Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.alignment;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@@ -35,6 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
 
@@ -72,12 +72,13 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
 
     /**
      * Aligns a read to the given reference.
+     *
      * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
      * @param read Read to align.
      * @return Number of reads aligned by this map (aka 1).
      */
     @Override
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         //logger.info(String.format("examining read %s", read.getReadName()));
 
         byte[] bases = read.getReadBases();

public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
 
@@ -92,12 +93,13 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
 
     /**
      * Aligns a read to the given reference.
+     *
      * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
      * @param read Read to align.
      * @return Number of alignments found for this read.
      */
     @Override
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         SAMRecord alignedRead = aligner.align(read,header);
         out.addAlignment(alignedRead);
         return 1;

public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.alignment;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@@ -34,6 +33,7 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.util.Iterator;
@@ -79,12 +79,13 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
 
     /**
      * Aligns a read to the given reference.
+     *
      * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
      * @param read Read to align.
      * @return Number of alignments found for this read.
      */
     @Override
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
         if(alignmentIterator.hasNext()) {
             int numAlignments = alignmentIterator.next().length;

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

@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.List;
 
@@ -130,7 +130,7 @@ public class AlignmentContext implements HasGenomeLocation {
      */
     @Deprecated
     //todo: unsafe and tailored for current usage only; both pileups can be null or worse, bot can be not null in theory
-    public List<SAMRecord> getReads() { return ( basePileup.getReads() ); }
+    public List<GATKSAMRecord> getReads() { return ( basePileup.getReads() ); }
 
     /**
      * Are there any reads associated with this locus?

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

@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Collections;
 import java.util.List;
@@ -132,7 +132,7 @@ public class AllLocusView extends LocusView {
      * @param site Site at which to create the blank locus context.
      * @return empty context.
      */
-    private final static List<SAMRecord> EMPTY_PILEUP_READS = Collections.emptyList();
+    private final static List<GATKSAMRecord> EMPTY_PILEUP_READS = Collections.emptyList();
     private final static List<Integer> EMPTY_PILEUP_OFFSETS = Collections.emptyList();
     private AlignmentContext createEmptyLocus( GenomeLoc site ) {
         return new AlignmentContext(site,new ReadBackedPileupImpl(site, EMPTY_PILEUP_READS, EMPTY_PILEUP_OFFSETS));

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

@@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileupImpl;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
@@ -377,10 +378,7 @@ public class LocusIteratorByState extends LocusIterator {
                                 maxDeletionLength = Math.max(maxDeletionLength,state.getEventLength());
                             }
                             else nInsertions++;
-                            indelPile.add ( new ExtendedEventPileupElement(state.getRead(),
+                            indelPile.add ( new ExtendedEventPileupElement((GATKSAMRecord) state.getRead(), state.getReadEventStartOffset(), state.getEventLength(), state.getEventBases()) );
-                                                                           state.getReadEventStartOffset(),
-                                                                           state.getEventLength(),
-                                                                           state.getEventBases()) );
 
                         }   else {
                             // HACK: The readahead mechanism for LocusIteratorByState will effectively read past the current position
@@ -402,9 +400,7 @@ public class LocusIteratorByState extends LocusIterator {
                                     // we count such reads (with a longer deletion spanning over a deletion at the previous base we are
                                     // about to report) only if includeReadsWithDeletionAtLoci is true.
                                     size++;
-                                    indelPile.add ( new ExtendedEventPileupElement(state.getRead(),
+                                    indelPile.add ( new ExtendedEventPileupElement((GATKSAMRecord) state.getRead(), state.getReadOffset()-1, -1) // length=-1 --> noevent
-                                                                           state.getReadOffset()-1,
-                                                                           -1) // length=-1 --> noevent
                                             );
                                 }
                             }
@@ -442,12 +438,12 @@ public class LocusIteratorByState extends LocusIterator {
                                 continue;
                             } else {
                                 //observed_bases++;
-                                pile.add(new PileupElement(state.getRead(), state.getReadOffset()));
+                                pile.add(new PileupElement((GATKSAMRecord) state.getRead(), state.getReadOffset()));
                                 size++;
                             }
                         } else if ( readInfo.includeReadsWithDeletionAtLoci() && state.getCurrentCigarOperator() != CigarOperator.N ) {
                             size++;
-                            pile.add(new PileupElement(state.getRead(), -1));
+                            pile.add(new PileupElement((GATKSAMRecord) state.getRead(), -1));
                             nDeletions++;
                         }
 

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

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.*;
 
@@ -57,9 +58,9 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
         return "dups";
     }
 
-    private List<SAMRecord> readsAtLoc(final SAMRecord read, PushbackIterator<SAMRecord> iter) {
+    private List<GATKSAMRecord> readsAtLoc(final GATKSAMRecord read, PushbackIterator<SAMRecord> iter) {
         GenomeLoc site = engine.getGenomeLocParser().createGenomeLoc(read);
-        ArrayList<SAMRecord> l = new ArrayList<SAMRecord>();
+        ArrayList<GATKSAMRecord> l = new ArrayList<GATKSAMRecord>();
 
         l.add(read);
         for (SAMRecord read2 : iter) {
@@ -70,7 +71,7 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
                 iter.pushback(read2);
                 break;
             } else {
-                l.add(read2);
+                l.add((GATKSAMRecord) read2);
             }
         }
 
@@ -84,15 +85,15 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
      * @param reads the list of reads to split into unique molecular samples
      * @return
      */
-    protected Set<List<SAMRecord>> uniqueReadSets(List<SAMRecord> reads) {
+    protected Set<List<GATKSAMRecord>> uniqueReadSets(List<GATKSAMRecord> reads) {
-        Set<List<SAMRecord>> readSets = new LinkedHashSet<List<SAMRecord>>();
+        Set<List<GATKSAMRecord>> readSets = new LinkedHashSet<List<GATKSAMRecord>>();
 
         // for each read, find duplicates, and either add the read to its duplicate list or start a new one
-        for ( SAMRecord read : reads ) {
+        for ( GATKSAMRecord read : reads ) {
-            List<SAMRecord> readSet = findDuplicateReads(read, readSets);
+            List<GATKSAMRecord> readSet = findDuplicateReads(read, readSets);
 
             if ( readSet == null ) {
-                readSets.add(new ArrayList<SAMRecord>(Arrays.asList(read)));    // copy so I can add to the list
+                readSets.add(new ArrayList<GATKSAMRecord>(Arrays.asList(read)));    // copy so I can add to the list
             } else {
                 readSet.add(read);
             }
@@ -110,13 +111,13 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
      * @param readSets
      * @return The list of duplicate reads that read is a member of, or null if it's the only one of its kind
      */
-    protected List<SAMRecord> findDuplicateReads(SAMRecord read, Set<List<SAMRecord>> readSets ) {
+    protected List<GATKSAMRecord> findDuplicateReads(GATKSAMRecord read, Set<List<GATKSAMRecord>> readSets ) {
         if ( read.getReadPairedFlag() ) {
             // paired
             final GenomeLoc readMateLoc = engine.getGenomeLocParser().createGenomeLoc(read.getMateReferenceName(), read.getMateAlignmentStart(), read.getMateAlignmentStart());
 
-            for (List<SAMRecord> reads : readSets) {
+            for (List<GATKSAMRecord> reads : readSets) {
-                SAMRecord key = reads.get(0);
+                GATKSAMRecord key = reads.get(0);
 
                 // read and key start at the same place, and either the this read and the key
                 // share a mate location or the read is flagged as a duplicate
@@ -131,8 +132,8 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
                 }
             }
         } else {
-            for (List<SAMRecord> reads : readSets) {
+            for (List<GATKSAMRecord> reads : readSets) {
-                SAMRecord key = reads.get(0);
+                GATKSAMRecord key = reads.get(0);
                 boolean v = (! key.getReadPairedFlag()) && read.getAlignmentStart() == key.getAlignmentStart() && ( key.getDuplicateReadFlag() || read.getDuplicateReadFlag() ) && read.getReadLength() == key.getReadLength();
                 //System.out.printf("%s %s %b %b %d %d %d %d => %b%n",
                 //        read.getReadPairedFlag(), key.getReadPairedFlag(), read.getDuplicateReadFlag(), key.getDuplicateReadFlag(),
@@ -179,7 +180,7 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
             // get the genome loc from the read
             GenomeLoc site = engine.getGenomeLocParser().createGenomeLoc(read);
 
-            Set<List<SAMRecord>> readSets = uniqueReadSets(readsAtLoc(read, iter));
+            Set<List<GATKSAMRecord>> readSets = uniqueReadSets(readsAtLoc((GATKSAMRecord) read, iter));
             if ( DEBUG ) logger.debug(String.format("*** TraverseDuplicates.traverse at %s with %d read sets", site, readSets.size()));
 
             // Jump forward in the reference to this locus location

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

@@ -13,6 +13,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -100,9 +101,9 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
             // if the read is mapped, create a metadata tracker
             ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;
 
-            final boolean keepMeP = walker.filter(refContext, read);
+            final boolean keepMeP = walker.filter(refContext, (GATKSAMRecord) read);
             if (keepMeP) {
-                M x = walker.map(refContext, read, tracker); // the tracker can be null
+                M x = walker.map(refContext, (GATKSAMRecord) read, tracker); // the tracker can be null
                 sum = walker.reduce(x, sum);
             }
 

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

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.commandline.Advanced;
 import org.broadinstitute.sting.commandline.Argument;
@@ -43,6 +42,7 @@ import org.broadinstitute.sting.utils.clipreads.ClippingOp;
 import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
 import org.broadinstitute.sting.utils.clipreads.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.io.File;
@@ -292,11 +292,12 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
     /**
      * The reads map function.
      *
+     *
      * @param ref  the reference bases that correspond to our read, if a reference was provided
-     * @param read the read itself, as a SAMRecord
+     * @param read the read itself, as a GATKSAMRecord
      * @return the ReadClipper object describing what should be done to clip this read
      */
-    public ReadClipperWithData map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
             if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES ) {
                 read = ReadUtils.replaceSoftClipsWithMatches(read);
@@ -323,7 +324,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
      */
     private void clipSequences(ReadClipperWithData clipper) {
         if (sequencesToClip != null) {                // don't bother if we don't have any sequences to clip
-            SAMRecord read = clipper.getRead();
+            GATKSAMRecord read = clipper.getRead();
             ClippingData data = clipper.getData();
 
             for (SeqToClip stc : sequencesToClip) {
@@ -360,7 +361,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
      * @param stop
      * @return
      */
-    private Pair<Integer, Integer> strandAwarePositions(SAMRecord read, int start, int stop) {
+    private Pair<Integer, Integer> strandAwarePositions(GATKSAMRecord read, int start, int stop) {
         if (read.getReadNegativeStrandFlag())
             return new Pair<Integer, Integer>(read.getReadLength() - stop - 1, read.getReadLength() - start - 1);
         else
@@ -374,7 +375,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
      */
     private void clipCycles(ReadClipperWithData clipper) {
         if (cyclesToClip != null) {
-            SAMRecord read = clipper.getRead();
+            GATKSAMRecord read = clipper.getRead();
             ClippingData data = clipper.getData();
 
             for (Pair<Integer, Integer> p : cyclesToClip) {   // iterate over each cycle range
@@ -416,7 +417,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
      * @param clipper
      */
     private void clipBadQualityScores(ReadClipperWithData clipper) {
-        SAMRecord read = clipper.getRead();
+        GATKSAMRecord read = clipper.getRead();
         ClippingData data = clipper.getData();
         int readLen = read.getReadBases().length;
         byte[] quals = read.getBaseQualities();
@@ -458,7 +459,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
         if ( clipper == null )
             return data;
 
-        SAMRecord clippedRead = clipper.clipRead(clippingRepresentation);
+        GATKSAMRecord clippedRead = clipper.clipRead(clippingRepresentation);
         if (outputBam != null) {
             outputBam.addAlignment(clippedRead);
         } else {
@@ -575,7 +576,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
     public class ReadClipperWithData extends ReadClipper {
         private ClippingData data;
 
