zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
View File

@ -94,7 +94,8 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
throw new IllegalArgumentException("Only VCFVariationCall objects should be passed in to the VCF writers");
VCFParameters params = new VCFParameters();
params.addFormatItem(VCFGenotypeRecord.GENOTYPE_KEY);
if ( genotypes.size() > 0 )
params.addFormatItem(VCFGenotypeRecord.GENOTYPE_KEY);
// get the location and reference
if ( genotypes.size() == 0 ) {

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
View File

@ -567,7 +567,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
builder.append(FIELD_SEPERATOR);
builder.append(createInfoString());
if ( hasGenotypeData() ) {
if ( mGenotypeFormatString != null && mGenotypeFormatString.length() > 0 ) {
try {
addGenotypeData(builder, header);
} catch (Exception e) {

4
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java
View File

@ -17,11 +17,11 @@ import java.util.List;
public class SequenomToVCFIntegrationTest extends WalkerTest {
@Test
public void testSequenomToVCFWithoutSmartHardy() {
String testMD5 = "ed121c7a27270ddefeded21b06fcb96d";
String testMD5 = "c6c2055d304674c2f7014c50f5cc160e";
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 "+
"-T SequenomToVCF -b36contig -ns 10 -sPed "+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs,1, Arrays.asList(testMD5));
//List<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst();
List<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst();
}
}