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Soft clip probability propagation is capped by the MAX_PROB_PROPAGATION_DISTANCE, which is 50 bp

This commit is contained in:
Mark DePristo 2013-01-23 15:52:00 -05:00
parent 0c94e3d96e
commit c96b64973a
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
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@ -40,7 +40,7 @@ import java.util.*;
* @since Date created * @since Date created
*/ */
public class ActivityProfile { 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 private final static double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author
protected final List<ActivityProfileState> stateList; protected final List<ActivityProfileState> stateList;
@ -259,7 +259,8 @@ public class ActivityProfile {
if ( justAddedState.resultState.equals(ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS) ) { 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 // special code to deal with the problem that high quality soft clipped bases aren't added to pileups
final List<ActivityProfileState> states = new LinkedList<ActivityProfileState>(); final List<ActivityProfileState> states = new LinkedList<ActivityProfileState>();
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++ ) { for( int jjj = - numHQClips; jjj <= numHQClips; jjj++ ) {
final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj); final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj);
if ( loc != null ) if ( loc != null )