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reallow MNP events through 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3740 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-08 06:26:52 +00:00
parent ed0d0d78fa
commit 6e6ad36523
2 changed files with 8 additions and 9 deletions
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13
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
View File

@ -387,7 +387,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
// find out our current location, and clip the alleles down to their minimum length
Pair<GenomeLoc, List<Allele>> locAndAlleles;
if ( hasIndel(alleles) ) {
if ( !isSingleNucleotideEvent(alleles) ) {
attributes.put(ORIGINAL_ALLELE_LIST,alleles);
locAndAlleles = clipAlleles(contig, pos, ref, alleles);
} else {
@ -405,13 +405,12 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
return new VariantContext(name, locAndAlleles.first, locAndAlleles.second, genotypes, qual, filters, attributes);
}
private boolean hasIndel(List<Allele> alleles) {
int lengthOfFirstEntry = alleles.get(0).length();
for ( int i = 1; i < alleles.size(); i++ ) {
if ( alleles.get(i).length() != lengthOfFirstEntry )
return true;
private boolean isSingleNucleotideEvent(List<Allele> alleles) {
for ( Allele a : alleles ) {
if ( a.length() > 1 )
return false;
}
return false;
return true;
}
class VCFParserException extends StingException {

4
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
View File

@ -11,7 +11,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
String testVCF = validationDataLocation + "complexExample.vcf";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("368f6f61e7a99b33f74aab2cf055554e"));
Arrays.asList("0f356354a4a78ff62b2848431ec11262"));
executeTest("Test probes", spec);
}
@ -26,4 +26,4 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
Arrays.asList("cb1f57e8bcaec4b599be075b6d5288a1"));
executeTest("Test probes", spec);
}
}
}