diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java new file mode 100755 index 000000000..9607b8226 --- /dev/null +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java @@ -0,0 +1,34 @@ +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)]; + } + +}