Moving reduced read functionality into GATKSAMRecord

-- More functions take / produce GATKSAMRecords instead of SAMRecord

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java

@@ -393,7 +393,7 @@ public class PairHMMIndelErrorModel {
 
         for (PileupElement p: pileup) {
             // > 1 when the read is a consensus read representing multiple independent observations
-            final boolean isReduced = ReadUtils.isReducedRead(p.getRead());
+            final boolean isReduced = p.isReducedRead();
             readCounts[readIdx] = isReduced ? p.getReducedCount() : 1;
 
             // check if we've already computed likelihoods for this pileup element (i.e. for this read at this location)

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

@@ -4,6 +4,7 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
@@ -82,16 +83,16 @@ public class PileupElement {
     // --------------------------------------------------------------------------
 
     public boolean isReducedRead() {
-        return ReadUtils.isReducedRead(getRead());
+        return ((GATKSAMRecord)read).isReducedRead();
     }
 
     public int getReducedCount() {
         if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced count for non-reduced read " + getRead().getReadName());
-        return ReadUtils.getReducedCount(getRead(), offset);
+        return ((GATKSAMRecord)read).getReducedCount(offset);
     }
 
     public byte getReducedQual() {
         if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced qual for non-reduced read " + getRead().getReadName());
-        return ReadUtils.getReducedQual(getRead(), offset);
+        return getQual();
     }
 }

public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java

@@ -134,6 +134,7 @@ public class ArtificialSAMUtils {
     /**
      * Create an artificial read based on the parameters.  The cigar string will be *M, where * is the length of the read
      *
+     *
      * @param header         the SAM header to associate the read with
      * @param name           the name of the read
      * @param refIndex       the reference index, i.e. what chromosome to associate it with
@@ -142,11 +143,11 @@ public class ArtificialSAMUtils {
      *
      * @return the artificial read
      */
-    public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
+    public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, int length) {
         if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
             (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
             throw new ReviewedStingException("Invalid alignment start for artificial read, start = " + alignmentStart);
-        SAMRecord record = new GATKSAMRecord(header);
+        GATKSAMRecord record = new GATKSAMRecord(header);
         record.setReadName(name);
         record.setReferenceIndex(refIndex);
         record.setAlignmentStart(alignmentStart);
@@ -166,6 +167,7 @@ public class ArtificialSAMUtils {
         if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
             record.setReadUnmappedFlag(true);
         }
+
         return record;
     }
 
@@ -181,16 +183,17 @@ public class ArtificialSAMUtils {
      *
      * @return the artificial read
      */
-    public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) {
+    public static GATKSAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) {
         if (bases.length != qual.length) {
             throw new ReviewedStingException("Passed in read string is different length then the quality array");
         }
-        SAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
+        GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
         rec.setReadBases(bases);
         rec.setBaseQualities(qual);
         if (refIndex == -1) {
             rec.setReadUnmappedFlag(true);
         }
+
         return rec;
     }
 

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -45,9 +45,11 @@ public class GATKSAMRecord extends BAMRecord {
     // the SAMRecord data we're caching
     private String mReadString = null;
     private GATKSAMReadGroupRecord mReadGroup = null;
+    private byte[] reducedReadCounts = null;
 
     // because some values can be null, we don't want to duplicate effort
     private boolean retrievedReadGroup = false;
+    private boolean retrievedReduceReadCounts = false;
 
     // These temporary attributes were added here to make life easier for
     // certain algorithms by providing a way to label or attach arbitrary data to
@@ -60,8 +62,27 @@ public class GATKSAMRecord extends BAMRecord {
      * @param header
      */
     public GATKSAMRecord(final SAMFileHeader header) {
-        super(header, SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, SAMRecord.NO_ALIGNMENT_START,
+        this(new SAMRecord(header));
-                (short)0, (short)255, 0, 1, 0, 1, 0, 0, 0, null);
+    }
+
+    /**
+     * HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
+     * @param read
+     */
+    public GATKSAMRecord(final SAMRecord read) {
+        super(read.getHeader(), read.getMateReferenceIndex(),
+                read.getAlignmentStart(),
+                read.getReadName() != null ? (short)read.getReadNameLength() : 0,
+                (short)read.getMappingQuality(),
+                0,
+                read.getCigarLength(),
+                read.getFlags(),
+                read.getReadLength(),
+                read.getMateReferenceIndex(),
+                read.getMateAlignmentStart(),
+                read.getInferredInsertSize(),
+                new byte[]{});
+        super.clearAttributes();
     }
 
     public GATKSAMRecord(final SAMFileHeader header,
@@ -121,6 +142,29 @@ public class GATKSAMRecord extends BAMRecord {
         retrievedReadGroup = true;
     }
 
