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Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed.

This commit is contained in:
Eric Banks 2011-10-27 20:43:50 -04:00
parent c2f343773e
commit ccfd853b34
3 changed files with 83 additions and 15 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -385,7 +385,7 @@ public class GenomeAnalysisEngine {
// this was very likely unintentional, the user should be informed of this. Note that this is different
// from the case where intervals == null, which indicates either that there were no interval arguments,
// or that -L all was specified.
if ( intervals != null && intervals.isEmpty() ) {
if ( intervals != null && intervals.isEmpty() && argCollection.excludeIntervals != null ) {
throw new ArgumentException("The given combination of -L and -XL options results in an empty set. " +
"No intervals to process.");
}

19
public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
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@ -109,20 +109,6 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
};
}
@Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
public void testInvalidBedIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
String contig, int intervalStart, int intervalEnd ) throws Exception {
// We need to adjust intervalStart, since BED intervals are 0-based. We don't need to adjust intervalEnd,
// since the ending point is an open interval.
File bedFile = createTempFile("testInvalidBedIntervalHandling", ".bed",
String.format("%s %d %d", contig, intervalStart -1, intervalEnd));
List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
intervalArgs.add(new IntervalBinding<Feature>(bedFile.getAbsolutePath()));
testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
}
@Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
public void testInvalidPicardIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
String contig, int intervalStart, int intervalEnd ) throws Exception {
@ -154,6 +140,11 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
}
private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception {
File tempFile = File.createTempFile(tempFilePrefix, tempFileExtension);
tempFile.deleteOnExit();

77
public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.utils.interval;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.commandline.ArgumentException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.io.File;
@ -161,4 +163,79 @@ public class IntervalIntegrationTest extends WalkerTest {
Arrays.asList(md5));
executeTest("testMixedIntervalMerging", spec);
}
@Test(enabled = true)
public void testComplexVCF() {
String md5 = "166d77ac1b46a1ec38aa35ab7e628ab5";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -L " + validationDataLocation + "intervalTest.3.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testComplexVCF", spec);
}
@Test(enabled = true)
public void testMergingWithComplexVCF() {
String md5 = "6d7fce9fee471194aa8b5b6e47267f03";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -L " + validationDataLocation + "intervalTest.1.vcf" +
" -XL " + validationDataLocation + "intervalTest.3.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testMergingWithComplexVCF", spec);
}
@Test(enabled = true, expectedExceptions = RuntimeException.class)
public void testEmptyVCFError() {
String md5 = "";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -L " + validationDataLocation + "intervalTest.empty.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testEmptyVCFError", spec);
}
@Test(enabled = true)
public void testEmptyVCFNoError() {
String md5 = "";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -U ALLOW_EMPTY_INTERVAL_LIST" +
" -L " + validationDataLocation + "intervalTest.empty.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testEmptyVCFNoError", spec);
}
@Test(enabled = true, expectedExceptions = RuntimeException.class)
public void testIncludeExcludeIsTheSame() {
String md5 = "";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -L " + validationDataLocation + "intervalTest.1.vcf" +
" -XL " + validationDataLocation + "intervalTest.1.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testIncludeExcludeIsTheSame", spec);
}
}