-        public ReadClipperWithData(SAMRecord read, List<SeqToClip> clipSeqs) {
+        public ReadClipperWithData(GATKSAMRecord read, List<SeqToClip> clipSeqs) {
             super(read);
             data = new ClippingData(clipSeqs);
         }

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

@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.List;
 import java.util.Set;
@@ -20,11 +20,11 @@ import java.util.Set;
 @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class})
 public abstract class DuplicateWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?
-    public boolean filter(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets ) {
+    public boolean filter(GenomeLoc loc, AlignmentContext context, Set<List<GATKSAMRecord>> readSets ) {
         return true;    // We are keeping all the reads
     }
 
-    public abstract MapType map(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets );
+    public abstract MapType map(GenomeLoc loc, AlignmentContext context, Set<List<GATKSAMRecord>> readSets );
 
     // Given result of map function
     public abstract ReduceType reduceInit();

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

@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
@@ -71,21 +72,23 @@ public class FindReadsWithNamesWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
     /**
      * The reads filter function.
+     *
      * @param ref the reference bases that correspond to our read, if a reference was provided
      * @param read the read itself, as a SAMRecord
      * @return true if the read passes the filter, false if it doesn't
      */
-    public boolean filter(ReferenceContext ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
         return namesToKeep.contains(read.getReadName());
 	}
 
     /**
      * The reads map function.
+     *
      * @param ref the reference bases that correspond to our read, if a reference was provided
      * @param read the read itself, as a SAMRecord
      * @return the read itself
      */
-    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         return read;
     }
 

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

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.text.DecimalFormat;
@@ -119,7 +119,7 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
 
     private FlagStat myStat = new FlagStat();
 
-    public Integer map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public Integer map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         myStat.readCount++;
         if (read.getReadFailsVendorQualityCheckFlag()) {
             myStat.QC_failure++;

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

@@ -40,6 +40,7 @@ import java.util.TreeSet;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.
@@ -136,11 +137,12 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
 
     /**
      * The reads filter function.
+     *
      * @param ref the reference bases that correspond to our read, if a reference was provided
      * @param read the read itself, as a SAMRecord
      * @return true if the read passes the filter, false if it doesn't
      */
-    public boolean filter(ReferenceContext ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
         // check the read group
         if  ( readGroup != null ) {
             SAMReadGroupRecord myReadGroup = read.getReadGroup();
@@ -180,11 +182,12 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
 
     /**
      * The reads map function.
+     *
      * @param ref the reference bases that correspond to our read, if a reference was provided
      * @param read the read itself, as a SAMRecord
      * @return the read itself
      */
-    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         return read;
     }
 

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

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
  * Created by IntelliJ IDEA.
@@ -20,11 +21,11 @@ public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, Re
     /** Must return true for reads that need to be processed. Reads, for which this method return false will
      * be skipped by the engine and never passed to the walker.
      */
-    public boolean filter(ReferenceContext ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
         // We are keeping all the reads
         return true;
     }
 
     // Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
-    public abstract MapType map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker);
+    public abstract MapType map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker);
 }

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

@@ -33,6 +33,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.ArrayList;
@@ -60,7 +61,7 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
         logger.info("SplitSamFile version: " + VERSION);
     }
 
-    public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public SAMRecord map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         return read;
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java

@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.diagnostics;
 
 import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.util.List;
@@ -69,12 +69,12 @@ public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
 
     }
 
-    public boolean filter(ReferenceContext ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
         return ( !read.getReadPairedFlag() || read.getReadPairedFlag() && read.getFirstOfPairFlag());
     }
 
     @Override
-    public Integer map(ReferenceContext referenceContext, SAMRecord samRecord, ReadMetaDataTracker readMetaDataTracker) {
+    public Integer map(ReferenceContext referenceContext, GATKSAMRecord samRecord, ReadMetaDataTracker readMetaDataTracker) {
         GATKReportTable table = report.getTable("ReadLengthDistribution");
 
         int length = Math.abs(samRecord.getReadLength());

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

@@ -9,6 +9,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.*;
 
@@ -180,8 +181,8 @@ public class ConstrainedMateFixingManager {
         addRead(newRead, readWasModified, true);
     }
 
-    public void addReads(List<SAMRecord> newReads, Set<SAMRecord> modifiedReads) {
+    public void addReads(List<GATKSAMRecord> newReads, Set<GATKSAMRecord> modifiedReads) {
-        for ( SAMRecord newRead : newReads )
+        for ( GATKSAMRecord newRead : newReads )
             addRead(newRead, modifiedReads.contains(newRead), false);
     }
 

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

@@ -47,6 +47,7 @@ import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@@ -281,10 +282,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     // the reads and known indels that fall into the current interval
     private final ReadBin readsToClean = new ReadBin();
-    private final ArrayList<SAMRecord> readsNotToClean = new ArrayList<SAMRecord>();
+    private final ArrayList<GATKSAMRecord> readsNotToClean = new ArrayList<GATKSAMRecord>();
     private final ArrayList<VariantContext> knownIndelsToTry = new ArrayList<VariantContext>();
     private final HashSet<Object> indelRodsSeen = new HashSet<Object>();
-    private final HashSet<SAMRecord> readsActuallyCleaned = new HashSet<SAMRecord>();
+    private final HashSet<GATKSAMRecord> readsActuallyCleaned = new HashSet<GATKSAMRecord>();
 
     private static final int MAX_QUAL = 99;
 
@@ -469,7 +470,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         readsActuallyCleaned.clear();
     }
 
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( currentInterval == null ) {
             emit(read);
             return 0;
@@ -535,7 +536,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         // TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
     }
 
-    private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
+    private void cleanAndCallMap(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
         if ( readsToClean.size() > 0 ) {
             GenomeLoc earliestPossibleMove = getToolkit().getGenomeLocParser().createGenomeLoc(readsToClean.getReads().get(0));
             if ( manager.canMoveReads(earliestPossibleMove) )
@@ -656,14 +657,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     private void clean(ReadBin readsToClean) {
 
-        final List<SAMRecord> reads = readsToClean.getReads();
+        final List<GATKSAMRecord> reads = readsToClean.getReads();
         if ( reads.size() == 0 )
             return;
 
         byte[] reference = readsToClean.getReference(referenceReader);
         int leftmostIndex = readsToClean.getLocation().getStart();
 
-        final ArrayList<SAMRecord> refReads = new ArrayList<SAMRecord>();                 // reads that perfectly match ref
+        final ArrayList<GATKSAMRecord> refReads = new ArrayList<GATKSAMRecord>();                 // reads that perfectly match ref
         final ArrayList<AlignedRead> altReads = new ArrayList<AlignedRead>();               // reads that don't perfectly match
         final LinkedList<AlignedRead> altAlignmentsToTest = new LinkedList<AlignedRead>();  // should we try to make an alt consensus from the read?
         final Set<Consensus> altConsenses = new LinkedHashSet<Consensus>();               // list of alt consenses
@@ -815,7 +816,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         // however we don't have enough info to use the proper MAQ scoring system.
                         // For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
                         // TODO -- we need a better solution here
-                        SAMRecord read = aRead.getRead();
+                        GATKSAMRecord read = aRead.getRead();
                         read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
 
                         // before we fix the attribute tags we first need to make sure we have enough of the reference sequence
@@ -874,8 +875,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         }
     }
 
-    private long determineReadsThatNeedCleaning(final List<SAMRecord> reads,
+    private long determineReadsThatNeedCleaning(final List<GATKSAMRecord> reads,
-                                                final ArrayList<SAMRecord> refReadsToPopulate,
+                                                final ArrayList<GATKSAMRecord> refReadsToPopulate,
                                                 final ArrayList<AlignedRead> altReadsToPopulate,
                                                 final LinkedList<AlignedRead> altAlignmentsToTest,
                                                 final Set<Consensus> altConsenses,
@@ -884,7 +885,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
         long totalRawMismatchSum = 0L;
 
-        for ( final SAMRecord read : reads ) {
+        for ( final GATKSAMRecord read : reads ) {
 
             // we can not deal with screwy records
             if ( read.getCigar().numCigarElements() == 0 ) {
@@ -1372,7 +1373,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     }
 
     private class AlignedRead {
-        private final SAMRecord read;
+        private final GATKSAMRecord read;
         private byte[] readBases = null;
         private byte[] baseQuals = null;
         private Cigar newCigar = null;
@@ -1380,12 +1381,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         private int mismatchScoreToReference = 0;
         private long alignerMismatchScore = 0;
 
-        public AlignedRead(SAMRecord read) {
+        public AlignedRead(GATKSAMRecord read) {
             this.read = read;
             mismatchScoreToReference = 0;
         }
 
-        public SAMRecord getRead() {
+        public GATKSAMRecord getRead() {
                return read;
         }
 
@@ -1569,7 +1570,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     private class ReadBin implements HasGenomeLocation {
 
-        private final ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
+        private final ArrayList<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>();
         private byte[] reference = null;
         private GenomeLoc loc = null;
 
@@ -1577,7 +1578,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
         // Return false if we can't process this read bin because the reads are not correctly overlapping.
         // This can happen if e.g. there's a large known indel with no overlapping reads.
-        public void add(SAMRecord read) {
+        public void add(GATKSAMRecord read) {
 
             GenomeLoc locForRead = getToolkit().getGenomeLocParser().createGenomeLoc(read);
             if ( loc == null )
@@ -1588,7 +1589,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             reads.add(read);
         }
 
-        public List<SAMRecord> getReads() { return reads; }
+        public List<GATKSAMRecord> getReads() { return reads; }
 
         public byte[] getReference(IndexedFastaSequenceFile referenceReader) {
             // set up the reference if we haven't done so yet

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

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 
 /**
@@ -88,7 +89,7 @@ public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
             writer.addAlignment(read);
     }
 
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         // we can not deal with screwy records
         if ( read.getCigar().numCigarElements() == 0 ) {
             emit(read);

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

@@ -57,6 +57,7 @@ import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -394,7 +395,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
 
 
 	@Override
-	public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+	public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
     //        if ( read.getReadName().equals("428EFAAXX090610:2:36:1384:639#0") ) System.out.println("GOT READ");
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java

@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.samples.Gender;
@@ -32,6 +31,7 @@ import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
@@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountMalesWalker extends ReadWalker<Integer, Integer> {
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
         Sample sample = getSampleDB().getSample(read);
         return sample.getGender() == Gender.MALE ? 1 : 0;
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java

