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Bug fix in adjustment of the shift position. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-11-03 16:08:11 +00:00
parent d60c632099
commit 55f61b1f88
1 changed files with 4 additions and 2 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -286,6 +286,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request); if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request);
attempts++; attempts++;
if ( attempts == 4 ) { if ( attempts == 4 ) {
System.out.println("DEBUG>> attempts to preserve full NQS window failed; now trying to find any suitable position.") ;
failure = true; failure = true;
break; break;
} }
@ -297,14 +298,15 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
// first position after the shift (this is bad for other reasons); if it breaks a nqs window, so be it // first position after the shift (this is bad for other reasons); if it breaks a nqs window, so be it
request = initial_request; request = initial_request;
attempts = 0; attempts = 0;
while ( tumor_context.hasIndelsInInterval(request,request) || while ( tumor_context.hasIndelsInInterval(request,request+1) ||
normal_context.hasIndelsInInterval(request,request) ) { normal_context.hasIndelsInInterval(request,request+1) ) {
request--; request--;
if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request); if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request);
attempts++; attempts++;
if ( attempts == 50 ) throw new StingException("Indel at every position in the interval ["+request+", "+initial_request+"]. Can not find a break to shift context window to"); if ( attempts == 50 ) throw new StingException("Indel at every position in the interval ["+request+", "+initial_request+"]. Can not find a break to shift context window to");
} }
} }
if ( DEBUG ) System.out.println("DEBUG>> Found acceptable target position "+request);
return request; return request;
} }