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Fix when specifying preset active regions with -AR argument

This commit is contained in:
Ryan Poplin 2012-02-02 16:34:26 -05:00
parent f596377e73
commit 601e53d633
1 changed files with 5 additions and 5 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -124,7 +124,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// Take the individual isActive calls and integrate them into contiguous active regions and // Take the individual isActive calls and integrate them into contiguous active regions and
// add these blocks of work to the work queue // add these blocks of work to the work queue
final ArrayList<ActiveRegion> activeRegions = integrateActiveList( isActiveList, firstIsActiveStart, activeRegionExtension ); final ArrayList<ActiveRegion> activeRegions = integrateActiveList( isActiveList, firstIsActiveStart, activeRegionExtension, walker.presetActiveRegions != null );
logger.debug("Integrated " + isActiveList.size() + " isActive calls into " + activeRegions.size() + " regions." ); logger.debug("Integrated " + isActiveList.size() + " isActive calls into " + activeRegions.size() + " regions." );
if( walker.activeRegionOutStream == null ) { if( walker.activeRegionOutStream == null ) {
workQueue.addAll( activeRegions ); workQueue.addAll( activeRegions );
@ -214,7 +214,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
} }
// band-pass filter the list of isActive probabilities and turn into active regions // band-pass filter the list of isActive probabilities and turn into active regions
private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension ) { private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension, final boolean presetRegions ) {
final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author
final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>(); final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>();
@ -227,11 +227,11 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
} else { } else {
final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]); final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]);
final double[] filteredProbArray = new double[activeProbArray.length]; final double[] filteredProbArray = new double[activeProbArray.length];
final int FILTER_SIZE = 50; // BUGBUG: needs to be set-able by the walker author final int FILTER_SIZE = ( presetRegions ? 0 : 50 ); // BUGBUG: needs to be set-able by the walker author
final int MAX_ACTIVE_REGION = 425; // BUGBUG: needs to be set-able by the walker author final int MAX_ACTIVE_REGION = ( presetRegions ? 16001 : 425 ); // BUGBUG: needs to be set-able by the walker author
for( int iii = 0; iii < activeProbArray.length; iii++ ) { for( int iii = 0; iii < activeProbArray.length; iii++ ) {
double maxVal = 0; double maxVal = 0;
for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE); jjj++ ) { for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE+1); jjj++ ) {
if( activeProbArray[jjj] > maxVal ) { maxVal = activeProbArray[jjj]; } if( activeProbArray[jjj] > maxVal ) { maxVal = activeProbArray[jjj]; }
} }
filteredProbArray[iii] = maxVal; filteredProbArray[iii] = maxVal;