+    //
+    //
+    // Reduced read functions
+    //
+    //
+
+    public byte[] getReducedReadCounts() {
+        if ( ! retrievedReduceReadCounts ) {
+            reducedReadCounts = getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
+            retrievedReduceReadCounts = true;
+        }
+
+        return reducedReadCounts;
+    }
+
+    public boolean isReducedRead() {
+        return getReducedReadCounts() != null;
+    }
+
+    public final byte getReducedCount(final int i) {
+        return getReducedReadCounts()[i];
+    }
+
     /**
      * Checks whether an attribute has been set for the given key.
      *

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -52,24 +52,6 @@ public class ReadUtils {
     // ----------------------------------------------------------------------------------------------------
 
     public static final String REDUCED_READ_QUALITY_TAG = "RQ";
-    public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC";
-
-    public final static byte[] getReducedReadQualityTagValue(final SAMRecord read) {
-        // TODO -- warning of performance problem.  Should be cached in GATKSAMRecord
-        return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
-    }
-
-    public final static boolean isReducedRead(final SAMRecord read) {
-        return getReducedReadQualityTagValue(read) != null;
-    }
-
-    public final static byte getReducedQual(final SAMRecord read, final int i) {
-        return read.getBaseQualities()[i];
-    }
-
-    public final static byte getReducedCount(final SAMRecord read, final int i) {
-        return getReducedReadQualityTagValue(read)[i];
-    }
 
     // ----------------------------------------------------------------------------------------------------
     //

public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java

@@ -5,6 +5,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeTest;
@@ -12,7 +13,7 @@ import org.testng.annotations.Test;
 
 
 public class ReadUtilsUnitTest extends BaseTest {
-    SAMRecord read, reducedRead;
+    GATKSAMRecord read, reducedRead;
     final static String BASES = "ACTG";
     final static String QUALS = "!+5?";
     final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40};
@@ -47,13 +48,12 @@ public class ReadUtilsUnitTest extends BaseTest {
 
     @Test
     public void testReducedReads() {
-        Assert.assertFalse(ReadUtils.isReducedRead(read), "isReducedRead is false for normal read");
+        Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");
-        Assert.assertEquals(ReadUtils.getReducedReadQualityTagValue(read), null, "No reduced read tag in normal read");
+        Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
 
-        Assert.assertTrue(ReadUtils.isReducedRead(reducedRead), "isReducedRead is true for reduced read");
+        Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
         for ( int i = 0; i < reducedRead.getReadLength(); i++) {
-            Assert.assertEquals(ReadUtils.getReducedQual(reducedRead, i), read.getBaseQualities()[i], "Reduced read quality not set to the expected value at " + i);
+            Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
-            Assert.assertEquals(ReadUtils.getReducedCount(reducedRead, i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
         }
     }
 

public/java/test/org/broadinstitute/sting/utils/ReservoirDownsamplerUnitTest.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.utils;
 
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@@ -28,7 +29,7 @@ public class ReservoirDownsamplerUnitTest {
 
     @Test
     public void testOneElementWithPoolSizeOne() {
-        List<SAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
+        List<GATKSAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
         ReservoirDownsampler<SAMRecord> downsampler = new ReservoirDownsampler<SAMRecord>(1);
         downsampler.addAll(reads);
 
@@ -40,7 +41,7 @@ public class ReservoirDownsamplerUnitTest {
 
     @Test
     public void testOneElementWithPoolSizeGreaterThanOne() {
-        List<SAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
+        List<GATKSAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
         ReservoirDownsampler<SAMRecord> downsampler = new ReservoirDownsampler<SAMRecord>(5);
         downsampler.addAll(reads);