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Merge pull request #195 from broadinstitute/eb_exclude_sample_file_bug_in_select_variants 

Fixed bug reported on the forum where using the --exclude_sample_file ar...
This commit is contained in:
Mark DePristo 2013-04-26 09:47:38 -07:00
parent b749f06ba6 360e2ba87e
commit 92a6c7b561
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
public void testSampleExclusion() {
public void testSampleExclusionFromFileAndSeparateSample() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
@ -158,6 +158,21 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
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
public void testSampleInclusionWithNonexistingSamples() {
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
Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
final Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
samples.removeAll(XLsamplesFromFile);
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 )
throw new UserException("All samples requested to be included were also requested to be excluded.");