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ART optimization: BandPassActivityProfile only applies the gaussian filter if the state probability > 0

This commit is contained in:
Mark DePristo 2013-01-25 17:20:13 -05:00
parent 705cccaf63
commit 52a28968a9
1 changed files with 9 additions and 5 deletions
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14
public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java
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@ -153,12 +153,16 @@ public class BandPassActivityProfile extends ActivityProfile {
final Collection<ActivityProfileState> states = new LinkedList<ActivityProfileState>();
for ( final ActivityProfileState superState : super.processState(justAddedState) ) {
for( int jjj = -filterSize; jjj <= filterSize; jjj++ ) {
final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj);
if ( loc != null ) {
final double newProb = superState.isActiveProb * GaussianKernel[jjj + filterSize];
states.add(new ActivityProfileState(loc, newProb));
if ( superState.isActiveProb > 0.0 ) {
for( int jjj = -filterSize; jjj <= filterSize; jjj++ ) {
final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj);
if ( loc != null ) {
final double newProb = superState.isActiveProb * GaussianKernel[jjj + filterSize];
states.add(new ActivityProfileState(loc, newProb));
}
}
} else {
states.add(justAddedState);
}
}