Moved hasPileupBeenDownsampled() based on Eric's request. Also eliminated

@Deprecated constructors from AlignmentContext.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4142 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java

@@ -46,6 +46,7 @@ import java.util.*;
 public class AlignmentContext {
     protected GenomeLoc loc = null;
     protected ReadBackedPileup basePileup = null;
+    protected boolean hasPileupBeenDownsampled;
 
     /**
      * The number of bases we've skipped over in the reference since the last map invocation.
@@ -53,40 +54,19 @@ public class AlignmentContext {
      */
     private long skippedBases = 0;
 
-    /**
-     * Default constructor for AlignmentContext object
-     * since private objects are already set to null we
-     * don't need to do anything
-     */
-    public AlignmentContext() { /*   private objects already set to null    */  }
-
-    /**
-     * Create a new AlignmentContext object
-     *
-     * @param loc
-     * @param reads
-     * @param offsets
-     */
-    @Deprecated
-    public AlignmentContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets) {
-        this(loc, reads, offsets, 0);
-    }
-
-    @Deprecated
-    public AlignmentContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets, long skippedBases ) {
-        if ( loc == null ) throw new StingException("BUG: GenomeLoc in Alignment context is null");
-        if ( skippedBases < 0 ) throw new StingException("BUG: skippedBases is -1 in Alignment context");
-
-        this.loc = loc;
-        this.basePileup = new ReadBackedPileupImpl(loc, reads, offsets);
-        this.skippedBases = skippedBases;
-    }
-
     public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup) {
-        this(loc, basePileup, 0);
+        this(loc, basePileup, 0, false);
     }
 
-    public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases ) {
+    public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, boolean hasPileupBeenDownsampled) {
+        this(loc, basePileup, 0, hasPileupBeenDownsampled);
+    }
+
+    public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases) {
+        this(loc, basePileup, skippedBases, false);
+    }
+
+    public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases,boolean hasPileupBeenDownsampled ) {
         if ( loc == null ) throw new StingException("BUG: GenomeLoc in Alignment context is null");
         if ( basePileup == null ) throw new StingException("BUG: ReadBackedPileup in Alignment context is null");
         if ( skippedBases < 0 ) throw new StingException("BUG: skippedBases is -1 in Alignment context");
@@ -94,6 +74,7 @@ public class AlignmentContext {
         this.loc = loc;
         this.basePileup = basePileup;
         this.skippedBases = skippedBases;
+        this.hasPileupBeenDownsampled = hasPileupBeenDownsampled;
     }
 
     /** Returns base pileup over the current genomic location. Deprectated. Use getBasePileup() to make your intentions
@@ -136,6 +117,12 @@ public class AlignmentContext {
      */
     public boolean hasExtendedEventPileup() { return basePileup instanceof ReadBackedExtendedEventPileup; }
 
+    /**
+     * Returns true if any reads have been filtered out of the pileup due to excess DoC.
+     * @return True if reads have been filtered out.  False otherwise.
+     */
+    public boolean hasPileupBeenDownsampled() { return hasPileupBeenDownsampled; }
+
     /**
      * get all of the reads within this context
      * 
@@ -178,6 +165,7 @@ public class AlignmentContext {
 
     public void downsampleToCoverage(int coverage) {
         basePileup = basePileup.getDownsampledPileup(coverage);
+        hasPileupBeenDownsampled = true;
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java

@@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 /**
  * User: hanna
  * Date: May 13, 2009
@@ -96,6 +97,6 @@ public class AllLocusView extends LocusView {
      * @return empty context.
      */
     private AlignmentContext createEmptyLocus( GenomeLoc site ) {        
-        return new AlignmentContext(site, new ArrayList<SAMRecord>(), new ArrayList<Integer>());
+        return new AlignmentContext(site,new ReadBackedPileupImpl(site,new ArrayList<SAMRecord>(), new ArrayList<Integer>()));
     }
 }

java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -358,10 +358,11 @@ public class LocusIteratorByState extends LocusIterator {
                 // are associated with the *previous* reference base
                 GenomeLoc loc = GenomeLocParser.incPos(our1stState.getLocation(),-1);
 
