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This somehow didn't make it into subversion the last time. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1814 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-12 21:11:13 +00:00
parent ecbb11e017
commit ec83bc6ec5
1 changed files with 34 additions and 0 deletions
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34
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java 100755
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package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Oct 9, 2009
* Time: 11:39:34 AM
* To change this template use File | Settings | File Templates.
*/
class LocalMapType {
public AlignmentContext context;
public ReferenceContext ref;
public RefMetaDataTracker tracker;
public LocalMapType(AlignmentContext context, ReferenceContext ref, RefMetaDataTracker tracker) {
this.context = context;
this.ref = ref;
this.tracker = tracker;
}
public int numReads() {
return context.numReads();
}
public int qScore(int read) {
return (int) context.getReads().get(read).getBaseQualities()[context.getOffsets().get(read)];
}
}