Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs.

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java

@@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSamRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -125,7 +125,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
             for ( ExtendedEventPileupElement p : indelPileup.toExtendedIterable() ) {
                 //SAMRecord read = p.getRead();
-                 GATKSamRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
+                 GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
                 if (read == null)
                     continue;     
                 if(ReadUtils.is454Read(read)) {

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.sam.GATKSamRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.util.ArrayList;
@@ -352,7 +352,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
         if( tracker.getValues(knownSites).size() == 0 ) { // If something here is in one of the knownSites tracks then skip over it, otherwise proceed
             // For each read at this locus
             for( final PileupElement p : context.getBasePileup() ) {
-                final GATKSamRecord gatkRead = (GATKSamRecord) p.getRead();
+                final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
                 int offset = p.getOffset();
 
                 if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE  ) ) {
@@ -445,7 +445,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
      * @param offset The offset in the read for this locus
      * @param refBase The reference base at this locus
      */
-    private void updateDataFromRead(CountedData counter, final GATKSamRecord gatkRead, final int offset, final byte refBase) {
+    private void updateDataFromRead(CountedData counter, final GATKSAMRecord gatkRead, final int offset, final byte refBase) {
         final Object[][] covars = (Comparable[][]) gatkRead.getTemporaryAttribute(COVARS_ATTRIBUTE);
         final Object[] key = covars[offset];
 

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java

@@ -4,7 +4,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSamRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Arrays;
 import java.util.EnumSet;
@@ -71,7 +71,7 @@ public class CycleCovariate implements StandardCovariate {
         // Illumina, Solid, PacBio, and Complete Genomics
         //-----------------------------
 
-        final NGSPlatform ngsPlatform = ((GATKSamRecord)read).getNGSPlatform();
+        final NGSPlatform ngsPlatform = ((GATKSAMRecord)read).getNGSPlatform();
         if( DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform) ) {
             final int init;
             final int increment;

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java

@@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
-import org.broadinstitute.sting.utils.sam.GATKSamRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -229,7 +229,7 @@ public class RecalDataManager {
      * @param RAC The list of shared command line arguments
      */
     public static void parseSAMRecord( final SAMRecord read, final RecalibrationArgumentCollection RAC ) {
-        GATKSAMReadGroupRecord readGroup = ((GATKSamRecord)read).getReadGroup();
+        GATKSAMReadGroupRecord readGroup = ((GATKSAMRecord)read).getReadGroup();
 
         // If there are no read groups we have to default to something, and that something could be specified by the user using command line arguments
         if( readGroup == null ) {
@@ -243,7 +243,7 @@ public class RecalDataManager {
                 // There is no readGroup so defaulting to these values
                 readGroup = new GATKSAMReadGroupRecord( RAC.DEFAULT_READ_GROUP );
                 readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
-                ((GATKSamRecord)read).setReadGroup( readGroup );
+                ((GATKSAMRecord)read).setReadGroup( readGroup );
             } else {
                 throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() );
             }
@@ -253,7 +253,7 @@ public class RecalDataManager {
             final String oldPlatform = readGroup.getPlatform();
             readGroup = new GATKSAMReadGroupRecord( RAC.FORCE_READ_GROUP );
             readGroup.setPlatform( oldPlatform );
-            ((GATKSamRecord)read).setReadGroup( readGroup );
+            ((GATKSAMRecord)read).setReadGroup( readGroup );
         }
 
         if( RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
@@ -572,7 +572,7 @@ public class RecalDataManager {
      * value for the ith position in the read and the jth covariate in
      * reqeustedCovariates list.
      */
-     public static Comparable[][] computeCovariates(final GATKSamRecord gatkRead, final List<Covariate> requestedCovariates) {
+     public static Comparable[][] computeCovariates(final GATKSAMRecord gatkRead, final List<Covariate> requestedCovariates) {
          //compute all covariates for this read
          final List<Covariate> requestedCovariatesRef = requestedCovariates;
          final int numRequestedCovariates = requestedCovariatesRef.size();

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSamRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
@@ -398,7 +398,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         //compute all covariate values for this read
         final Comparable[][] covariateValues_offset_x_covar =
-            RecalDataManager.computeCovariates((GATKSamRecord) read, requestedCovariates);
+            RecalDataManager.computeCovariates((GATKSAMRecord) read, requestedCovariates);
 
         // For each base in the read
         for( int offset = 0; offset < read.getReadLength(); offset++ ) {

public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java

@@ -29,7 +29,7 @@ import net.sf.samtools.SAMRecord;
 
 /**
  * A canonical, master list of the standard NGS platforms.  These values
- * can be obtained (efficiently) from a GATKSamRecord object with the
+ * can be obtained (efficiently) from a GATKSAMRecord object with the
  * getNGSPlatform method.
  *
  * @author Mark DePristo
@@ -65,7 +65,7 @@ public enum NGSPlatform {
 
     /**
      * Convenience constructor -- calculates the NGSPlatfrom from a SAMRecord.
-     * Note you should not use this function if you have a GATKSamRecord -- use the
+     * Note you should not use this function if you have a GATKSAMRecord -- use the
      * accessor method instead.
      *
      * @param read

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

@@ -146,7 +146,7 @@ public class ArtificialSAMUtils {
         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);
+        SAMRecord record = new GATKSAMRecord(header);
         record.setReadName(name);
         record.setReferenceIndex(refIndex);
         record.setAlignmentStart(alignmentStart);

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

@@ -1,3 +1,27 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
@@ -7,23 +31,17 @@ import java.util.HashMap;
 import java.util.Map;
 