+                boolean hasBeenSampled = false;
                 for(String sampleName: sampleNames) {
                     Iterator<SAMRecordState> iterator = readStates.iteratorForSample(sampleName);
                     ArrayList<ExtendedEventPileupElement> indelPile = new ArrayList<ExtendedEventPileupElement>(readStates.size());
-                    boolean hasBeenSampled = loc.getStart() <= readStates.readStatesBySample.get(sampleName).getDownsamplingExtent();
+                    hasBeenSampled |= loc.getStart() <= readStates.readStatesBySample.get(sampleName).getDownsamplingExtent();
 
                     size = 0;
                     nDeletions = 0;
@@ -414,21 +415,22 @@ public class LocusIteratorByState extends LocusIterator {
                             nMQ0Reads++;
                         }
                     }
-                    if( indelPile.size() != 0 ) fullExtendedEventPileup.put(sampleName,new ReadBackedExtendedEventPileupImpl(loc,indelPile,size,maxDeletionLength,nInsertions,nDeletions,nMQ0Reads,hasBeenSampled));
+                    if( indelPile.size() != 0 ) fullExtendedEventPileup.put(sampleName,new ReadBackedExtendedEventPileupImpl(loc,indelPile,size,maxDeletionLength,nInsertions,nDeletions,nMQ0Reads));
                 }
                 hasExtendedEvents = false; // we are done with extended events prior to current ref base
 //                System.out.println("Indel(s) at "+loc);
 //               for ( ExtendedEventPileupElement pe : indelPile ) { if ( pe.isIndel() ) System.out.println("  "+pe.toString()); }
-                nextAlignmentContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileupImpl(loc, fullExtendedEventPileup));
+                nextAlignmentContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileupImpl(loc, fullExtendedEventPileup), hasBeenSampled);
             }  else {
                 GenomeLoc location = getLocation();
                 Map<String,ReadBackedPileupImpl> fullPileup = new HashMap<String,ReadBackedPileupImpl>();
 
                 // todo -- performance problem -- should be lazy, really
+                boolean hasBeenSampled = false;
                 for(String sampleName: sampleNames) {
                     Iterator<SAMRecordState> iterator = readStates.iteratorForSample(sampleName);
                     ArrayList<PileupElement> pile = new ArrayList<PileupElement>(readStates.size());
-                    boolean hasBeenSampled = location.getStart() <= readStates.readStatesBySample.get(sampleName).getDownsamplingExtent();
+                    hasBeenSampled |= location.getStart() <= readStates.readStatesBySample.get(sampleName).getDownsamplingExtent();
 
                     size = 0;
                     nDeletions = 0;
@@ -458,12 +460,12 @@ public class LocusIteratorByState extends LocusIterator {
                             nMQ0Reads++;
                         }
                     }
-                    if( pile.size() != 0 ) fullPileup.put(sampleName,new ReadBackedPileupImpl(location,pile,size,nDeletions,nMQ0Reads,hasBeenSampled));
+                    if( pile.size() != 0 ) fullPileup.put(sampleName,new ReadBackedPileupImpl(location,pile,size,nDeletions,nMQ0Reads));
                 }
 
                 updateReadStates(); // critical - must be called after we get the current state offsets and location
                 // if we got reads with non-D/N over the current position, we are done
-                if ( !fullPileup.isEmpty() ) nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileupImpl(location,fullPileup));
+                if ( !fullPileup.isEmpty() ) nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileupImpl(location,fullPileup),hasBeenSampled);
             }
         }
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java

@@ -37,9 +37,11 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Collection;
@@ -114,7 +116,7 @@ public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, Strin
                         List<SAMRecord> sub_reads = MathUtils.sliceListByIndices(subset_indices, reads);
                         List<Integer> sub_offsets = MathUtils.sliceListByIndices(subset_indices, offsets);
 
-                        AlignmentContext subContext = new AlignmentContext(context.getLocation(), sub_reads, sub_offsets);
+                        AlignmentContext subContext = new AlignmentContext(context.getLocation(), new ReadBackedPileupImpl(context.getLocation(),sub_reads, sub_offsets));
 
                         VariantCallContext calls = UG.runGenotyper(tracker, ref, subContext);
 

java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -46,7 +46,6 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
     protected int size = 0;                   // cached value of the size of the pileup
     protected int nDeletions = 0;             // cached value of the number of deletions
     protected int nMQ0Reads = 0;              // cached value of the number of MQ0 reads
-    protected boolean hasPileupBeenDownsampled;
 