@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
@@ -38,7 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReadsWalker extends ReadWalker<Integer, Integer> {
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
 
         return 1;
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java

@@ -1,434 +1,434 @@
-/*
+/*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2010 The Broad Institute
- *
+ *
- * Permission is hereby granted, free of charge, to any person
+ * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+ * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+ * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+ * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+ * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
+ * Software is furnished to do so, subject to the following
- * conditions:
+ * conditions:
- *
+ *
- * The above copyright notice and this permission notice shall be
+ * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+ * included in all copies or substantial portions of the Software.
- *
+ *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * OTHER DEALINGS IN THE SOFTWARE.
- */
+ */
-
+
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.sting.gatk.walkers.qc;
-
+
-import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.collections.PrimitivePair;
-import org.broadinstitute.sting.utils.collections.PrimitivePair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
+
-import java.io.*;
+import java.io.*;
-import java.util.*;
+import java.util.*;
-
+
-/**
+/**
- * Created by IntelliJ IDEA.
+ * Created by IntelliJ IDEA.
- * User: asivache
+ * User: asivache
- * Date: Apr 9, 2010
+ * Date: Apr 9, 2010
- * Time: 12:16:41 PM
+ * Time: 12:16:41 PM
- * To change this template use File | Settings | File Templates.
+ * To change this template use File | Settings | File Templates.
- */
+ */
-
+
-/**
+/**
- * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
+ * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
- * Can also count the number of reads matching a given criterion using read filters (see the
+ * Can also count the number of reads matching a given criterion using read filters (see the
- * --read-filter command line argument).  Simplest example of a read-backed analysis.
+ * --read-filter command line argument).  Simplest example of a read-backed analysis.
- */
+ */
-@Requires({DataSource.READS})
+@Requires({DataSource.READS})
-public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
+public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
-    @Output
+    @Output
-    protected PrintStream out;
+    protected PrintStream out;
-
+
-    @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
+    @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
-                "on mapped reads only, while unmapped reads will be discarded", required=false)
+                "on mapped reads only, while unmapped reads will be discarded", required=false)
-    protected boolean MAPPED_ONLY = true;
+    protected boolean MAPPED_ONLY = true;
-    @Argument(fullName="maxReadLength", shortName="rl", doc="maximum read length", required=false)
+    @Argument(fullName="maxReadLength", shortName="rl", doc="maximum read length", required=false)
-    protected int MAX_READ_LENGTH = 500;
+    protected int MAX_READ_LENGTH = 500;
-    @Argument(fullName="out_prefix",shortName="p",doc="prefix for output report and statistics files",required=true)
+    @Argument(fullName="out_prefix",shortName="p",doc="prefix for output report and statistics files",required=true)
-    protected String PREFIX = null;
+    protected String PREFIX = null;
-//    @Argument(fullName="html",shortName="html",doc="produce html-formatted output (starting with h3-level tags) rather than plain text",required=false)
+//    @Argument(fullName="html",shortName="html",doc="produce html-formatted output (starting with h3-level tags) rather than plain text",required=false)
-    protected boolean HTML = false;
+    protected boolean HTML = false;
-    @Argument(fullName="qualThreshold", shortName="Q",doc="flag as problematic all cycles with av. qualities below the threshold (applies only to the generated report)",required=false)
+    @Argument(fullName="qualThreshold", shortName="Q",doc="flag as problematic all cycles with av. qualities below the threshold (applies only to the generated report)",required=false)
-    protected double QTHRESHOLD = 10.0;
+    protected double QTHRESHOLD = 10.0;
-    @Argument(fullName="useBothQualities",shortName="bothQ",required=false,doc="Generate statistics both for currently set and for "+
+    @Argument(fullName="useBothQualities",shortName="bothQ",required=false,doc="Generate statistics both for currently set and for "+
-        "original base qualities (OQ tag, must be present in the bam); two separate data files will be generated.")
+        "original base qualities (OQ tag, must be present in the bam); two separate data files will be generated.")
-    protected boolean ASSESS_BOTH_QUALS = false;
+    protected boolean ASSESS_BOTH_QUALS = false;
-
+
-    private Map<String,CycleStats[]> cyclesByLaneMap = null;
+    private Map<String,CycleStats[]> cyclesByLaneMap = null;
-    private Map<String,CycleStats[]> cyclesByLibraryMap = null;
+    private Map<String,CycleStats[]> cyclesByLibraryMap = null;
-    private Map<String,CycleStats[]> cyclesByLaneMapOrig = null;
+    private Map<String,CycleStats[]> cyclesByLaneMapOrig = null;
-    private Map<String,CycleStats[]> cyclesByLibraryMapOrig = null;
+    private Map<String,CycleStats[]> cyclesByLibraryMapOrig = null;
-
+
-    public void initialize() {
+    public void initialize() {
-        if ( PREFIX == null ) throw new ReviewedStingException("Prefix for output file(s) must be specified");
+        if ( PREFIX == null ) throw new ReviewedStingException("Prefix for output file(s) must be specified");
-        cyclesByLaneMap = new HashMap<String,CycleStats[]>();
+        cyclesByLaneMap = new HashMap<String,CycleStats[]>();
-        cyclesByLibraryMap = new HashMap<String,CycleStats[]>();
+        cyclesByLibraryMap = new HashMap<String,CycleStats[]>();
-        cyclesByLaneMapOrig = new HashMap<String,CycleStats[]>();
+        cyclesByLaneMapOrig = new HashMap<String,CycleStats[]>();
-        cyclesByLibraryMapOrig = new HashMap<String,CycleStats[]>();
+        cyclesByLibraryMapOrig = new HashMap<String,CycleStats[]>();
-    }
+    }
-
+
-
+
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
-
+
-        if ( AlignmentUtils.isReadUnmapped(read) ) return 0;
+        if ( AlignmentUtils.isReadUnmapped(read) ) return 0;
-
+
-        SAMReadGroupRecord rg = read.getReadGroup();
+        SAMReadGroupRecord rg = read.getReadGroup();
-
+
-        if ( rg == null ) throw new UserException.ReadMissingReadGroup(read);
+        if ( rg == null ) throw new UserException.ReadMissingReadGroup(read);
-
+
-        String lane = read.getReadGroup().getPlatformUnit();
+        String lane = read.getReadGroup().getPlatformUnit();
-        String library = read.getReadGroup().getLibrary();
+        String library = read.getReadGroup().getLibrary();
-
+
-        if ( lane == null ) throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has no platform unit information");
+        if ( lane == null ) throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has no platform unit information");
-        if ( library == null ) throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has no library information");
+        if ( library == null ) throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has no library information");
-
+
-        int end = 0;
+        int end = 0;
-
+
-        if ( read.getReadPairedFlag() ) {
+        if ( read.getReadPairedFlag() ) {
-
+
-            if ( read.getFirstOfPairFlag() ) {
+            if ( read.getFirstOfPairFlag() ) {
-                if ( read.getSecondOfPairFlag() )
+                if ( read.getSecondOfPairFlag() )
-                    throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes");
+                    throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes");
-                end = 1;
+                end = 1;
-            } else {
+            } else {
-                if ( ! read.getSecondOfPairFlag() )
+                if ( ! read.getSecondOfPairFlag() )
-                    throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes");
+                    throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes");
-                end = 2;
+                end = 2;
-            }
+            }
-        }
+        }
-
+
-        CycleStats[] byLane = cyclesByLaneMap.get(lane);
+        CycleStats[] byLane = cyclesByLaneMap.get(lane);
-        CycleStats[] byLib = cyclesByLibraryMap.get(library);
+        CycleStats[] byLib = cyclesByLibraryMap.get(library);
-
+
-        //byte [] quals = USE_ORIGINAL_QUALS ? AlignmentUtils.getOriginalQualsInCycleOrder(read) : AlignmentUtils.getQualsInCycleOrder(read);
+        //byte [] quals = USE_ORIGINAL_QUALS ? AlignmentUtils.getOriginalQualsInCycleOrder(read) : AlignmentUtils.getQualsInCycleOrder(read);
-
+
-        byte [] quals = AlignmentUtils.getQualsInCycleOrder(read);
+        byte [] quals = AlignmentUtils.getQualsInCycleOrder(read);
-
+
-        // if end == 0 (single end lane), we allocate array of length 1, otherwise we need two
+        // if end == 0 (single end lane), we allocate array of length 1, otherwise we need two
-        // elements in the array in order to be able to collect statistics for each end in the pair independently
+        // elements in the array in order to be able to collect statistics for each end in the pair independently
-        if ( byLane == null ) cyclesByLaneMap.put(lane,byLane = new CycleStats[(end==0?1:2)]);
+        if ( byLane == null ) cyclesByLaneMap.put(lane,byLane = new CycleStats[(end==0?1:2)]);
-        if ( byLib == null ) cyclesByLibraryMap.put(library, byLib =new CycleStats[2]);
+        if ( byLib == null ) cyclesByLibraryMap.put(library, byLib =new CycleStats[2]);
-
+
-        if ( end != 0 ) end--; // we will now use 'end' as index into the array of stats
+        if ( end != 0 ) end--; // we will now use 'end' as index into the array of stats
-
+
-        if ( byLane[end] == null ) byLane[end] = new CycleStats(MAX_READ_LENGTH);
+        if ( byLane[end] == null ) byLane[end] = new CycleStats(MAX_READ_LENGTH);
-        if ( byLib[end] == null ) byLib[end] =new CycleStats(MAX_READ_LENGTH);
+        if ( byLib[end] == null ) byLib[end] =new CycleStats(MAX_READ_LENGTH);
-        byLane[end].add(quals);
+        byLane[end].add(quals);
-        byLib[end].add(quals);
+        byLib[end].add(quals);
-
+
-        return 1;  //To change body of implemented methods use File | Settings | File Templates.
+        return 1;  //To change body of implemented methods use File | Settings | File Templates.
-    }
+    }
-
+
-    /**
+    /**
-     * Provide an initial value for reduce computations.
+     * Provide an initial value for reduce computations.
-     *
+     *
-     * @return Initial value of reduce.
+     * @return Initial value of reduce.
-     */
+     */
-    public Integer reduceInit() {
+    public Integer reduceInit() {
-        return 0;  //To change body of implemented methods use File | Settings | File Templates.
+        return 0;  //To change body of implemented methods use File | Settings | File Templates.
-    }
+    }
-
+
-    /**
+    /**
-     * Reduces a single map with the accumulator provided as the ReduceType.
+     * Reduces a single map with the accumulator provided as the ReduceType.
-     *
+     *
-     * @param value result of the map.
+     * @param value result of the map.
-     * @param sum   accumulator for the reduce.
+     * @param sum   accumulator for the reduce.
-     * @return accumulator with result of the map taken into account.
+     * @return accumulator with result of the map taken into account.
-     */
+     */
-    public Integer reduce(Integer value, Integer sum) {
+    public Integer reduce(Integer value, Integer sum) {
-        return sum.intValue()+value.intValue();  //To change body of implemented methods use File | Settings | File Templates.
