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Fixed bug reported on the forum where using the --exclude_sample_file argument in SV was giving bad results. 

Added integration test.
https://www.pivotaltracker.com/s/projects/793457/stories/47399245
This commit is contained in:
Eric Banks 2013-04-26 12:23:11 -04:00
parent 43f1746eb9
commit 360e2ba87e
2 changed files with 18 additions and 3 deletions
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17
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -144,7 +144,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
} }
@Test @Test
public void testSampleExclusion() { public void testSampleExclusionFromFileAndSeparateSample() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
@ -158,6 +158,21 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testSampleExclusion--" + testfile, spec); executeTest("testSampleExclusion--" + testfile, spec);
} }
@Test
public void testSampleExclusionJustFromFile() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sf " + samplesFile + " --variant " + testfile,
1,
Arrays.asList("875d7e00ac8081e87ab9fb1b20c83677")
);
spec.disableShadowBCF();
executeTest("testSampleExclusion--" + testfile, spec);
}
@Test @Test
public void testSampleInclusionWithNonexistingSamples() { public void testSampleInclusionWithNonexistingSamples() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -377,10 +377,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
// now, exclude any requested samples // now, exclude any requested samples
Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles); final Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
samples.removeAll(XLsamplesFromFile); samples.removeAll(XLsamplesFromFile);
samples.removeAll(XLsampleNames); samples.removeAll(XLsampleNames);
NO_SAMPLES_SPECIFIED = NO_SAMPLES_SPECIFIED && XLsampleNames.isEmpty(); NO_SAMPLES_SPECIFIED = NO_SAMPLES_SPECIFIED && XLsampleNames.isEmpty() && XLsamplesFromFile.isEmpty();
if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED ) if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
throw new UserException("All samples requested to be included were also requested to be excluded."); throw new UserException("All samples requested to be included were also requested to be excluded.");