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Do not build alt consensuses from insertions that have an N in the inserted sequence. Seems to cause problems rather than solve any 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2880 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-24 03:00:26 +00:00
parent 94d74d4f78
commit d73bc490c2
1 changed files with 7 additions and 1 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -676,8 +676,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
altIdx += elementLength;
break;
case I:
for (int j = 0; j < elementLength; j++)
for (int j = 0; j < elementLength; j++) {
if ( ! BaseUtils.isRegularBase(readStr[altIdx+j]) ) {
// Insertions with N's in them cause real problems sometimes; it's better to drop them altogether
ok_flag=false;
break;
}
sb.append((char)readStr[altIdx + j]);
}
altIdx += elementLength;
indelCount++;
break;