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Merge pull request #1046 from broadinstitute/rhl_catvariants_sort 

Fix for mis-sorted VCF files in CatVariants
This commit is contained in:
Eric Banks 2015-07-21 17:37:27 -04:00
parent 9360e1d293 8fc631b7ae
commit 178bf12b27
2 changed files with 40 additions and 12 deletions
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29
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.gatk.tools;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.reference.ReferenceSequenceFile;
import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
import org.apache.log4j.BasicConfigurator;
@ -47,6 +48,7 @@ import htsjdk.variant.vcf.VCFCodec;
import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextComparator;
import htsjdk.variant.variantcontext.writer.Options;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
@ -228,9 +230,9 @@ public class CatVariants extends CommandLineProgram {
variant = parseVariantList(variant);
Comparator<Pair<Integer,File>> positionComparator = new PositionComparator();
Comparator<Pair<VariantContext,File>> positionComparator = new PositionComparator(ref.getSequenceDictionary());
Queue<Pair<Integer,File>> priorityQueue;
Queue<Pair<VariantContext,File>> priorityQueue;
if (assumeSorted)
priorityQueue = new LinkedList<>();
else
@ -244,7 +246,7 @@ public class CatVariants extends CommandLineProgram {
return 1;
if (assumeSorted){
priorityQueue.add(new Pair<>(0,file));
priorityQueue.add(new Pair<VariantContext,File>(null,file));
}
else{
if (!file.exists()) {
@ -257,9 +259,8 @@ public class CatVariants extends CommandLineProgram {
continue;
}
VariantContext vc = it.next();
int firstPosition = vc.getStart();
reader.close();
priorityQueue.add(new Pair<>(firstPosition,file));
priorityQueue.add(new Pair<>(vc,file));
}
}
@ -318,15 +319,19 @@ public class CatVariants extends CommandLineProgram {
}
}
private static class PositionComparator implements Comparator<Pair<Integer,File>> {
private static class PositionComparator implements Comparator<Pair<VariantContext,File>> {
VariantContextComparator comp;
public PositionComparator(final SAMSequenceDictionary dict){
comp = new VariantContextComparator(dict);
}
@Override
public int compare(Pair<Integer,File> p1, Pair<Integer,File> p2) {
int startPositionP1 = p1.getFirst();
int startPositionP2 = p2.getFirst();
if (startPositionP1 == startPositionP2)
return 0;
return startPositionP1 < startPositionP2 ? -1 : 1 ;
public int compare(final Pair<VariantContext,File> p1, final Pair<VariantContext,File> p2) {
final VariantContext startPositionP1 = p1.getFirst();
final VariantContext startPositionP2 = p2.getFirst();
return comp.compare(startPositionP1, startPositionP2);
}
}
}

23
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
View File

@ -57,6 +57,8 @@ public class CatVariantsIntegrationTest {
private final File CatVariantsVcf2 = new File(CatVariantsDir, "CatVariantsTest2.vcf");
private final File CatVariantsBcf1 = new File(CatVariantsDir, "CatVariantsTest1.bcf");
private final File CatVariantsBcf2 = new File(CatVariantsDir, "CatVariantsTest2.bcf");
private final File CatVariantsVcf3 = new File(CatVariantsDir, "CatVariantsTest3.vcf");
private final File CatVariantsVcf4 = new File(CatVariantsDir, "CatVariantsTest4.vcf");
private class CatVariantsTestProvider extends BaseTest.TestDataProvider {
private final File file1;
@ -126,6 +128,27 @@ public class CatVariantsIntegrationTest {
}
}
@DataProvider(name = "SortOrderTest")
public Object[][] makeSortOrderTestProvider() {
new CatVariantsTestProvider(CatVariantsVcf3, CatVariantsVcf4, BaseTest.createTempFile("CatVariantsSortOrderTest", ".vcf"), "7bfe34c78b9f1b56a28cc33262cdfd97");
return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
}
@Test(dataProvider = "SortOrderTest")
public void testSortOrder(final CatVariantsTestProvider cfg) throws IOException {
ProcessController pc = ProcessController.getThreadLocal();
ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cfg.getCmdLine()));
pc.execAndCheck(ps);
MD5DB.MD5Match result = md5db.testFileMD5("testSortOrder", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
if(result.failed) {
final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
Assert.fail(failure.toString());
}
}
@DataProvider(name = "MismatchedExtensionsTest")
public Object[][] makeMismatchedExtensionsTestProvider() {
return new Object[][]{