+        return sum.intValue()+value.intValue();  //To change body of implemented methods use File | Settings | File Templates.
-    }
+    }
-
+
-    public void onTraversalDone(Integer result) {
+    public void onTraversalDone(Integer result) {
-        if ( HTML ) {
+        if ( HTML ) {
-            out.println("<h3>Cycle Quality QC</h3>\n");
+            out.println("<h3>Cycle Quality QC</h3>\n");
-            out.println("File(s) analyzed: <br>");
+            out.println("File(s) analyzed: <br>");
-            for ( String fileName : getToolkit().getArguments().samFiles) out.println(fileName+"<br>");
+            for ( String fileName : getToolkit().getArguments().samFiles) out.println(fileName+"<br>");
-            out.println("<br>");
+            out.println("<br>");
-        }
+        }
-        if ( HTML ) out.println("<br><br>");
+        if ( HTML ) out.println("<br><br>");
-        out.println("\n"+result+" reads analyzed\n");
+        out.println("\n"+result+" reads analyzed\n");
-        if ( HTML ) out.println("<br><br>");
+        if ( HTML ) out.println("<br><br>");
-        out.println("by platform unit:");
+        out.println("by platform unit:");
-        if ( HTML ) out.println("<br>");
+        if ( HTML ) out.println("<br>");
-        report2(cyclesByLaneMap, new File(PREFIX+".byLane.txt"),true);
+        report2(cyclesByLaneMap, new File(PREFIX+".byLane.txt"),true);
-        out.println();
+        out.println();
-        if ( HTML ) out.println("<br><br>");
+        if ( HTML ) out.println("<br><br>");
-        out.println("\nby library:");
+        out.println("\nby library:");
-        if ( HTML ) out.println("<br>");
+        if ( HTML ) out.println("<br>");
-        report2(cyclesByLibraryMap, new File(PREFIX+".byLibrary.txt"),true);
+        report2(cyclesByLibraryMap, new File(PREFIX+".byLibrary.txt"),true);
-        out.println();
+        out.println();
-        if ( HTML ) out.println("<br><br>");
+        if ( HTML ) out.println("<br><br>");
-    }
+    }
-
+
- 
+ 
-
+
-    private void report2(Map<String,CycleStats[]> m, File f,boolean summaryReport) {
+    private void report2(Map<String,CycleStats[]> m, File f,boolean summaryReport) {
-        long totalReads_1 =0;
+        long totalReads_1 =0;
-        long totalReads_2 =0;
+        long totalReads_2 =0;
-        long totalReads_unpaired = 0;
+        long totalReads_unpaired = 0;
-        SortedSet<String> columns = new TreeSet<String>();
+        SortedSet<String> columns = new TreeSet<String>();
-        int maxLength = 0; // maximum read length across all lanes/read ends analyzed
+        int maxLength = 0; // maximum read length across all lanes/read ends analyzed
-
+
-        for( Map.Entry<String,CycleStats[]> e : m.entrySet() ) {
+        for( Map.Entry<String,CycleStats[]> e : m.entrySet() ) {
-            if ( e.getValue()[0].getMaxReadLength() > maxLength ) maxLength = e.getValue()[0].getMaxReadLength();
+            if ( e.getValue()[0].getMaxReadLength() > maxLength ) maxLength = e.getValue()[0].getMaxReadLength();
-
+
-            if ( e.getValue().length == 1 || e.getValue().length == 2 && e.getValue()[1] == null ) {
+            if ( e.getValue().length == 1 || e.getValue().length == 2 && e.getValue()[1] == null ) {
-                totalReads_unpaired += e.getValue()[0].getReadCount(); // single end lane
+                totalReads_unpaired += e.getValue()[0].getReadCount(); // single end lane
-            } else {
+            } else {
-                totalReads_1 += e.getValue()[0].getReadCount();
+                totalReads_1 += e.getValue()[0].getReadCount();
-                totalReads_2 += e.getValue()[1].getReadCount();
+                totalReads_2 += e.getValue()[1].getReadCount();
-                if ( e.getValue()[1].getMaxReadLength() > maxLength ) maxLength = e.getValue()[1].getMaxReadLength();
+                if ( e.getValue()[1].getMaxReadLength() > maxLength ) maxLength = e.getValue()[1].getMaxReadLength();
-            }
+            }
-
+
-            columns.add(e.getKey());
+            columns.add(e.getKey());
-        }
+        }
-
+
-        if ( summaryReport ) {
+        if ( summaryReport ) {
-            if ( totalReads_1 == 0 && totalReads_2 != 0) {
+            if ( totalReads_1 == 0 && totalReads_2 != 0) {
-                out.println("   End 1: No reads");
+                out.println("   End 1: No reads");
-                if ( HTML ) out.println("<br>");
+                if ( HTML ) out.println("<br>");
-            }
+            }
-            if ( totalReads_2 == 0 && totalReads_1 != 0 ) {
+            if ( totalReads_2 == 0 && totalReads_1 != 0 ) {
-                out.println("   End 2: No reads");
+                out.println("   End 2: No reads");
-                if ( HTML ) out.println("<br>");
+                if ( HTML ) out.println("<br>");
-            }
+            }
-            if ( totalReads_1 == 0 && totalReads_2 == 0 && totalReads_unpaired == 0 ) {
+            if ( totalReads_1 == 0 && totalReads_2 == 0 && totalReads_unpaired == 0 ) {
-                out.println("   No reads found.");
+                out.println("   No reads found.");
-                if ( HTML ) out.println("<br>");
+                if ( HTML ) out.println("<br>");
-            }
+            }
-        }
+        }
-
+
-        if ( totalReads_1 == 0 && totalReads_2 == 0 && totalReads_unpaired == 0 ) return;
+        if ( totalReads_1 == 0 && totalReads_2 == 0 && totalReads_unpaired == 0 ) return;
-
+
-        try {
+        try {
-            BufferedWriter w = new BufferedWriter(new FileWriter(f));
+            BufferedWriter w = new BufferedWriter(new FileWriter(f));
-
+
-            w.write("cycle");
+            w.write("cycle");
-
+
-            for( String col : columns ) {
+            for( String col : columns ) {
-                CycleStats[] data = m.get(col);
+                CycleStats[] data = m.get(col);
-                if ( summaryReport ) {
+                if ( summaryReport ) {
-                    out.print("   ");
+                    out.print("   ");
-                    out.print(col);
+                    out.print(col);
-                }
+                }
-
+
-                CycleStats end1 = data[0];
+                CycleStats end1 = data[0];
-                int minL = ( end1 == null ? 0 : end1.getMinReadLength() );
+                int minL = ( end1 == null ? 0 : end1.getMinReadLength() );
-                int maxL = ( end1 == null ? 0 : end1.getMaxReadLength() );
+                int maxL = ( end1 == null ? 0 : end1.getMaxReadLength() );
-
+
-                if ( data.length == 2 && data[1] != null ) {
+                if ( data.length == 2 && data[1] != null ) {
-                    if ( summaryReport ) {
+                    if ( summaryReport ) {
-                        out.println(": paired");
+                        out.println(": paired");
-                        if ( HTML ) out.println("<br>");
+                        if ( HTML ) out.println("<br>");
-                        out.println("    Reads analyzed:");
+                        out.println("    Reads analyzed:");
-                        if ( HTML ) out.println("<br>");
+                        if ( HTML ) out.println("<br>");
-                    }
+                    }
-                    CycleStats end2 = data[1];
+                    CycleStats end2 = data[1];
-
+
-                    out.print( "      End 1: "+ ( end1 == null ? 0 : end1.getReadCount()) );
+                    out.print( "      End 1: "+ ( end1 == null ? 0 : end1.getReadCount()) );
-                    if ( minL == maxL ) out.println("; read length = "+minL);
+                    if ( minL == maxL ) out.println("; read length = "+minL);
-                    else out.println("; WARNING: variable read length = "+minL+"-"+maxL);
+                    else out.println("; WARNING: variable read length = "+minL+"-"+maxL);
-                    if ( HTML ) out.println("<br>");
+                    if ( HTML ) out.println("<br>");
-
+
-                    out.print( "      End 2: "+ ( end2 == null ? 0 : end2.getReadCount()) );
+                    out.print( "      End 2: "+ ( end2 == null ? 0 : end2.getReadCount()) );
-                    minL = ( end2 == null ? 0 : end2.getMinReadLength() );
+                    minL = ( end2 == null ? 0 : end2.getMinReadLength() );
-                    maxL = ( end2 == null ? 0 : end2.getMaxReadLength() );
+                    maxL = ( end2 == null ? 0 : end2.getMaxReadLength() );
-                    if ( minL == maxL ) out.println("; read length = "+minL);
+                    if ( minL == maxL ) out.println("; read length = "+minL);
-                    else out.println("; WARNING: variable read length = "+minL+"-"+maxL);
+                    else out.println("; WARNING: variable read length = "+minL+"-"+maxL);
-                    if ( HTML ) out.println("<br>");
+                    if ( HTML ) out.println("<br>");
-                }
+                }
-                else {
+                else {
-                    out.println(": unpaired");
+                    out.println(": unpaired");
-                    if ( HTML ) out.println("<br>");
+                    if ( HTML ) out.println("<br>");
-                    out.print( "      Reads analyzed: "+ ( end1 == null ? 0 : end1.getReadCount()) );
+                    out.print( "      Reads analyzed: "+ ( end1 == null ? 0 : end1.getReadCount()) );
-                    if ( minL == maxL ) out.println("; read length = "+minL);
+                    if ( minL == maxL ) out.println("; read length = "+minL);
-                    else out.println("; WARNING: variable read length = "+minL+"-"+maxL);
+                    else out.println("; WARNING: variable read length = "+minL+"-"+maxL);
-                    if ( HTML ) out.println("<br>");
+                    if ( HTML ) out.println("<br>");
-                }
+                }
-
+
-                w.write('\t') ;
+                w.write('\t') ;
-                w.write(col);
+                w.write(col);
-                if ( data.length == 1 || data.length == 2 && data[1] == null ) {
+                if ( data.length == 1 || data.length == 2 && data[1] == null ) {
-                    w.write(".unpaired");
+                    w.write(".unpaired");
-                    w.write('\t');
+                    w.write('\t');
-                    w.write(col);
+                    w.write(col);
-                    w.write(".unpaired.stddev");
+                    w.write(".unpaired.stddev");
-                }  else {
+                }  else {
-                    w.write(".end1");
+                    w.write(".end1");
-                    w.write('\t');
+                    w.write('\t');
-                    w.write(col);
+                    w.write(col);
-                    w.write(".end1.stddev");
+                    w.write(".end1.stddev");
-                    w.write('\t') ;
+                    w.write('\t') ;
-                    w.write(col);
+                    w.write(col);
-                    w.write(".end2");
+                    w.write(".end2");
-                    w.write('\t');
+                    w.write('\t');
-                    w.write(col);
+                    w.write(col);
-                    w.write(".end2.stddev");
+                    w.write(".end2.stddev");
-                }
+                }
-            }
+            }
-
+
-            w.write('\n');
+            w.write('\n');
-
+
-            int cycle = 0;
+            int cycle = 0;
-
+
-            Map<String,List<PrimitivePair.Int>> problems = new HashMap<String,List<PrimitivePair.Int>>();
+            Map<String,List<PrimitivePair.Int>> problems = new HashMap<String,List<PrimitivePair.Int>>();
-
+
-            while ( cycle < maxLength ) {
+            while ( cycle < maxLength ) {
-                w.write(Integer.toString(cycle+1));
+                w.write(Integer.toString(cycle+1));
-                for ( String col : columns ) {
+                for ( String col : columns ) {
-
+
-                    CycleStats[] data = m.get(col);
+                    CycleStats[] data = m.get(col);
