Renaming IncrementalActivityProfile to ActivityProfile

-- Also adding a work in progress functionality to make it easy to visualize activity profiles and active regions in IGV

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java

@@ -77,7 +77,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
 
     private LinkedList<GATKSAMRecord> myReads = new LinkedList<GATKSAMRecord>();
     private GenomeLoc spanOfLastReadSeen = null;
-    private IncrementalActivityProfile activityProfile = null;
+    private ActivityProfile activityProfile = null;
     int maxReadsInMemory = 0;
 
     @Override
@@ -94,7 +94,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
         maxRegionSize = walker.getClass().getAnnotation(ActiveRegionExtension.class).maxRegion();
         walkerHasPresetRegions = arWalker.hasPresetActiveRegions();
 
-        activityProfile = new IncrementalActivityProfile(engine.getGenomeLocParser());
+        activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser());
         if ( walkerHasPresetRegions ) {
             // we load all of the preset locations into the
             for ( final GenomeLoc loc : arWalker.getPresetActiveRegions()) {
@@ -349,6 +349,12 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
         if ( ! walkerHasPresetRegions ) {
             activityProfile.add(state);
         }
+
+        if ( walker.activityProfileOutStream != null )
+            walker.activityProfileOutStream.printf("%s\t%d\t%d\t%.2f%n",
+                    locus.getLocation().getContig(), locus.getLocation().getStart(), locus.getLocation().getStart(),
+                    state.isActiveProb);
+
     }
 
     /**
@@ -375,7 +381,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
             // We don't have preset regions, so we get our regions from the activity profile
             final Collection<ActiveRegion> activeRegions = activityProfile.popReadyActiveRegions(getActiveRegionExtension(), getMaxRegionSize(), flushActivityProfile);
             workQueue.addAll(activeRegions);
-            if ( logger.isDebugEnabled() ) logger.debug("Integrated " + activityProfile.size() + " isActive calls into " + activeRegions.size() + " regions." );
+            if ( ! activeRegions.isEmpty() && logger.isDebugEnabled() ) logger.debug("Integrated " + activityProfile.size() + " isActive calls into " + activeRegions.size() + " regions." );
         }
 
         if ( walker.activeRegionOutStream != null ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java

@@ -61,6 +61,8 @@ import java.util.*;
 @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, MappingQualityUnavailableFilter.class})
 @RemoveProgramRecords
 public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
+    @Output(fullName="activityProfileOut", shortName="APO", doc="Output the raw activity profile results bed file", required = false)
+    public PrintStream activityProfileOutStream = null;
 
     @Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this interval list file", required = false)
     public PrintStream activeRegionOutStream = null;

public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java

@@ -26,12 +26,11 @@
 package org.broadinstitute.sting.utils.activeregion;
 
 /**
- * Created with IntelliJ IDEA.
+ * Describes how a read relates to an assigned ActiveRegion
+ *
  * User: thibault
  * Date: 11/26/12
  * Time: 2:35 PM
- *
- * Describes how a read relates to an assigned ActiveRegion
  */
 public enum ActiveRegionReadState {
     PRIMARY,        // This is the read's primary region

public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java

@@ -39,7 +39,7 @@ import java.util.*;
  * @author Mark DePristo
  * @since Date created
  */
-public class IncrementalActivityProfile {
+public class ActivityProfile {
     private final static int MAX_PROB_PROPOGATION_DISTANCE = 10;
     private final static double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author
 
@@ -50,10 +50,10 @@ public class IncrementalActivityProfile {
     protected GenomeLoc regionStopLoc = null;
 
     /**
-     * Create a new empty IncrementalActivityProfile
+     * Create a new empty ActivityProfile
      * @param parser the parser we can use to create genome locs, cannot be null
      */
-    public IncrementalActivityProfile(final GenomeLocParser parser) {
+    public ActivityProfile(final GenomeLocParser parser) {
         if ( parser == null ) throw new IllegalArgumentException("parser cannot be null");
 
         this.parser = parser;
@@ -79,7 +79,7 @@ public class IncrementalActivityProfile {
      * @return a positive integer distance in bp
      */
     @Ensures("result >= 0")
-    public int getMaxProbPropogationDistance() {
+    public int getMaxProbPropagationDistance() {
         return MAX_PROB_PROPOGATION_DISTANCE;
     }
 
