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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mauricio Carneiro 2011-07-13 15:14:06 -04:00
parent df996a1a73 0c54c796ed
commit a4ab19d040
4 changed files with 38 additions and 9 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -199,8 +199,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
//hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
//hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
for ( VCFHeaderLine field : hInfo ) {

7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
View File

@ -444,9 +444,10 @@ public class StandardVCFWriter implements VCFWriter {
break;
}
for (String s : attrs ) {
mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
mWriter.write(s);
for (int i = 0; i < attrs.size(); i++) {
if ( i > 0 || genotypeFormatKeys.contains(VCFConstants.GENOTYPE_KEY) )
mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
mWriter.write(attrs.get(i));
}
}
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
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@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testVariantsToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("815b82fff92aab41c209eedce2d7e7d9");
md5.add("4accae035d271b35ee2ec58f403c68c6");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("22336ee9c12aa222ce29c3c5babca7d0");
md5.add("71e8c98d7c3a73b6287ecc339086fe03");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingHapMapInput() {
List<String> md5 = new ArrayList<String>();
md5.add("9bedaa7670b86a07be5191898c3727cf");
md5.add("f343085305e80c7a2493422e4eaad983");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingVCFInput() {
List<String> md5 = new ArrayList<String>();
md5.add("cc215edec9ca28e5c79ab1b67506f9f7");
md5.add("86f02e2e764ba35854cff2aa05a1fdd8");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +

28
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java 100644
View File

@ -0,0 +1,28 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.List;
public class VCFIntegrationTest extends WalkerTest {
@Test
public void testReadingAndWritingWitHNoChanges() {
String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447";
String testVCF = validationDataLocation + "vcf4.1.example.vcf";
String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
String test1 = baseCommand + "-T VariantAnnotator -BTI variant -B:variant,vcf " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
String test2 = baseCommand + "-T VariantsToVCF -B:variant,vcf " + result.get(0).getAbsolutePath();
WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
executeTest("Test Variants To VCF from new output", spec2);
}
}