-                    CycleStats end1 = data[0];
+                    CycleStats end1 = data[0];
-                    w.write('\t');
+                    w.write('\t');
-                    if ( end1 == null || cycle >= end1.getMaxReadLength() ) w.write(".\t.");
+                    if ( end1 == null || cycle >= end1.getMaxReadLength() ) w.write(".\t.");
-                    else {
+                    else {
-                        double aq = end1.getCycleQualAverage(cycle);
+                        double aq = end1.getCycleQualAverage(cycle);
-                        w.write(String.format("%.4f\t%.4f",aq,end1.getCycleQualStdDev(cycle)));
+                        w.write(String.format("%.4f\t%.4f",aq,end1.getCycleQualStdDev(cycle)));
-                        recordProblem(aq,cycle, problems,col+".End1");
+                        recordProblem(aq,cycle, problems,col+".End1");
-                    }
+                    }
-                    if ( data.length > 1 && data[1] != null ) {
+                    if ( data.length > 1 && data[1] != null ) {
-                        w.write('\t');
+                        w.write('\t');
-                        CycleStats end2 = data[1];
+                        CycleStats end2 = data[1];
-                        if ( end2 == null || cycle >= end2.getMaxReadLength() ) w.write(".\t.");
+                        if ( end2 == null || cycle >= end2.getMaxReadLength() ) w.write(".\t.");
-                        else {
+                        else {
-                            double aq = end2.getCycleQualAverage(cycle);
+                            double aq = end2.getCycleQualAverage(cycle);
-                            w.write(String.format("%.4f\t%.4f",aq,end2.getCycleQualStdDev(cycle)));
+                            w.write(String.format("%.4f\t%.4f",aq,end2.getCycleQualStdDev(cycle)));
-                            recordProblem(aq,cycle, problems,col+".End2");
+                            recordProblem(aq,cycle, problems,col+".End2");
-                        }
+                        }
-                    }
+                    }
-                }
+                }
-                w.write('\n');
+                w.write('\n');
-                cycle++;
+                cycle++;
-            }
+            }
-            w.close();
+            w.close();
-
+
-            if ( HTML ) out.println("<hr>");
+            if ( HTML ) out.println("<hr>");
-
+
-            if ( HTML ) out.println("<br>");
+            if ( HTML ) out.println("<br>");
-            out.println("\nOUTCOME (threshold at Q="+QTHRESHOLD+"):");
+            out.println("\nOUTCOME (threshold at Q="+QTHRESHOLD+"):");
-            if ( HTML ) out.println("<br>");
+            if ( HTML ) out.println("<br>");
-            for ( String col : columns ) {
+            for ( String col : columns ) {
-                List<PrimitivePair.Int> lp = problems.get(col+".End1");
+                List<PrimitivePair.Int> lp = problems.get(col+".End1");
-                out.print("  "+col+" End1:");
+                out.print("  "+col+" End1:");
-                if ( lp == null ) {
+                if ( lp == null ) {
-                    out.print(" GOOD");
+                    out.print(" GOOD");
-                } else {
+                } else {
-                    for ( PrimitivePair.Int p : lp ) {
+                    for ( PrimitivePair.Int p : lp ) {
-                        out.print(" "+(p.first+1)+"-");
+                        out.print(" "+(p.first+1)+"-");
-                        if ( p.second >= 0 ) out.print((p.second+1));
+                        if ( p.second >= 0 ) out.print((p.second+1));
-                        else out.print("END");
+                        else out.print("END");
-                    }
+                    }
-                }
+                }
-                out.println();
+                out.println();
-                if ( HTML ) out.println("<br>");
+                if ( HTML ) out.println("<br>");
-
+
-                lp = problems.get(col+".End2");
+                lp = problems.get(col+".End2");
-                out.print("  "+col+" End2:");
+                out.print("  "+col+" End2:");
-                if ( lp == null ) {
+                if ( lp == null ) {
-                    out.print(" GOOD");
+                    out.print(" GOOD");
-                } else {
+                } else {
-                    for ( PrimitivePair.Int p : lp ) {
+                    for ( PrimitivePair.Int p : lp ) {
-                        out.print(" "+(p.first+1)+"-");
+                        out.print(" "+(p.first+1)+"-");
-                        if ( p.second >= 0 ) out.print(p.second);
+                        if ( p.second >= 0 ) out.print(p.second);
-                        else out.print("END");
+                        else out.print("END");
-                    }
+                    }
-                }
+                }
-                out.println();
+                out.println();
-                if ( HTML ) out.println("<br>");
+                if ( HTML ) out.println("<br>");
-            }
+            }
-
+
-        } catch (IOException ioe) {
+        } catch (IOException ioe) {
-            throw new UserException.CouldNotCreateOutputFile(f, "Failed to write report", ioe);
+            throw new UserException.CouldNotCreateOutputFile(f, "Failed to write report", ioe);
-        }
+        }
-    }
+    }
-
+
-
+
-    private void recordProblem(double q, int cycle, Map<String,List<PrimitivePair.Int>> problems, String name) {
+    private void recordProblem(double q, int cycle, Map<String,List<PrimitivePair.Int>> problems, String name) {
-
+
-        PrimitivePair.Int p = null;
+        PrimitivePair.Int p = null;
-        List<PrimitivePair.Int> lp = null;
+        List<PrimitivePair.Int> lp = null;
-        if ( q < QTHRESHOLD ) { // there is a problem
+        if ( q < QTHRESHOLD ) { // there is a problem
-               if ( ! problems.containsKey(name) ) {
+               if ( ! problems.containsKey(name) ) {
-                   lp = new ArrayList<PrimitivePair.Int>();
+                   lp = new ArrayList<PrimitivePair.Int>();
-                   p = new PrimitivePair.Int(cycle,-1);
+                   p = new PrimitivePair.Int(cycle,-1);
-                   lp.add(p);
+                   lp.add(p);
-                   problems.put(name,lp);
+                   problems.put(name,lp);
-               } else {
+               } else {
-                   lp = problems.get(name);
+                   lp = problems.get(name);
-                   p = lp.get(lp.size()-1);
+                   p = lp.get(lp.size()-1);
-               }
+               }
-               if ( p.second != -1 ) { // if we are not already inside a run of bad qual bases
+               if ( p.second != -1 ) { // if we are not already inside a run of bad qual bases
-                   lp.add(new PrimitivePair.Int(cycle,-1)); // start new run
+                   lp.add(new PrimitivePair.Int(cycle,-1)); // start new run
-               }
+               }
-        } else { // good base
+        } else { // good base
-              if ( problems.containsKey(name) ) { // only if we had problem intervals at all, we need to check if the last one needs to be closed
+              if ( problems.containsKey(name) ) { // only if we had problem intervals at all, we need to check if the last one needs to be closed
-                  lp = problems.get(name);
+                  lp = problems.get(name);
-                  p = lp.get(lp.size()-1);
+                  p = lp.get(lp.size()-1);
-                  if ( p.second == -1 ) p.second = cycle - 1;
+                  if ( p.second == -1 ) p.second = cycle - 1;
-              }
+              }
-        }
+        }
-    }
+    }
-
+
-
+
-    static class CycleStats {
+    static class CycleStats {
-        private long readCount = 0;
+        private long readCount = 0;
-        private double[] cycleQualsAv = null;
+        private double[] cycleQualsAv = null;
-        private double[] cycleQualsSd = null;
+        private double[] cycleQualsSd = null;
-        private int minL = 1000000000; // read min. length
+        private int minL = 1000000000; // read min. length
-        private int maxL = 0; // read max. length
+        private int maxL = 0; // read max. length
-
+
-        public CycleStats(int N) {
+        public CycleStats(int N) {
-            readCount = 0;
+            readCount = 0;
-            cycleQualsAv = new double[N];
+            cycleQualsAv = new double[N];
-            cycleQualsSd = new double[N];
+            cycleQualsSd = new double[N];
-        }
+        }
-
+
-        public void add(byte[] quals) {
+        public void add(byte[] quals) {
-            if ( quals.length > cycleQualsAv.length )
+            if ( quals.length > cycleQualsAv.length )
-                throw new UserException("A read of length "+quals.length+" encountered, which exceeds specified maximum read length");
+                throw new UserException("A read of length "+quals.length+" encountered, which exceeds specified maximum read length");
-            if ( quals.length > maxL ) maxL = quals.length;
+            if ( quals.length > maxL ) maxL = quals.length;
-            if ( quals.length < minL ) minL = quals.length;
+            if ( quals.length < minL ) minL = quals.length;
-            readCount++;
+            readCount++;
-            for ( int i = 0 ; i < quals.length ; i++ ) {
+            for ( int i = 0 ; i < quals.length ; i++ ) {
-                // NOTE: in the update equaltions below, there is no need to check if readCount == 1 (i.e.
+                // NOTE: in the update equaltions below, there is no need to check if readCount == 1 (i.e.
-                // we are initializing with the very first record) or not. Indeed, the arrays are initialized with
+                // we are initializing with the very first record) or not. Indeed, the arrays are initialized with
-                // 0; when the very first value arrives, readCount is 1 and cycleQuals[i] gets set to quals[i] (correct!);
+                // 0; when the very first value arrives, readCount is 1 and cycleQuals[i] gets set to quals[i] (correct!);
-                // this will also make the second term in the update equation for Sd (quals[i]-cycleQualsAv[i]) equal
+                // this will also make the second term in the update equation for Sd (quals[i]-cycleQualsAv[i]) equal
-                // to 0, so Sd will be initially set to 0.
+                // to 0, so Sd will be initially set to 0.
-                double oldAvg = cycleQualsAv[i]; // save old mean, will need it for calculation of the variance
+                double oldAvg = cycleQualsAv[i]; // save old mean, will need it for calculation of the variance
-                cycleQualsAv[i] += ( quals[i] - cycleQualsAv[i] ) / readCount; // update mean
+                cycleQualsAv[i] += ( quals[i] - cycleQualsAv[i] ) / readCount; // update mean
-                cycleQualsSd[i] += ( quals[i] - oldAvg ) * ( quals[i] - cycleQualsAv[i] );
+                cycleQualsSd[i] += ( quals[i] - oldAvg ) * ( quals[i] - cycleQualsAv[i] );
-            }
+            }
-        }
+        }
-
+
-        public long getReadCount() { return readCount; }
+        public long getReadCount() { return readCount; }
-        public int getMaxReadLength() { return maxL; }
+        public int getMaxReadLength() { return maxL; }
-        public int getMinReadLength() { return minL; }
+        public int getMinReadLength() { return minL; }
-//        long [] getCycleQualSums() { return cycleQuals; }
+//        long [] getCycleQualSums() { return cycleQuals; }
-//        long getCycleQualSum(int i) { return cycleQuals[i]; }
+//        long getCycleQualSum(int i) { return cycleQuals[i]; }
-        double getCycleQualAverage(int i) { return cycleQualsAv[i]; }
+        double getCycleQualAverage(int i) { return cycleQualsAv[i]; }
-        double getCycleQualStdDev(int i) { return Math.sqrt( cycleQualsSd[i]/(readCount-1) ); }
+        double getCycleQualStdDev(int i) { return Math.sqrt( cycleQualsSd[i]/(readCount-1) ); }
-    }
+    }
-}
+}

