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

indel-related fixes to the strict validator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4725 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-24 04:08:34 +00:00
parent 9cdc341be5
commit 816c33c821
1 changed files with 8 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
View File

@ -95,17 +95,11 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
Allele reportedRefAllele = vc.getReference(); Allele reportedRefAllele = vc.getReference();
Allele observedRefAllele; Allele observedRefAllele;
// insertions // insertions
if ( reportedRefAllele.isNull() ) { if ( vc.isInsertion() ) {
observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING); observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING);
} }
// SNPs
else if ( reportedRefAllele.length() == 1 ) {
byte[] refByte = new byte[1];
refByte[0] = ref.getBase();
observedRefAllele = Allele.create(refByte, true);
}
// deletions // deletions
else { else if ( vc.isDeletion() || vc.isMixed() || vc.getType() == VariantContext.Type.MNP ) {
// we can't validate arbitrarily long deletions // we can't validate arbitrarily long deletions
if ( reportedRefAllele.length() > 100 ) { if ( reportedRefAllele.length() > 100 ) {
logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart())); logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart()));
@ -118,6 +112,12 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
trueRef[i] = refBytes[i+1]; trueRef[i] = refBytes[i+1];
observedRefAllele = Allele.create(trueRef, true); observedRefAllele = Allele.create(trueRef, true);
} }
// SNPs, etc.
else {
byte[] refByte = new byte[1];
refByte[0] = ref.getBase();
observedRefAllele = Allele.create(refByte, true);
}
// get the RS IDs // get the RS IDs
Set<String> rsIDs = null; Set<String> rsIDs = null;