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We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test). 

SequenomToVCF now correctly has no-calls when probes fail.
Re-enabled SequenomToVCF integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2572 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-13 15:40:27 +00:00
parent 6d1107a4ed
commit 8ca5bba738
3 changed files with 5 additions and 4 deletions
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3
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
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@ -94,7 +94,8 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
throw new IllegalArgumentException("Only VCFVariationCall objects should be passed in to the VCF writers"); throw new IllegalArgumentException("Only VCFVariationCall objects should be passed in to the VCF writers");
VCFParameters params = new VCFParameters(); VCFParameters params = new VCFParameters();
params.addFormatItem(VCFGenotypeRecord.GENOTYPE_KEY); if ( genotypes.size() > 0 )
params.addFormatItem(VCFGenotypeRecord.GENOTYPE_KEY);
// get the location and reference // get the location and reference
if ( genotypes.size() == 0 ) { if ( genotypes.size() == 0 ) {

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
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@ -567,7 +567,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
builder.append(FIELD_SEPERATOR); builder.append(FIELD_SEPERATOR);
builder.append(createInfoString()); builder.append(createInfoString());
if ( hasGenotypeData() ) { if ( mGenotypeFormatString != null && mGenotypeFormatString.length() > 0 ) {
try { try {
addGenotypeData(builder, header); addGenotypeData(builder, header);
} catch (Exception e) { } catch (Exception e) {

4
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java
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@ -17,11 +17,11 @@ import java.util.List;
public class SequenomToVCFIntegrationTest extends WalkerTest { public class SequenomToVCFIntegrationTest extends WalkerTest {
@Test @Test
public void testSequenomToVCFWithoutSmartHardy() { public void testSequenomToVCFWithoutSmartHardy() {
String testMD5 = "ed121c7a27270ddefeded21b06fcb96d"; String testMD5 = "c6c2055d304674c2f7014c50f5cc160e";
String testPedFile = "/humgen/gsa-hpprojects/GATK/data/Validation_Data/Sequenom_Test_File.txt"; String testPedFile = "/humgen/gsa-hpprojects/GATK/data/Validation_Data/Sequenom_Test_File.txt";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -L 1:1000000-2000000 "+ String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -L 1:1000000-2000000 "+
"-T SequenomToVCF -b36contig -ns 10 -sPed "+testPedFile+" -vcf %s"; "-T SequenomToVCF -b36contig -ns 10 -sPed "+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs,1, Arrays.asList(testMD5)); WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs,1, Arrays.asList(testMD5));
//List<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst(); List<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst();
} }
} }