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java

@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.util.Arrays;
@@ -40,7 +40,7 @@ public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integ
         return lhs + rhs;
     }
 
-    private String[] getReadNames( List<SAMRecord> reads ) {
+    private String[] getReadNames( List<GATKSAMRecord> reads ) {
         String[] readNames = new String[ reads.size() ];
         for( int i = 0; i < reads.size(); i++ ) {
             readNames[i] = String.format("%nname = %s, start = %d, end = %d", reads.get(i).getReadName(), reads.get(i).getAlignmentStart(), reads.get(i).getAlignmentEnd());

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java

@@ -1,142 +1,142 @@
-/*
+/*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2009 The Broad Institute
- *  Permission is hereby granted, free of charge, to any person
+ *  Permission is hereby granted, free of charge, to any person
- *  obtaining a copy of this software and associated documentation
+ *  obtaining a copy of this software and associated documentation
- *  files (the "Software"), to deal in the Software without
+ *  files (the "Software"), to deal in the Software without
- *  restriction, including without limitation the rights to use,
+ *  restriction, including without limitation the rights to use,
- *  copy, modify, merge, publish, distribute, sublicense, and/or sell
+ *  copy, modify, merge, publish, distribute, sublicense, and/or sell
- *  copies of the Software, and to permit persons to whom the
+ *  copies of the Software, and to permit persons to whom the
- *  Software is furnished to do so, subject to the following
+ *  Software is furnished to do so, subject to the following
- *  conditions:
+ *  conditions:
- *  The above copyright notice and this permission notice shall be
+ *  The above copyright notice and this permission notice shall be
- *  included in all copies or substantial portions of the Software.
+ *  included in all copies or substantial portions of the Software.
- *  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ *  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- *  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ *  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- *  OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ *  OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- *  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ *  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- *  HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ *  HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- *  WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ *  WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- *  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ *  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- *  * OTHER DEALINGS IN THE SOFTWARE.
+ *  * OTHER DEALINGS IN THE SOFTWARE.
- */
+ */
-
+
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.sting.gatk.walkers.qc;
-
+
-import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
+import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
+
-import java.io.PrintStream;
+import java.io.PrintStream;
-import java.util.Arrays;
+import java.util.Arrays;
-
+
-/**
+/**
- * User: depristo
+ * User: depristo
- * Date: May 5, 2010
+ * Date: May 5, 2010
- * Time: 12:16:41 PM
+ * Time: 12:16:41 PM
- */
+ */
-
+
-/**
+/**
- * Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
+ * Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
- * of the clipping to the output stream.
+ * of the clipping to the output stream.
- */
+ */
-@Requires({DataSource.READS})
+@Requires({DataSource.READS})
-public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.ReadClippingInfo,Integer> {
+public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.ReadClippingInfo,Integer> {
-    @Output
+    @Output
-    protected PrintStream out;
+    protected PrintStream out;
-
+
-    @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
+    @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
-                "on mapped reads only, while unmapped reads will be discarded", required=false)
+                "on mapped reads only, while unmapped reads will be discarded", required=false)
-    protected boolean MAPPED_ONLY = true;
+    protected boolean MAPPED_ONLY = true;
-
+
-    @Argument(fullName="skip", shortName="skip", doc="When provided, only every skip reads are analyzed", required=false)
+    @Argument(fullName="skip", shortName="skip", doc="When provided, only every skip reads are analyzed", required=false)
-    protected int SKIP = 1;
+    protected int SKIP = 1;
-
+
-//    public void initialize() {
+//    public void initialize() {
-//
+//
-//    }
+//    }
-
+
-    public class ReadClippingInfo {
+    public class ReadClippingInfo {
-        SAMReadGroupRecord rg;
+        SAMReadGroupRecord rg;
-        int readLength, nClippingEvents, nClippedBases;
+        int readLength, nClippingEvents, nClippedBases;
-    }
+    }
-
+
-    public ReadClippingInfo map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public ReadClippingInfo map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
-        if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
+        if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
-            return null;
+            return null;
-
+
-        ReadClippingInfo info = new ReadClippingInfo();
+        ReadClippingInfo info = new ReadClippingInfo();
-        info.rg = read.getReadGroup();
+        info.rg = read.getReadGroup();
-
+
-        if ( info.rg == null ) throw new UserException.ReadMissingReadGroup(read);
+        if ( info.rg == null ) throw new UserException.ReadMissingReadGroup(read);
-
+
-        for ( CigarElement elt : read.getCigar().getCigarElements() ) {
+        for ( CigarElement elt : read.getCigar().getCigarElements() ) {
-            if ( elt.getOperator() != CigarOperator.N )
+            if ( elt.getOperator() != CigarOperator.N )
-
+
-            switch ( elt.getOperator()) {
+            switch ( elt.getOperator()) {
-                case H : // ignore hard clips
+                case H : // ignore hard clips
-                case S : // soft clip
+                case S : // soft clip
-                    info.nClippingEvents++;
+                    info.nClippingEvents++;
-                    info.nClippedBases += elt.getLength();
+                    info.nClippedBases += elt.getLength();
-                    // note the fall through here
+                    // note the fall through here
-                case M :
+                case M :
-                case D : // deletion w.r.t. the reference
+                case D : // deletion w.r.t. the reference
-                case P : // ignore pads
+                case P : // ignore pads
-                case I : // insertion w.r.t. the reference
+                case I : // insertion w.r.t. the reference
-                    info.readLength += elt.getLength(); // Unless we have a reference skip, the read gets longer
+                    info.readLength += elt.getLength(); // Unless we have a reference skip, the read gets longer
-                    break;
+                    break;
-                case N : // reference skip (looks and gets processed just like a "deletion", just different logical meaning)
+                case N : // reference skip (looks and gets processed just like a "deletion", just different logical meaning)
-                    break;
+                    break;
-                default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + elt.getOperator());
+                default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + elt.getOperator());
-            }
+            }
-        }
+        }
-
+
-        return info;  //To change body of implemented methods use File | Settings | File Templates.
+        return info;  //To change body of implemented methods use File | Settings | File Templates.
-    }
+    }
-
+
-    /**
+    /**
-     * Provide an initial value for reduce computations.
+     * Provide an initial value for reduce computations.
-     *
+     *
-     * @return Initial value of reduce.
+     * @return Initial value of reduce.
-     */
+     */
-    public Integer reduceInit() {
+    public Integer reduceInit() {
-        out.println(Utils.join(" \t", Arrays.asList("ReadGroup", "ReadLength", "NClippingEvents", "NClippedBases", "PercentClipped")));
+        out.println(Utils.join(" \t", Arrays.asList("ReadGroup", "ReadLength", "NClippingEvents", "NClippedBases", "PercentClipped")));
-        return 0;
+        return 0;
-    }
+    }
-
+
-    /**
+    /**
-     * Reduces a single map with the accumulator provided as the ReduceType.
+     * Reduces a single map with the accumulator provided as the ReduceType.
-     *
+     *
-     * @param info  result of the map.
+     * @param info  result of the map.
-     * @param sum   accumulator for the reduce.
+     * @param sum   accumulator for the reduce.
-     * @return accumulator with result of the map taken into account.
+     * @return accumulator with result of the map taken into account.
-     */
+     */
-    public Integer reduce(ReadClippingInfo info, Integer sum) {
+    public Integer reduce(ReadClippingInfo info, Integer sum) {
-        if ( info != null ) {
+        if ( info != null ) {
-            if ( sum % SKIP == 0 ) {
+            if ( sum % SKIP == 0 ) {
-                String id = info.rg.getReadGroupId();
+                String id = info.rg.getReadGroupId();
-                out.printf("%s\t %d\t %d\t %d\t %.2f%n",
+                out.printf("%s\t %d\t %d\t %d\t %.2f%n",
-                        id, info.readLength, info.nClippingEvents, info.nClippedBases,
+                        id, info.readLength, info.nClippingEvents, info.nClippedBases,
-                        100.0 * MathUtils.ratio(info.nClippedBases, info.readLength));
+                        100.0 * MathUtils.ratio(info.nClippedBases, info.readLength));
-            }
+            }
-            return sum + 1;  //To change body of implemented methods use File | Settings | File Templates.
+            return sum + 1;  //To change body of implemented methods use File | Settings | File Templates.
-        } else {
+        } else {
-            return sum;
+            return sum;
-        }
+        }
-    }
+    }
-
+
-    public void onTraversalDone(Integer result) {
+    public void onTraversalDone(Integer result) {
-
+
-    }
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
@@ -64,21 +65,23 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
 
     /**
      * The reads filter function.
+     *
      * @param ref the reference bases that correspond to our read, if a reference was provided
      * @param read the read itself, as a SAMRecord
      * @return true if the read passes the filter, false if it doesn't
      */
-    public boolean filter(ReferenceContext ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
         return true;
 	}
 
     /**
      * The reads map function.
+     *
      * @param ref the reference bases that correspond to our read, if a reference was provided
      * @param read the read itself, as a SAMRecord
      * @return the read itself
      */
-    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         return read;
     }
 

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

@@ -364,11 +364,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
     /**
      * For each base in the read calculate a new recalibrated quality score and replace the quality scores in the read
+     *
      * @param refBases References bases over the length of the read
      * @param read The read to be recalibrated
      * @return The read with quality scores replaced
      */
-    public SAMRecord map( ReferenceContext refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker  ) {
+    public SAMRecord map( ReferenceContext refBases, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker  ) {
 
         if( read.getReadLength() == 0 ) { // Some reads have '*' as the SEQ field and samtools returns length zero. We don't touch these reads.
             return read;

public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java

@@ -4,9 +4,9 @@ import com.google.java.contract.Requires;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
 import java.util.Stack;
@@ -39,14 +39,14 @@ public class ClippingOp {
      * @param algorithm
      * @param read
      */
-    public SAMRecord apply(ClippingRepresentation algorithm, SAMRecord read) {
+    public GATKSAMRecord apply(ClippingRepresentation algorithm, GATKSAMRecord read) {
         byte[] quals = read.getBaseQualities();
         byte[] bases = read.getReadBases();
 
         switch (algorithm) {
             // important note:
             //   it's not safe to call read.getReadBases()[i] = 'N' or read.getBaseQualities()[i] = 0
-            //   because you're not guaranteed to get a pointer to the actual array of bytes in the SAMRecord
+            //   because you're not guaranteed to get a pointer to the actual array of bytes in the GATKSAMRecord
             case WRITE_NS:
                 for (int i = start; i <= stop; i++)
                     bases[i] = 'N';
@@ -248,9 +248,9 @@ public class ClippingOp {
     }
 
     @Requires({"start <= stop", "start == 0 || stop == read.getReadLength() - 1", "!read.getReadUnmappedFlag()"})
-    private SAMRecord hardClip (SAMRecord read, int start, int stop) {
+    private GATKSAMRecord hardClip (GATKSAMRecord read, int start, int stop) {
         if (start == 0 && stop == read.getReadLength() - 1)
-            return new SAMRecord(read.getHeader());
+            return new GATKSAMRecord(read.getHeader());
 
         // If the read is unmapped there is no Cigar string and neither should we create a new cigar string
         CigarShift cigarShift = (read.getReadUnmappedFlag()) ? new CigarShift(new Cigar(), 0, 0) : hardClipCigar(read.getCigar(), start, stop);
@@ -265,9 +265,9 @@ public class ClippingOp {
         System.arraycopy(read.getReadBases(), copyStart, newBases, 0, newLength);
         System.arraycopy(read.getBaseQualities(), copyStart, newQuals, 0, newLength);
 
-        SAMRecord hardClippedRead;
+        GATKSAMRecord hardClippedRead;
         try {
-            hardClippedRead = (SAMRecord) read.clone();
+            hardClippedRead = (GATKSAMRecord) read.clone();
         } catch (CloneNotSupportedException e) {
             throw new ReviewedStingException("Where did the clone go?");
         }

public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java

@@ -3,8 +3,8 @@ package org.broadinstitute.sting.utils.clipreads;
 import com.google.java.contract.Requires;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.ArrayList;
@@ -14,7 +14,7 @@ import java.util.List;
  * A simple collection of the clipping operations to apply to a read along with its read
  */
 public class ReadClipper {
-    SAMRecord read;
+    GATKSAMRecord read;
     boolean wasClipped;
     List<ClippingOp> ops = null;
 
@@ -23,7 +23,7 @@ public class ReadClipper {
      *
      * @param read
      */
-    public ReadClipper(final SAMRecord read) {
+    public ReadClipper(final GATKSAMRecord read) {
         this.read = read;
         this.wasClipped = false;
     }
@@ -46,19 +46,19 @@ public class ReadClipper {
         return wasClipped;
     }
 
-    public SAMRecord getRead() {
+    public GATKSAMRecord getRead() {
         return read;
     }
 
-    public SAMRecord hardClipByReferenceCoordinatesLeftTail(int refStop) {
+    public GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(int refStop) {
         return hardClipByReferenceCoordinates(-1, refStop);
     }
 
-    public SAMRecord hardClipByReferenceCoordinatesRightTail(int refStart) {
+    public GATKSAMRecord hardClipByReferenceCoordinatesRightTail(int refStart) {
         return hardClipByReferenceCoordinates(refStart, -1);
     }
 
-    private int numDeletions(SAMRecord read) {
+    private int numDeletions(GATKSAMRecord read) {
         int result = 0;
         for (CigarElement e: read.getCigar().getCigarElements()) {
             if ( e.getOperator() == CigarOperator.DELETION || e.getOperator() == CigarOperator.D )
@@ -67,7 +67,7 @@ public class ReadClipper {
         return result;
     }
 
-    protected SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
+    protected GATKSAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
         int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL);
         int stop =  (refStop  < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ReadUtils.ClippingTail.LEFT_TAIL);
 
@@ -78,32 +78,32 @@ public class ReadClipper {
             throw new ReviewedStingException("START > STOP -- this should never happen -- call Mauricio!");
 
         this.addOp(new ClippingOp(start, stop));
-        SAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);
+        GATKSAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);
         this.ops = null;
         return clippedRead;
     }
 
-    public SAMRecord hardClipByReadCoordinates(int start, int stop) {
+    public GATKSAMRecord hardClipByReadCoordinates(int start, int stop) {
         this.addOp(new ClippingOp(start, stop));
         return clipRead(ClippingRepresentation.HARDCLIP_BASES);
     }
 
     @Requires("left <= right")
-    public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
+    public GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
         if (left == right)
-            return new SAMRecord(read.getHeader());
+            return new GATKSAMRecord(read.getHeader());
-        SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
+        GATKSAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
 
         // after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
         // make the left cut index no longer part of the read. In that case, clip the read entirely.
         if (left > leftTailRead.getAlignmentEnd())
-            return new SAMRecord(read.getHeader());
+            return new GATKSAMRecord(read.getHeader());
 
         ReadClipper clipper = new ReadClipper(leftTailRead);
         return clipper.hardClipByReferenceCoordinatesLeftTail(left);
     }
 
-    public SAMRecord hardClipLowQualEnds(byte lowQual) {
+    public GATKSAMRecord hardClipLowQualEnds(byte lowQual) {
         byte [] quals = read.getBaseQualities();
         int leftClipIndex = 0;
         int rightClipIndex = read.getReadLength() - 1;
@@ -114,7 +114,7 @@ public class ReadClipper {
 
         // if the entire read should be clipped, then return an empty read. (--todo: maybe null is better? testing this for now)
         if (leftClipIndex > rightClipIndex)
-            return (new SAMRecord(read.getHeader()));
+            return (new GATKSAMRecord(read.getHeader()));
 
         if (rightClipIndex < read.getReadLength() - 1) {
             this.addOp(new ClippingOp(rightClipIndex + 1, read.getReadLength() - 1));
@@ -125,7 +125,7 @@ public class ReadClipper {
         return this.clipRead(ClippingRepresentation.HARDCLIP_BASES);
     }
 
