence dictionary
*/
public class Contig extends VariantStratifier {
public Contig(VariantEvalEngine engine) {
super(engine);

states.addAll(getContigNames(getEngine().getSequenceDictionaryForDrivingVariants()));
states.addAll(getContigNames());
states.add("all");
}

private Set<String> getContigNames(SAMSequenceDictionary dict) {
/**
* @return The list of contig names to be traversed, preferentially taking user supplied intervals, but otherwise defaulting to driving variants
*/
private List<String> getContigNames() {
final TreeSet<String> contigs = new TreeSet<>();
for( final SAMSequenceRecord r : dict.getSequences()) {
contigs.add(r.getSequenceName());
if (getEngine().getTraversalIntervals() == null) {
getEngine().getSequenceDictionaryForDrivingVariants().getSequences().stream().map(SAMSequenceRecord::getSequenceName).forEach(contigs::add);
}
return contigs;
else {
getEngine().getTraversalIntervals().stream().map(SimpleInterval::getContig).forEach(contigs::add);
}

return new ArrayList<>(contigs);
}

@Override
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40 changes: 35 additions & 5 deletions ...a/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEvalIntegrationTest.java
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@@ -1,21 +1,27 @@
package org.broadinstitute.hellbender.tools.walkers.varianteval;

import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.util.IOUtil;
import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.barclay.argparser.CommandLineException;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.reference.ReferenceUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.*;
import java.util.stream.Collectors;

public class VariantEvalIntegrationTest extends CommandLineProgramTest {

Expand Down Expand Up @@ -106,6 +112,31 @@ public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() throws IOExc
spec.executeTest(name, this);
}

@DataProvider(name = "testContigStratWithUserSuppliedIntervalsData")
public Object[][] testContigStratWithUserSuppliedIntervalsData() {
return new Object[][]{
new Object[]{"1:1-1480226", "testContigStratWithUserSuppliedIntervals"},
new Object[]{"1", "testContigStratWithUserSuppliedIntervals2"},
new Object[]{null, "testContigStratWithUserSuppliedIntervals3"}
};
}
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The original version of these tests was much easier to understand - it just needed a data provider, which for the old version of the tests would just be:

    @DataProvider(name = "testContigStratWithIntervals")
    public Object[][] testContigStratWithIntervals() {
        return new Object[][] {
                { "testContigStratWithUserSuppliedIntervals", "-L 1:1-1480226" },
                { "testContigStratWithUserSuppliedIntervals2", "-L 1" },
                { "testContigStratWithUserSuppliedIntervals3", null },
        };
    }

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discussed below - made the change


@Test(dataProvider = "testContigStratWithUserSuppliedIntervalsData")
public void testContigStratWithUserSuppliedIntervals(String intervalString, String expectedOutputFile) throws IOException {
IntegrationTestSpec spec = new IntegrationTestSpec(
" -R " + b37Reference +
" --eval " + snpEffVcf +
" -no-ev" +
" -EV CountVariants" +
" -no-st" +
" -ST Contig" +
(intervalString == null ? "" : " -L " + intervalString) +
" -O %s",
Arrays.asList(getExpectedFile(expectedOutputFile))
);
spec.executeTest(expectedOutputFile, this);
}

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These two tests are identical except for the file name and interval, so they can be replaced with a single test that uses a @DataProvider. That will also nicely document the test files contents. Also please add a test case with no intervals specified.

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Not sure if you've used data providers before - if not let me know and I'll add one here.

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yes, i've used them. i reworked the test so it doesnt need the static test files anymore. i dont know what GATK's vision is in terms of having the full output checked in vs. testing specific features of the output. most of VariantEvalIntegration test uses the former since it was ported from GATK3, but i assume you dont want infinite test outputs checked in.

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This seems much more convoluted and error-prone than the previous version, which was much easier to comprehend.

@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() throws IOException {
String name = "testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter";
Expand Down Expand Up @@ -636,7 +667,6 @@ public Object[][] testValidationReportData() {
return tests.toArray(new Object[][]{});
}


@Test
public void testPrintMissingComp() throws IOException {
String name = "testPrintMissingComp";
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6 changes: 6 additions & 0 deletions ...rs/varianteval/VariantEval/expected/testContigStratWithUserSuppliedIntervals.expected.txt
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#:GATKReport.v1.1:1
#:GATKTable:29:2:%s:%s:%s:%s:%d:%d:%d:%d:%.8f:%.8f:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f:;
#:GATKTable:CountVariants:Counts different classes of variants in the sample
CountVariants CompFeatureInput Contig EvalFeatureInput nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp insertionDeletionRatio
CountVariants none 1 eval 1480226 969 0 969 0.00065463 1527.00000000 920 0 16 33 0 0 0 7519 12011 123783 6882 287 0 8.11e-03 123.00 1.75 3.31e-05 30208.00 0.48
CountVariants none all eval 1480226 969 0 969 0.00065463 1527.00000000 920 0 16 33 0 0 0 7519 12011 123783 6882 287 0 8.11e-03 123.00 1.75 3.31e-05 30208.00 0.48
7 changes: 7 additions & 0 deletions ...s/varianteval/VariantEval/expected/testContigStratWithUserSuppliedIntervals2.expected.txt
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#:GATKReport.v1.1:1
#:GATKTable:29:2:%s:%s:%s:%s:%d:%d:%d:%d:%.8f:%.8f:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f:;
#:GATKTable:CountVariants:Counts different classes of variants in the sample
CountVariants CompFeatureInput Contig EvalFeatureInput nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp insertionDeletionRatio
CountVariants none 1 eval 249250621 969 0 969 0.00000389 257224.00000000 920 0 16 33 0 0 0 7519 12011 123783 6882 287 0 4.82e-05 20751.00 1.75 1.97e-07 5086747.00 0.48
CountVariants none all eval 249250621 969 0 969 0.00000389 257224.00000000 920 0 16 33 0 0 0 7519 12011 123783 6882 287 0 4.82e-05 20751.00 1.75 1.97e-07 5086747.00 0.48

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