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AnalyzeCovariates also has to skip over NO_DINUC 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2461 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2009-12-29 14:36:05 +00:00
parent a34c2442c0
commit 29a3d9b47a
1 changed files with 9 additions and 6 deletions
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15
java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
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@ -60,12 +60,15 @@ public class AnalysisDataManager {
if( iii == 0 || !(qscore < IGNORE_QSCORES_LESS_THAN) ) { // use all data for the plot versus reported quality, but not for the other plots versus cycle and etc.
newKey = new ArrayList<Comparable>();
newKey.add( key.get(0) ); // Make a new key with the read group ...
newKey.add( key.get(iii + 1) ); // and the given covariate
collapsedDatum = dataCollapsedByCovariate.get(iii).get( newKey );
if( collapsedDatum == null ) {
dataCollapsedByCovariate.get(iii).put( newKey, new RecalDatum(fullDatum) );
} else {
collapsedDatum.combine( fullDatum );
Comparable theCovariateElement = key.get(iii + 1); // and the given covariate
if( theCovariateElement != null ) {
newKey.add( theCovariateElement );
collapsedDatum = dataCollapsedByCovariate.get(iii).get( newKey );
if( collapsedDatum == null ) {
dataCollapsedByCovariate.get(iii).put( newKey, new RecalDatum(fullDatum) );
} else {
collapsedDatum.combine( fullDatum );
}
}
}
}