-    public SAMRecord hardClipSoftClippedBases () {
+    public GATKSAMRecord hardClipSoftClippedBases () {
         int readIndex = 0;
         int cutLeft = -1;            // first position to hard clip (inclusive)
         int cutRight = -1;           // first position to hard clip (inclusive)
@@ -164,12 +164,12 @@ public class ReadClipper {
      * @param algorithm
      * @return
      */
-    public SAMRecord clipRead(ClippingRepresentation algorithm) {
+    public GATKSAMRecord clipRead(ClippingRepresentation algorithm) {
         if (ops == null)
             return getRead();
         else {
             try {
-                SAMRecord clippedRead = (SAMRecord) read.clone();
+                GATKSAMRecord clippedRead = (GATKSAMRecord) read.clone();
                 for (ClippingOp op : getOps()) {
                     clippedRead = op.apply(algorithm, clippedRead);
                 }
@@ -181,7 +181,7 @@ public class ReadClipper {
         }
     }
 
-    public SAMRecord hardClipLeadingInsertions() {
+    public GATKSAMRecord hardClipLeadingInsertions() {
         for(CigarElement cigarElement : read.getCigar().getCigarElements()) {
             if (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP &&
                 cigarElement.getOperator() != CigarOperator.INSERTION && cigarElement.getOperator() != CigarOperator.DELETION)

public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.utils.duplicates;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -35,27 +34,28 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Arrays;
 import java.util.List;
 
 public class DupUtils {
-    private static SAMRecord tmpCopyRead(SAMRecord read) {
+    private static GATKSAMRecord tmpCopyRead(GATKSAMRecord read) {
         try {
-            return (SAMRecord)read.clone();
+            return (GATKSAMRecord)read.clone();
         } catch ( CloneNotSupportedException e ) {
             throw new ReviewedStingException("Unexpected Clone failure!");
         }
     }
 
-    public static SAMRecord combineDuplicates(GenomeLocParser genomeLocParser,List<SAMRecord> duplicates, int maxQScore) {
+    public static GATKSAMRecord combineDuplicates(GenomeLocParser genomeLocParser,List<GATKSAMRecord> duplicates, int maxQScore) {
         if ( duplicates.size() == 0 )
             return null;
 
         // make the combined read by copying the first read and setting the
         // bases and quals to new arrays
-        SAMRecord comb = tmpCopyRead(duplicates.get(0));
+        GATKSAMRecord comb = tmpCopyRead(duplicates.get(0));
-        //SAMRecord comb = tmpCopyRead(duplicates.get(0));
+        //GATKSAMRecord comb = tmpCopyRead(duplicates.get(0));
         comb.setDuplicateReadFlag(false);
         int readLen = comb.getReadBases().length;
         byte[] bases = new byte[readLen];
@@ -63,7 +63,7 @@ public class DupUtils {
 
         for ( int i = 0; i < readLen; i++ ) {
             //System.out.printf("I is %d%n", i);
-            //for ( SAMRecord read : duplicates ) {
+            //for ( GATKSAMRecord read : duplicates ) {
             //    System.out.printf("dup base %c %d%n", (char)read.getReadBases()[i], read.getBaseQualities()[i]);
             //}
             Pair<Byte, Byte> baseAndQual = combineBaseProbs(genomeLocParser,duplicates, i, maxQScore);
@@ -117,7 +117,7 @@ public class DupUtils {
         System.out.printf("%n");
     }
 
-    private static Pair<Byte, Byte> combineBaseProbs(GenomeLocParser genomeLocParser,List<SAMRecord> duplicates, int readOffset, int maxQScore) {
+    private static Pair<Byte, Byte> combineBaseProbs(GenomeLocParser genomeLocParser,List<GATKSAMRecord> duplicates, int readOffset, int maxQScore) {
         GenomeLoc loc = genomeLocParser.createGenomeLoc(duplicates.get(0));
         ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, duplicates, readOffset);
 

public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.fragments;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.*;
 
@@ -35,17 +36,17 @@ public class FragmentUtils {
      * @param <T>
      */
     public interface ReadGetter<T> {
-        public SAMRecord get(T object);
+        public GATKSAMRecord get(T object);
     }
 
     /** Identify getter for SAMRecords themselves */
-    private final static ReadGetter<SAMRecord> SamRecordGetter = new ReadGetter<SAMRecord>() {
+    private final static ReadGetter<GATKSAMRecord> SamRecordGetter = new ReadGetter<GATKSAMRecord>() {
-        @Override public SAMRecord get(final SAMRecord object) { return object; }
+        @Override public GATKSAMRecord get(final GATKSAMRecord object) { return object; }
     };
 
     /** Gets the SAMRecord in a PileupElement */
     private final static ReadGetter<PileupElement> PileupElementGetter = new ReadGetter<PileupElement>() {
-        @Override public SAMRecord get(final PileupElement object) { return object.getRead(); }
+        @Override public GATKSAMRecord get(final PileupElement object) { return object.getRead(); }
     };
 
 
@@ -116,7 +117,7 @@ public class FragmentUtils {
         return create(rbp, rbp.getNumberOfElements(), PileupElementGetter);
     }
 
-    public final static FragmentCollection<SAMRecord> create(List<SAMRecord> reads) {
+    public final static FragmentCollection<GATKSAMRecord> create(List<GATKSAMRecord> reads) {
         return create(reads, reads.size(), SamRecordGetter);
     }
 

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

@@ -24,13 +24,13 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
 import org.broadinstitute.sting.utils.fragments.FragmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.*;
 
@@ -59,12 +59,12 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @param reads
      * @param offsets
      */
-    public AbstractReadBackedPileup(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets ) {
+    public AbstractReadBackedPileup(GenomeLoc loc, List<GATKSAMRecord> reads, List<Integer> offsets ) {
         this.loc = loc;
         this.pileupElementTracker = readsOffsets2Pileup(reads,offsets);
     }
 
-    public AbstractReadBackedPileup(GenomeLoc loc, List<SAMRecord> reads, int offset ) {
+    public AbstractReadBackedPileup(GenomeLoc loc, List<GATKSAMRecord> reads, int offset ) {
         this.loc = loc;
         this.pileupElementTracker = readsOffsets2Pileup(reads,offset);
     }
@@ -167,7 +167,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @param offsets
      * @return
      */
-    private PileupElementTracker<PE> readsOffsets2Pileup(List<SAMRecord> reads, List<Integer> offsets ) {
+    private PileupElementTracker<PE> readsOffsets2Pileup(List<GATKSAMRecord> reads, List<Integer> offsets ) {
         if ( reads == null ) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup");
         if ( offsets == null ) throw new ReviewedStingException("Illegal null offsets list in UnifiedReadBackedPileup");
         if ( reads.size() != offsets.size() ) throw new ReviewedStingException("Reads and offset lists have different sizes!");
@@ -187,7 +187,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @param offset
      * @return
      */
-    private PileupElementTracker<PE> readsOffsets2Pileup(List<SAMRecord> reads, int offset ) {
+    private PileupElementTracker<PE> readsOffsets2Pileup(List<GATKSAMRecord> reads, int offset ) {
         if ( reads == null ) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup");
         if ( offset < 0 ) throw new ReviewedStingException("Illegal offset < 0 UnifiedReadBackedPileup");
 
@@ -200,7 +200,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
     }
 
     protected abstract AbstractReadBackedPileup<RBP,PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
-    protected abstract PE createNewPileupElement(SAMRecord read, int offset);
+    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset);
 
     // --------------------------------------------------------
     //
@@ -512,7 +512,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         else {
             UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
             for(PE p: pileupElementTracker) {
-                SAMRecord read = p.getRead();
+                GATKSAMRecord read = p.getRead();
                 if(targetReadGroupId != null) {
                     if(read.getReadGroup() != null && targetReadGroupId.equals(read.getReadGroup().getReadGroupId()))
                         filteredTracker.add(p);
@@ -543,7 +543,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         else {
             UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
             for(PE p: pileupElementTracker) {
-                SAMRecord read = p.getRead();
+                GATKSAMRecord read = p.getRead();
                 if(laneID != null) {
                     if(read.getReadGroup() != null &&
                        (read.getReadGroup().getReadGroupId().startsWith(laneID + ".")) ||   // lane is the same, but sample identifier is different
@@ -567,7 +567,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         else {
             Collection<String> sampleNames = new HashSet<String>();
             for(PileupElement p: this) {
-                SAMRecord read = p.getRead();
+                GATKSAMRecord read = p.getRead();
                 String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
                 sampleNames.add(sampleName);
             }
@@ -644,7 +644,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
             HashSet<String> hashSampleNames = new HashSet<String>(sampleNames);    // to speed up the "contains" access in the for loop
             UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
             for(PE p: pileupElementTracker) {
-                SAMRecord read = p.getRead();
+                GATKSAMRecord read = p.getRead();
                 if(sampleNames != null) {                                          // still checking on sampleNames because hashSampleNames will never be null. And empty means something else.
                     if(read.getReadGroup() != null && hashSampleNames.contains(read.getReadGroup().getSample()))
                         filteredTracker.add(p);
@@ -669,7 +669,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         else {
             UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
             for(PE p: pileupElementTracker) {
-                SAMRecord read = p.getRead();
+                GATKSAMRecord read = p.getRead();
                 if(sampleName != null) {
                     if(read.getReadGroup() != null && sampleName.equals(read.getReadGroup().getSample()))
                         filteredTracker.add(p);
@@ -824,8 +824,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @return
      */
     @Override
-    public List<SAMRecord> getReads() {
+    public List<GATKSAMRecord> getReads() {
-        List<SAMRecord> reads = new ArrayList<SAMRecord>(getNumberOfElements());
+        List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>(getNumberOfElements());
         for ( PileupElement pile : this ) { reads.add(pile.getRead()); }
         return reads;
     }