@@ -377,6 +377,6 @@ public class IncrementalActivityProfile {
         }
 
         // we're one past the end, so i must be decremented
-        return forceConversion || i + getMaxProbPropogationDistance() < stateList.size() ? i - 1 : -1;
+        return forceConversion || i + getMaxProbPropagationDistance() < stateList.size() ? i - 1 : -1;
     }
 }

public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileState.java

@@ -30,7 +30,8 @@ import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 /**
- * Created with IntelliJ IDEA.
+ * The state of an active region walker's isActive call at a specific locus in the genome
+ *
  * User: rpoplin
  * Date: 7/27/12
  */

public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java

@@ -42,7 +42,7 @@ import java.util.LinkedList;
  * @author Mark DePristo
  * @since 2011
  */
-public class BandPassIncrementalActivityProfile extends IncrementalActivityProfile {
+public class BandPassActivityProfile extends ActivityProfile {
     public static final int DEFAULT_FILTER_SIZE = 80;
 
     private final int filterSize;
@@ -52,7 +52,7 @@ public class BandPassIncrementalActivityProfile extends IncrementalActivityProfi
      * Create a band pass activity profile with the default band size
      * @param parser our genome loc parser
      */
-    public BandPassIncrementalActivityProfile(final GenomeLocParser parser) {
+    public BandPassActivityProfile(final GenomeLocParser parser) {
         this(parser, DEFAULT_FILTER_SIZE);
     }
 
@@ -63,7 +63,7 @@ public class BandPassIncrementalActivityProfile extends IncrementalActivityProfi
      *                   side that are included in the band.  So a filter size of 1 implies that the actual band
      *                   is 3 bp, 1 for the center site and 1 on each size.  2 => 5, etc.
      */
-    public BandPassIncrementalActivityProfile(final GenomeLocParser parser, final int filterSize) {
+    public BandPassActivityProfile(final GenomeLocParser parser, final int filterSize) {
         super(parser);
 
         if ( filterSize < 0 ) throw new IllegalArgumentException("Filter size must be greater than or equal to 0 but got " + filterSize);
@@ -77,6 +77,19 @@ public class BandPassIncrementalActivityProfile extends IncrementalActivityProfi
         this.GaussianKernel = MathUtils.normalizeFromRealSpace(kernel);
     }
 
+    /**
+     * Our maximize propagation distance is whatever our parent's is, plus our filter size
+     *
+     * Stops the profile from interpreting sites that aren't yet fully determined due to
+     * propagation of the probabilities.
+     *
+     * @return the distance in bp we might move our probabilities around for some site i
+     */
+    @Override
+    public int getMaxProbPropagationDistance() {
+        return super.getMaxProbPropagationDistance() + filterSize;
+    }
+
     /**
      * Get the size (in bp) of the band pass filter
      * @return a positive integer

public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java

@@ -45,7 +45,7 @@ import java.io.FileNotFoundException;
 import java.util.*;
 
 
-public class IncrementalActivityProfileUnitTest extends BaseTest {
+public class ActivityProfileUnitTest extends BaseTest {
     private GenomeLocParser genomeLocParser;
     private GenomeLoc startLoc;
 
@@ -82,12 +82,12 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
             return String.format("type=%s probs=%s expectedRegions=%s", type, Utils.join(",", probs), Utils.join(",", expectedRegions));
         }
 
-        public IncrementalActivityProfile makeProfile() {
+        public ActivityProfile makeProfile() {
             switch ( type ) {
-                case Base: return new IncrementalActivityProfile(genomeLocParser);
+                case Base: return new ActivityProfile(genomeLocParser);
                 case BandPass:
-                    // zero size => equivalent to IncrementalActivityProfile
+                    // zero size => equivalent to ActivityProfile
-                    return new BandPassIncrementalActivityProfile(genomeLocParser, 0);
+                    return new BandPassActivityProfile(genomeLocParser, 0);
                 default: throw new IllegalStateException(type.toString());
             }
         }
@@ -125,7 +125,7 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
 
     @Test(dataProvider = "BasicActivityProfileTestProvider")
     public void testBasicActivityProfile(BasicActivityProfileTestProvider cfg) {
-        IncrementalActivityProfile profile = cfg.makeProfile();
+        ActivityProfile profile = cfg.makeProfile();
 
         Assert.assertTrue(profile.isEmpty());
 