     /**
      * Create a new version of a read backed pileup at loc, using the reads and their corresponding
@@ -96,7 +95,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @param loc
      * @param pileup
      */
-    public AbstractReadBackedPileup(GenomeLoc loc, List<PE> pileup, int size, int nDeletions, int nMQ0Reads, boolean hasPileupBeenDownsampled ) {
+    public AbstractReadBackedPileup(GenomeLoc loc, List<PE> pileup, int size, int nDeletions, int nMQ0Reads) {
         if ( loc == null ) throw new StingException("Illegal null genomeloc in UnifiedReadBackedPileup");
         if ( pileup == null ) throw new StingException("Illegal null pileup in UnifiedReadBackedPileup");
 
@@ -105,7 +104,6 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         this.size = size;
         this.nDeletions = nDeletions;
         this.nMQ0Reads = nMQ0Reads;
-        this.hasPileupBeenDownsampled = hasPileupBeenDownsampled;
     }
 
 
@@ -150,7 +148,6 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         size += pileup.size();
         nDeletions += pileup.getNumberOfDeletions();
         nMQ0Reads += pileup.getNumberOfMappingQualityZeroReads();
-        hasPileupBeenDownsampled |= pileup.hasPileupBeenDownsampled();
     }
 
     /**
@@ -675,11 +672,6 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         return loc;
     }
 
-    @Override
-    public boolean hasPileupBeenDownsampled() {
-        return hasPileupBeenDownsampled;
-    }
-
     /**
      * Somewhat expensive routine that returns true if any base in the pileup has secondary bases annotated
      * @return

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java

@@ -34,10 +34,6 @@ import net.sf.samtools.SAMRecord;
 public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<ReadBackedExtendedEventPileupImpl,ExtendedEventPileupElement> implements ReadBackedExtendedEventPileup {
     private int nInsertions;
     private int maxDeletionLength;      // cached value of the length of the longest deletion observed at the site
-    /**
-     * True if this pileup has been downsampled due to excessive coverage depth.  False otherwise.
-     */
-    private boolean hasBeenDownsampled;
 
     public ReadBackedExtendedEventPileupImpl(GenomeLoc loc, List<ExtendedEventPileupElement> pileupElements) {
         super(loc,pileupElements);
@@ -53,8 +49,8 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
      * @param pileup
      */
     public ReadBackedExtendedEventPileupImpl(GenomeLoc loc, List<ExtendedEventPileupElement> pileup, int size,
-                                         int maxDeletionLength, int nInsertions, int nDeletions, int nMQ0Reads, boolean hasPileupBeenDownsampled ) {
+                                         int maxDeletionLength, int nInsertions, int nDeletions, int nMQ0Reads) {
-        super(loc,pileup,size,nDeletions,nMQ0Reads,hasPileupBeenDownsampled);
+        super(loc,pileup,size,nDeletions,nMQ0Reads);
         this.maxDeletionLength = maxDeletionLength;
         this.nInsertions = nInsertions;
     }

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java

@@ -115,12 +115,6 @@ public interface ReadBackedPileup extends Iterable<PileupElement> {
      */
     public ReadBackedPileup getDownsampledPileup(int desiredCoverage);
 
-    /**
-     * Returns true if any reads have been filtered out of the pileup due to excess DoC.
-     * @return True if reads have been filtered out.  False otherwise.
-     */
-    public boolean hasPileupBeenDownsampled();
-
     /**
      * Gets a collection of all the read groups represented in this pileup.
      * @return A collection of all the read group ids represented in this pileup.

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java

@@ -56,8 +56,8 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
      * @param loc
      * @param pileup
      */
-    public ReadBackedPileupImpl(GenomeLoc loc, List<PileupElement> pileup, int size, int nDeletions, int nMQ0Reads, boolean hasPileupBeenDownsampled ) {
+    public ReadBackedPileupImpl(GenomeLoc loc, List<PileupElement> pileup, int size, int nDeletions, int nMQ0Reads) {
-        super(loc,pileup,size,nDeletions,nMQ0Reads,hasPileupBeenDownsampled);
+        super(loc,pileup,size,nDeletions,nMQ0Reads);
     }
 
     protected ReadBackedPileupImpl(GenomeLoc loc, PileupElementTracker<PileupElement> tracker) {