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orlicohen committed Jun 30, 2022
1 parent 9b956ba commit cb09924
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Showing 5 changed files with 3 additions and 172 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ public void onTraversalStart() {

// if fields specified, but none are genotype fields, set samples to empty
if (genotypeFieldsToTake.isEmpty() && asGenotypeFieldsToTake.isEmpty()) {
samples = Collections.emptySortedSet();
samples = Collections.emptySortedSet();
}
else {
final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
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Original file line number Diff line number Diff line change
Expand Up @@ -239,10 +239,10 @@ public void testMoltenOutputWithMultipleAlleles() throws IOException {
}

@Test
public void testNoFieldsSpecified() throws IOException {
public void testNoFieldsSpecifiedNoSamples() throws IOException {
final File inputFile = new File(getToolTestDataDir(), "VCFWithoutGenotypes_dbsnp_138.snippet.vcf");
final File outputFile = createTempFile("noFieldsSpecifiedOutput", ".table");
final File expectedFile = new File(getToolTestDataDir(), "expected.noFieldsSpecified.table");
final File expectedFile = new File(getToolTestDataDir(), "expected.noFieldsSpecifiedNoSamples.table");

final String[] args = new String[] {"--variant", inputFile.getAbsolutePath(),
"-O", outputFile.getAbsolutePath()};
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