@@ -228,7 +228,7 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
 
     @Test(enabled = true, dataProvider = "RegionCreationTests")
     public void testRegionCreation(final int start, final List<Boolean> probs, int maxRegionSize, final int nParts, final boolean forceConversion, final boolean waitUntilEnd) {
-        final IncrementalActivityProfile profile = new IncrementalActivityProfile(genomeLocParser);
+        final ActivityProfile profile = new ActivityProfile(genomeLocParser);
         Assert.assertNotNull(profile.toString());
 
         final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName();
@@ -253,7 +253,7 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
         }
 
         for ( int i = 0; i < probs.size(); i++ ) {
-            if ( forceConversion || (i + maxRegionSize + profile.getMaxProbPropogationDistance() < probs.size()))
+            if ( forceConversion || (i + maxRegionSize + profile.getMaxProbPropagationDistance() < probs.size()))
                 // only require a site to be seen if we are forcing conversion or the site is more than maxRegionSize from the end
                 Assert.assertTrue(seenSites.get(i), "Missed site " + i);
         }
@@ -314,7 +314,7 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
 
     @Test(dataProvider = "SoftClipsTest")
     public void testSoftClips(final int start, int nPrecedingSites, final int softClipSize) {
-        final IncrementalActivityProfile profile = new IncrementalActivityProfile(genomeLocParser);
+        final ActivityProfile profile = new ActivityProfile(genomeLocParser);
 
         final int contigLength = genomeLocParser.getContigs().getSequences().get(0).getSequenceLength();
         final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName();

public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java

@@ -35,7 +35,6 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -47,7 +46,7 @@ import java.io.FileNotFoundException;
 import java.util.*;
 
 
-public class BandPassIncrementalActivityProfileUnitTest extends BaseTest {
+public class BandPassActivityProfileUnitTest extends BaseTest {
     private GenomeLocParser genomeLocParser;
 
     @BeforeClass
@@ -80,7 +79,7 @@ public class BandPassIncrementalActivityProfileUnitTest extends BaseTest {
 
     @Test(dataProvider = "BandPassBasicTest")
     public void testBandPass(final int start, final boolean precedingIsActive, final int nPrecedingSites, final int bandPassSize) {
-        final BandPassIncrementalActivityProfile profile = new BandPassIncrementalActivityProfile(genomeLocParser, bandPassSize);
+        final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, bandPassSize);
 
         final int expectedBandSize = bandPassSize * 2 + 1;
         Assert.assertEquals(profile.getBandSize(), expectedBandSize, "Wrong expected band size");
@@ -103,7 +102,7 @@ public class BandPassIncrementalActivityProfileUnitTest extends BaseTest {
         }
     }
 
-    private double[] bandPassInOnePass(final BandPassIncrementalActivityProfile profile, final double[] activeProbArray) {
+    private double[] bandPassInOnePass(final BandPassActivityProfile profile, final double[] activeProbArray) {
         final double[] bandPassProbArray = new double[activeProbArray.length];
 
         // apply the band pass filter for activeProbArray into filteredProbArray
@@ -121,7 +120,7 @@ public class BandPassIncrementalActivityProfileUnitTest extends BaseTest {
     public Object[][] makeBandPassComposition() {
         final List<Object[]> tests = new LinkedList<Object[]>();
 
-        for ( int bandPassSize : Arrays.asList(0, 1, 10, 100, BandPassIncrementalActivityProfile.DEFAULT_FILTER_SIZE) ) {
+        for ( int bandPassSize : Arrays.asList(0, 1, 10, 100, BandPassActivityProfile.DEFAULT_FILTER_SIZE) ) {
             for ( int integrationLength : Arrays.asList(1, 10, 100, 1000) ) {
                 tests.add(new Object[]{ bandPassSize, integrationLength });
             }
@@ -133,7 +132,7 @@ public class BandPassIncrementalActivityProfileUnitTest extends BaseTest {
     @Test( dataProvider = "BandPassComposition")
     public void testBandPassComposition(final int bandPassSize, final int integrationLength) {
         final int start = 1;
-        final BandPassIncrementalActivityProfile profile = new BandPassIncrementalActivityProfile(genomeLocParser, bandPassSize);
+        final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, bandPassSize);
         final double[] rawActiveProbs = new double[integrationLength + bandPassSize * 2];
 
         // add a buffer so that we can get all of the band pass values