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Inject read group into covars_out file's toString output. Continue fixing systematic bug in the code where flattenData is not joined to the read group. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@924 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-06 20:43:28 +00:00
parent 0bb4565798
commit 40ac3b7816
1 changed files with 8 additions and 2 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -79,14 +79,14 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
}
public String headerString() {
return ("pos, dinuc, qual, emp_qual, qual_diff, n, b");
return ("pos, rg, dinuc, qual, emp_qual, qual_diff, n, b");
}
public String toString() {
double empiricalQual = -10 * Math.log10((double)B / N);
if (empiricalQual > MAX_QUAL_SCORE) empiricalQual = MAX_QUAL_SCORE;
return String.format("%3d,%s,%3d,%5.1f,%5.1f,%6d,%6d", pos, dinuc, qual, empiricalQual, qual-empiricalQual, N, B);
return String.format("%3d,%s,%s,%3d,%5.1f,%5.1f,%6d,%6d", pos, readGroup, dinuc, qual, empiricalQual, qual-empiricalQual, N, B);
//return String.format("%d\t%s\t%d\t%.1f\t%d\t%6d", pos, dinuc, qual, empiricalQual, N, B);
}
}
@ -241,6 +241,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
}
for ( RecalData datum: flattenData ) {
if( !datum.readGroup.equals(readGroup.getReadGroupId()) )
continue;
ByCycle.get(datum.pos).inc(datum.N, datum.B);
ByCycleReportedQ.get(datum.pos).inc(datum.qual, datum.N);
All.inc(datum.N, datum.B);
@ -277,6 +279,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
}
for ( RecalData datum: flattenData ) {
if( !datum.readGroup.equals(readGroup.getReadGroupId()) )
continue;
int dinucIndex = string2dinucIndex(datum.dinuc); //bases2dinucIndex(datum.dinuc.charAt(0), datum.dinuc.charAt(1), false);
ByCycle.get(dinucIndex).inc(datum.N, datum.B);
ByCycleReportedQ.get(dinucIndex).inc(datum.qual, datum.N);
@ -314,6 +318,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
}
for ( RecalData datum: flattenData ){
if( !datum.readGroup.equals(readGroup.getReadGroupId()) )
continue;
ByQ.get(datum.qual).inc(datum.N, datum.B);
ByQReportedQ.get(datum.qual).inc(datum.qual, datum.N);
All.inc(datum.N, datum.B);