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

bug fix for known-indels used as consenses 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-23 13:52:51 +00:00
parent f050beada6
commit 3adf7fbf64
1 changed files with 7 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -716,11 +716,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
break; break;
case I: case I:
for (int j = 0; j < elementLength; j++) { for (int j = 0; j < elementLength; j++) {
if ( ! BaseUtils.isRegularBase(readStr[altIdx+j]) ) { if ( ! BaseUtils.isRegularBase(readStr[altIdx+j]) ) {
// Insertions with N's in them cause real problems sometimes; it's better to drop them altogether // Insertions with N's in them cause real problems sometimes; it's better to drop them altogether
ok_flag=false; ok_flag=false;
break; break;
} }
sb.append((char)readStr[altIdx + j]); sb.append((char)readStr[altIdx + j]);
} }
altIdx += elementLength; altIdx += elementLength;
@ -759,7 +759,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
cigar.add(new CigarElement(indelStr.length, CigarOperator.D)); cigar.add(new CigarElement(indelStr.length, CigarOperator.D));
} }
else { else {
sb.append(indelStr); for ( byte b : indelStr )
sb.append((char)b);
cigar.add(new CigarElement(indelStr.length, CigarOperator.I)); cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
} }