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Added integration test for VCF writing. Also, bug fix for writing the GT-free records.

This commit is contained in:
Eric Banks 2011-07-13 14:57:21 -04:00
parent 6a431da554
commit bb0e3a26fc
2 changed files with 8 additions and 7 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
View File

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

8
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
View File

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