 /**
- * @author ebanks
+ * @author ebanks, depristo
  * GATKSAMRecord
  *
- * this class extends the samtools SAMRecord class and caches important
+ * this class extends the samtools BAMRecord class (and SAMRecord) and caches important
  * (and oft-accessed) data that's not already cached by the SAMRecord class
  *
  * IMPORTANT NOTE: Because ReadGroups are not set through the SAMRecord,
  *   if they are ever modified externally then one must also invoke the
  *   setReadGroup() method here to ensure that the cache is kept up-to-date.
- *
- * 13 Oct 2010 - mhanna - this class is fundamentally flawed: it uses a decorator
- *                        pattern to wrap a heavyweight object, which can lead
- *                        to heinous side effects if the wrapping is not carefully
- *                        done.  Hopefully SAMRecord will become an interface and
- *                        this will eventually be fixed.
  */
-public class GATKSamRecord extends BAMRecord {
+public class GATKSAMRecord extends BAMRecord {
     // the SAMRecord data we're caching
     private String mReadString = null;
     private GATKSAMReadGroupRecord mReadGroup = null;
@@ -41,13 +59,12 @@ public class GATKSamRecord extends BAMRecord {
      * HACK TO CREATE GATKSAMRECORD WITH ONLY A HEADER FOR TESTING PURPOSES ONLY
      * @param header
      */
-    public GATKSamRecord(final SAMFileHeader header) {
+    public GATKSAMRecord(final SAMFileHeader header) {
         super(header, SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, SAMRecord.NO_ALIGNMENT_START,
                 (short)0, (short)255, 0, 1, 0, 1, 0, 0, 0, null);
     }
 
-
+    public GATKSAMRecord(final SAMFileHeader header,
-    public GATKSamRecord(final SAMFileHeader header,
                          final int referenceSequenceIndex,
                          final int alignmentStart,
                          final short readNameLength,
@@ -91,6 +108,10 @@ public class GATKSamRecord extends BAMRecord {
         return mReadGroup;
     }
 
+    /**
+     * Efficient caching accessor that returns the GATK NGSPlatform of this read
+     * @return
+     */
     public NGSPlatform getNGSPlatform() {
         return getReadGroup().getNGSPlatform();
     }
@@ -153,12 +174,16 @@ public class GATKSamRecord extends BAMRecord {
         return null;
     }
 
+    @Override
+    public int hashCode() {
+        return super.hashCode();
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
 
-        // note -- this forbids a GATKSAMRecord being equal to its underlying SAMRecord
+        if (!(o instanceof GATKSAMRecord)) return false;
-        if (!(o instanceof GATKSamRecord)) return false;
 
         // note that we do not consider the GATKSAMRecord internal state at all
         return super.equals(o);

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

@@ -57,7 +57,7 @@ public class GATKSamRecordFactory implements SAMRecordFactory {
                                      final int mateAlignmentStart,
                                      final int insertSize,
                                      final byte[] variableLengthBlock) {
-        return new GATKSamRecord(header,
+        return new GATKSAMRecord(header,
                 referenceSequenceIndex,
                 alignmentStart,
                 readNameLength,

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

@@ -55,7 +55,7 @@ public class ReadUtils {
     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
+        // TODO -- warning of performance problem.  Should be cached in GATKSAMRecord
         return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
     }
 
@@ -260,10 +260,10 @@ public class ReadUtils {
      * @param adaptorLength  length of adaptor sequence
      * @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
      */
-    public static GATKSamRecord hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
+    public static GATKSAMRecord hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
 
         Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(rec, adaptorLength);
-        GATKSamRecord result = (GATKSamRecord)rec;
+        GATKSAMRecord result = (GATKSAMRecord)rec;
 
         if ( adaptorBoundaries != null ) {
             if ( rec.getReadNegativeStrandFlag() && adaptorBoundaries.second >= rec.getAlignmentStart() && adaptorBoundaries.first < rec.getAlignmentEnd() )
@@ -276,7 +276,7 @@ public class ReadUtils {
     }
 
     // return true if the read needs to be completely clipped
-    private static GATKSamRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
+    private static GATKSAMRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
 
         if ( stopPosition >= oldRec.getAlignmentEnd() ) {
             // BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
@@ -284,9 +284,9 @@ public class ReadUtils {
             return null;
         }
 
-        GATKSamRecord rec;
+        GATKSAMRecord rec;
         try {
-            rec = (GATKSamRecord)oldRec.clone();
+            rec = (GATKSAMRecord)oldRec.clone();
         } catch (Exception e) {
             return null;
         }
@@ -356,7 +356,7 @@ public class ReadUtils {
         return rec;
     }
 
-    private static GATKSamRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
+    private static GATKSAMRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
 
         if ( startPosition <= oldRec.getAlignmentStart() ) {
             // BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
@@ -364,9 +364,9 @@ public class ReadUtils {
             return null;
         }
 
-        GATKSamRecord rec;
+        GATKSAMRecord rec;
         try {
-            rec = (GATKSamRecord)oldRec.clone();
+            rec = (GATKSAMRecord)oldRec.clone();
         } catch (Exception e) {
             return null;
         }
@@ -584,7 +584,7 @@ public class ReadUtils {
      * @param rec  original SAM record
      * @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
      */
-    public static GATKSamRecord hardClipAdaptorSequence(final SAMRecord rec) {
+    public static GATKSAMRecord hardClipAdaptorSequence(final SAMRecord rec) {
         return hardClipAdaptorSequence(rec, DEFAULT_ADAPTOR_SIZE);
     }