diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 80484e12f..16cb2fd84 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -40,7 +40,7 @@ import java.util.*; * @since Date created */ public class ActivityProfile { - private final static int MAX_PROB_PROPOGATION_DISTANCE = 10; + private final static int MAX_PROB_PROPOGATION_DISTANCE = 50; private final static double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author protected final List stateList; @@ -259,7 +259,8 @@ public class ActivityProfile { if ( justAddedState.resultState.equals(ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS) ) { // special code to deal with the problem that high quality soft clipped bases aren't added to pileups final List states = new LinkedList(); - final int numHQClips = justAddedState.resultValue.intValue(); + // add no more than the max prob propagation distance num HQ clips + final int numHQClips = Math.min(justAddedState.resultValue.intValue(), getMaxProbPropagationDistance()); for( int jjj = - numHQClips; jjj <= numHQClips; jjj++ ) { final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj); if ( loc != null )