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

ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-10-19 18:21:00 +00:00
parent 3d50c72d74
commit cfa86d52c2
3 changed files with 24 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
View File

@ -77,6 +77,10 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return vcf;
}
public void assertBiAllelic() {
if (!this.isBiallelic()) throw new StingException("We're not bi-allelic.");
}
/**
* get the frequency of this variant
*
@ -116,8 +120,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override
public boolean isSNP() {
this.assertNotNull();
if (!mCurrentRecord.hasAlternateAllele())
return false;
assertBiAllelic();
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
if (alt.getType() != VCFGenotypeEncoding.TYPE.SINGLE_BASE)
return false;
@ -133,6 +136,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override
public boolean isInsertion() {
this.assertNotNull();
assertBiAllelic();
if (!mCurrentRecord.hasAlternateAllele())
return false;
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
@ -150,6 +154,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override
public boolean isDeletion() {
this.assertNotNull();
assertBiAllelic();
if (!mCurrentRecord.hasAlternateAllele())
return false;
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {

18
java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java
View File

@ -113,7 +113,7 @@ public class RodVCFTest extends BaseTest {
}
@Test
public void testType() {
public void testInsertion() {
RodVCF vcf = getVCFObject();
Iterator<RodVCF> iter = vcf.createIterator("VCF", vcfFile);
RodVCF rec = iter.next();
@ -123,10 +123,24 @@ public class RodVCFTest extends BaseTest {
rec = iter.next();
rec = iter.next();
Assert.assertTrue(rec.isIndel());
Assert.assertTrue(rec.isInsertion());
Assert.assertTrue(rec.isDeletion());
}
@Test
public void testDeletion() {
RodVCF vcf = getVCFObject();
Iterator<RodVCF> iter = vcf.createIterator("VCF", vcfFile);
RodVCF rec = iter.next();
Assert.assertTrue(rec.isSNP());
rec = iter.next();
rec = iter.next();
rec = iter.next();
rec = iter.next();
rec = iter.next();
Assert.assertTrue(rec.isIndel());
Assert.assertTrue(rec.isInsertion());
}
@Test
public void testGetGenotypes() {
RodVCF vcf = getVCFObject();

2
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
View File

@ -22,7 +22,7 @@ public class VCFReaderTest extends BaseTest {
counter++;
reader.next();
}
Assert.assertEquals(5, counter);
Assert.assertEquals(6, counter);
}
@Test