Support for reducedReads in the pileup and UG. Totally experimental -- the code interface could change, and so could the implementation. Only works for SNPs now. Pileup has contracts as well.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5936 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.pileup.FragmentPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
@@ -270,8 +271,18 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
     }
     public int add(PileupElement elt, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
         byte obsBase = elt.getBase();
-        byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
-        return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0) : 0;
+
+        if ( elt.isReducedRead() ) {
+            // reduced read representation
+            byte qual = elt.getReducedQual();
+            for ( int i = 0; i < elt.getReducedCount(); i++ ) {
+                add(obsBase, qual, (byte)0, (byte)0);
+            }
+            return elt.getQual();
+        } else {
+            byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
+            return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0) : 0;
+        }
     }
 
     public int add(FragmentPileup.TwoReadPileupElement twoRead, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -156,7 +156,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
             ReadBackedPileup pileup = useBAQedPileup ? createBAQedPileup( sample.getValue().getBasePileup() ) : sample.getValue().getBasePileup();
             for ( PileupElement p : pileup ) {
                 // ignore deletions
-                if ( p.isDeletion() || p.getQual() < UAC.MIN_BASE_QUALTY_SCORE )
+                if ( p.isDeletion() || (! p.isReducedRead() && p.getQual() < UAC.MIN_BASE_QUALTY_SCORE ))
                     continue;
 
                 final int index = BaseUtils.simpleBaseToBaseIndex(p.getBase());

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

@@ -2,13 +2,14 @@ package org.broadinstitute.sting.utils.pileup;
 
 import org.broadinstitute.sting.utils.*;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+import com.google.java.contract.*;
 
 /**
  * Created by IntelliJ IDEA.
  * User: depristo
  * Date: Apr 14, 2009
  * Time: 8:54:05 AM
- * To change this template use File | Settings | File Templates.
  */
 public class PileupElement {
     public static final byte DELETION_BASE = BaseUtils.D;
@@ -18,9 +19,13 @@ public class PileupElement {
     public static final byte T_FOLLOWED_BY_INSERTION_BASE = (byte) 89;
     public static final byte G_FOLLOWED_BY_INSERTION_BASE = (byte) 90;
 
-    protected SAMRecord read;
-    protected int offset;
+    protected final SAMRecord read;
+    protected final int offset;
 
+    @Requires({
+            "read != null",
+            "offset >= -1",
+            "offset <= read.getReadLength()"})
     public PileupElement( SAMRecord read, int offset ) {
         this.read = read;
         this.offset = offset;
@@ -30,7 +35,10 @@ public class PileupElement {
         return offset == -1;
     }
 
+    @Ensures("result != null")
     public SAMRecord getRead() { return read; }
+
+    @Ensures("result == offset")
     public int getOffset() { return offset; }
 
     public byte getBase() {
@@ -45,8 +53,11 @@ public class PileupElement {
         return getQual(offset);
     }
 
-    public int getMappingQual() { return read.getMappingQuality(); }
+    public int getMappingQual() {
+        return read.getMappingQuality();
+    }
 
+    @Ensures("result != null")
     public String toString() {
         return String.format("%s @ %d = %c Q%d", getRead().getReadName(), getOffset(), (char)getBase(), getQual());
     }
@@ -62,4 +73,27 @@ public class PileupElement {
     protected byte getQual(final int offset) {
         return isDeletion() ? DELETION_QUAL : read.getBaseQualities()[offset];
     }
+
+    // --------------------------------------------------------------------------
+    //
+    // Reduced read accessors
+    //
+    // --------------------------------------------------------------------------
+
+    private Integer getReducedReadQualityTagValue() {
+        return (Integer)getRead().getAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
+    }
+
+    public boolean isReducedRead() {
+        return getReducedReadQualityTagValue() != null;
+    }
+
+    public int getReducedCount() {
+        return (int)getQual();
+    }
+
+    public byte getReducedQual() {
+        return (byte)(int)getReducedReadQualityTagValue();
+    }
+
 }