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

@@ -1,131 +1,132 @@
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.sting.utils.pileup;
-
+
-import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecord;
-
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import java.util.Arrays;
+
-
+import java.util.Arrays;
-/**
+
- * In the "standard" locus traversal mode,
+/**
- * the traversal is performed striclty over the reference bases. Thus, only pileups of bases (and hence local events
+ * In the "standard" locus traversal mode,
- * such as point mutations) are "seen" at every invocation of the walker's map() function at every (genomic) locus. Deletions
+ * the traversal is performed striclty over the reference bases. Thus, only pileups of bases (and hence local events
- * are seen on the base-by-base basis (i.e. the pileup does keep the information about the current reference base being deleted
+ * such as point mutations) are "seen" at every invocation of the walker's map() function at every (genomic) locus. Deletions
- * in some reads), but the information about the extended event (deletion length, string of all deleted bases) is not kept.
+ * are seen on the base-by-base basis (i.e. the pileup does keep the information about the current reference base being deleted
- * The insertions that may be present in some reads are not seen at all in such strict reference traversal mode.
+ * in some reads), but the information about the extended event (deletion length, string of all deleted bases) is not kept.
- *
+ * The insertions that may be present in some reads are not seen at all in such strict reference traversal mode.
- * By convention, any extended event (indel) is mapped onto the reference at the last base prior to the event (i.e.
+ *
- * last base before the insertion or deletion). If the special "extended" traversal mode is turned on and there is
+ * By convention, any extended event (indel) is mapped onto the reference at the last base prior to the event (i.e.
- * an indel in at least one read that maps onto the reference position Z, the walker's map function will be called twice:
+ * last base before the insertion or deletion). If the special "extended" traversal mode is turned on and there is
- * first call will be performed in a "standard" mode, with a pileup of bases over the position Z, and then the additional
+ * an indel in at least one read that maps onto the reference position Z, the walker's map function will be called twice:
- * call will be made at the same position with a pileup of event/noevent calls, where events are extended and contain
+ * first call will be performed in a "standard" mode, with a pileup of bases over the position Z, and then the additional
- * full information about insertions/deletions. Then the next, "standard", call to map() will be performed at the next
+ * call will be made at the same position with a pileup of event/noevent calls, where events are extended and contain
- * (covered) reference position. Note that if the extended event at Z was a deletion, the "standard" base pileup at
+ * full information about insertions/deletions. Then the next, "standard", call to map() will be performed at the next
- * Z+1 and following bases may still contain deleted bases. However the fully extended event call will be performed
+ * (covered) reference position. Note that if the extended event at Z was a deletion, the "standard" base pileup at
- * only once, at the position where the indel maps (starts).
+ * Z+1 and following bases may still contain deleted bases. However the fully extended event call will be performed
- *
+ * only once, at the position where the indel maps (starts).
- * This class wraps an "extended" event (indel) so that in can be added to a pileup of events at a given location.
+ *
- *
+ * This class wraps an "extended" event (indel) so that in can be added to a pileup of events at a given location.
- * Created by IntelliJ IDEA.
+ *
- * User: asivache
+ * Created by IntelliJ IDEA.
- * Date: Dec 21, 2009
+ * User: asivache
- * Time: 2:57:55 PM
+ * Date: Dec 21, 2009
- * To change this template use File | Settings | File Templates.
+ * Time: 2:57:55 PM
- */
+ * To change this template use File | Settings | File Templates.
-public class ExtendedEventPileupElement extends PileupElement {
+ */
-    public enum Type {
+public class ExtendedEventPileupElement extends PileupElement {
-        NOEVENT, DELETION, INSERTION
+    public enum Type {
-    }
+        NOEVENT, DELETION, INSERTION
-
+    }
-    private Type type = null;
+
-    private int eventLength = -1;
+    private Type type = null;
-    private String eventBases = null; // if it is a deletion, we do not have information about the actual deleted bases
+    private int eventLength = -1;
-                               // in the read itself, so we fill the string with D's; for insertions we keep actual inserted bases
+    private String eventBases = null; // if it is a deletion, we do not have information about the actual deleted bases
-    private SAMRecord read;
+                               // in the read itself, so we fill the string with D's; for insertions we keep actual inserted bases
-    private int offset; // position in the read immediately BEFORE the event
+    private SAMRecord read;
-    // This is broken! offset is always zero because these member variables are shadowed by base class
+    private int offset; // position in the read immediately BEFORE the event
-
+    // This is broken! offset is always zero because these member variables are shadowed by base class
-    /** Constructor for extended pileup element (indel).
+
-     *
+    /** Constructor for extended pileup element (indel).
-     * @param read the read, in which the indel is observed
+     *
-     * @param offset position in the read immediately before the indel (can be -1 if read starts with an insertion)
+     * @param read the read, in which the indel is observed
-     * @param length length of the indel (number of inserted or deleted bases); length <=0 indicates that the read has no indel (NOEVENT)
+     * @param offset position in the read immediately before the indel (can be -1 if read starts with an insertion)
-     * @param eventBases inserted bases. null indicates that the event is a deletion; ignored if length<=0 (noevent)
+     * @param length length of the indel (number of inserted or deleted bases); length <=0 indicates that the read has no indel (NOEVENT)
-     */
+     * @param eventBases inserted bases. null indicates that the event is a deletion; ignored if length<=0 (noevent)
-    public ExtendedEventPileupElement( SAMRecord read, int offset, int length, byte[] eventBases ) {
+     */
-        super(read, offset);
+    public ExtendedEventPileupElement( GATKSAMRecord read, int offset, int length, byte[] eventBases ) {
-        this.eventLength = length;
+        super(read, offset);
-        if ( length <= 0 ) type = Type.NOEVENT;
+        this.eventLength = length;
-        else {
+        if ( length <= 0 ) type = Type.NOEVENT;
-            if ( eventBases != null ) {
+        else {
-                this.eventBases = new String(eventBases).toUpperCase();
+            if ( eventBases != null ) {
-                type = Type.INSERTION;
+                this.eventBases = new String(eventBases).toUpperCase();
-            } else {
+                type = Type.INSERTION;
-                type = Type.DELETION;
+            } else {
-            }
+                type = Type.DELETION;
-        }
+            }
-    }
+        }
-
+    }
-    /** Constructor for deletion or noevent calls - does not take event bases as an argument (as those should
+
-     * be null or are ignored in these cases anyway)
+    /** Constructor for deletion or noevent calls - does not take event bases as an argument (as those should
-     * @param read
+     * be null or are ignored in these cases anyway)
-     * @param offset
+     * @param read
-     * @param length
+     * @param offset
-     */
+     * @param length
-    public ExtendedEventPileupElement( SAMRecord read, int offset, int length ) {
+     */
-        this(read,offset, length, null);
+    public ExtendedEventPileupElement( GATKSAMRecord read, int offset, int length ) {
-    }
+        this(read,offset, length, null);
-
+    }
-    public boolean isDeletion() {
+
-        return type == Type.DELETION;
+    public boolean isDeletion() {
-    }
+        return type == Type.DELETION;
-
+    }
-    public boolean isInsertion() {
+
-        return type == Type.INSERTION;
+    public boolean isInsertion() {
-    }
+        return type == Type.INSERTION;
-
+    }
-    public boolean isIndel() {
+
-        return isDeletion() || isInsertion();
+    public boolean isIndel() {
-    }
+        return isDeletion() || isInsertion();
-
+    }
-    public Type getType() { return type; }
+
-
+    public Type getType() { return type; }
-    // The offset can be negative with insertions at the start of the read, but a valid base does exist at this position with
+
-    // a valid base quality.  The following code attempts to compensate for that.'
+    // The offset can be negative with insertions at the start of the read, but a valid base does exist at this position with
-
+    // a valid base quality.  The following code attempts to compensate for that.'
-    @Override
+
-    public byte getBase() {
+    @Override
-        return getBase(offset >= 0 ? offset : offset+eventLength);
+    public byte getBase() {
-    }
+        return getBase(offset >= 0 ? offset : offset+eventLength);
-
+    }
-    @Override
+
-    public int getBaseIndex() {
+    @Override
-        return getBaseIndex(offset >= 0 ? offset : offset+eventLength);
+    public int getBaseIndex() {
-    }
+        return getBaseIndex(offset >= 0 ? offset : offset+eventLength);
-
+    }
-    @Override
+
-    public byte getQual() {
+    @Override
-        return getQual(offset >= 0 ? offset : offset+eventLength);
+    public byte getQual() {
-    }
+        return getQual(offset >= 0 ? offset : offset+eventLength);
-
+    }
-    /** Returns length of the event (number of inserted or deleted bases */
+
-    public int getEventLength() { return eventLength; }
+    /** Returns length of the event (number of inserted or deleted bases */
-
+    public int getEventLength() { return eventLength; }
-    /** Returns actual sequence of inserted bases, or a null if the event is a deletion or if there is no event in the associated read.
+
-     *  */
+    /** Returns actual sequence of inserted bases, or a null if the event is a deletion or if there is no event in the associated read.
-    public String getEventBases() { return eventBases; }
+     *  */
-
+    public String getEventBases() { return eventBases; }
-    @Override
+
-    public String toString() {
+    @Override
-        char c = '.';
+    public String toString() {
-        String fillStr = null ;
+        char c = '.';
-        if ( isDeletion() ) {
+        String fillStr = null ;
-            c = '-';
+        if ( isDeletion() ) {
-            char [] filler = new char[eventLength];
+            c = '-';
-            Arrays.fill(filler, 'D');
+            char [] filler = new char[eventLength];
-            fillStr = new String(filler);
+            Arrays.fill(filler, 'D');
-        }
+            fillStr = new String(filler);
-        else if ( isInsertion() ) c = '+';
+        }
-        return String.format("%s @ %d = %c%s MQ%d", getRead().getReadName(), getOffset(), c, isIndel()?
+        else if ( isInsertion() ) c = '+';
-                (isInsertion() ? eventBases : fillStr ): "", getMappingQual());
+        return String.format("%s @ %d = %c%s MQ%d", getRead().getReadName(), getOffset(), c, isIndel()?
-    }
+                (isInsertion() ? eventBases : fillStr ): "", getMappingQual());
-
+    }
-}
+
+}

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

@@ -2,10 +2,8 @@ package org.broadinstitute.sting.utils.pileup;
 
 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;
 
 /**
  * Created by IntelliJ IDEA.
@@ -21,14 +19,14 @@ public class PileupElement implements Comparable<PileupElement> {
     public static final byte T_FOLLOWED_BY_INSERTION_BASE = (byte) 89;
     public static final byte G_FOLLOWED_BY_INSERTION_BASE = (byte) 90;
 
-    protected final SAMRecord read;
+    protected final GATKSAMRecord read;
     protected final int offset;
 
     @Requires({
             "read != null",
             "offset >= -1",
             "offset <= read.getReadLength()"})
-    public PileupElement( SAMRecord read, int offset ) {
+    public PileupElement( GATKSAMRecord read, int offset ) {
         this.read = read;
         this.offset = offset;
     }
@@ -38,7 +36,7 @@ public class PileupElement implements Comparable<PileupElement> {
     }
 
     @Ensures("result != null")
-    public SAMRecord getRead() { return read; }
+    public GATKSAMRecord getRead() { return read; }
 
     @Ensures("result == offset")
     public int getOffset() { return offset; }

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.pileup;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Collection;
 import java.util.List;
@@ -166,7 +167,7 @@ public interface ReadBackedExtendedEventPileup extends ReadBackedPileup {
      * Returns a list of the reads in this pileup. Note this call costs O(n) and allocates fresh lists each time
      * @return
      */
-    public List<SAMRecord> getReads();
+    public List<GATKSAMRecord> getReads();
 
     /**
      * Returns a list of the offsets in this pileup. Note this call costs O(n) and allocates fresh lists each time

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

@@ -23,10 +23,10 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.*;
 
@@ -95,7 +95,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
     }
 
     @Override
-    protected ExtendedEventPileupElement createNewPileupElement(SAMRecord read, int offset) {
+    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset) {
         throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
     }
 

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

@@ -24,10 +24,10 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Collection;
 import java.util.List;
@@ -202,7 +202,7 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
      * Returns a list of the reads in this pileup. Note this call costs O(n) and allocates fresh lists each time
      * @return
      */
-    public List<SAMRecord> getReads();
+    public List<GATKSAMRecord> getReads();
 
     /**
      * Returns a list of the offsets in this pileup. Note this call costs O(n) and allocates fresh lists each time

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

@@ -23,8 +23,8 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.List;
 import java.util.Map;
@@ -35,11 +35,11 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
         super(loc);
     }
 
-    public ReadBackedPileupImpl(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets ) {
+    public ReadBackedPileupImpl(GenomeLoc loc, List<GATKSAMRecord> reads, List<Integer> offsets ) {
         super(loc,reads,offsets);
     }
 
-    public ReadBackedPileupImpl(GenomeLoc loc, List<SAMRecord> reads, int offset ) {
+    public ReadBackedPileupImpl(GenomeLoc loc, List<GATKSAMRecord> reads, int offset ) {
         super(loc,reads,offset);
     }
 
@@ -70,7 +70,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
     }
 
     @Override
-    protected PileupElement createNewPileupElement(SAMRecord read, int offset) {
+    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset) {
         return new PileupElement(read,offset);
     }
 }

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

@@ -104,9 +104,9 @@ public class ArtificialReadsTraversal<M,T> extends TraversalEngine<M,T,Walker<M,
             // an array of characters that represent the reference
             ReferenceContext refSeq = null;
 
-            final boolean keepMeP = readWalker.filter(refSeq, read);
+            final boolean keepMeP = readWalker.filter(refSeq, (GATKSAMRecord) read);
             if (keepMeP) {
-                M x = readWalker.map(refSeq, read, null);  // TODO: fix me at some point, it would be nice to fake out ROD data too
+                M x = readWalker.map(refSeq, (GATKSAMRecord) read, null);  // TODO: fix me at some point, it would be nice to fake out ROD data too
                 sum = readWalker.reduce(x, sum);
             }
         }

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

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -201,9 +200,9 @@ public class ArtificialSAMUtils {
         return rec;
     }
 
-    public final static List<SAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
+    public final static List<GATKSAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
-        SAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen);
+        GATKSAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen);
-        SAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen);
+        GATKSAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen);
 
         left.setReadPairedFlag(true);
         right.setReadPairedFlag(true);
@@ -327,9 +326,9 @@ public class ArtificialSAMUtils {
 
             if ( rightStart <= 0 ) continue;
 
-            List<SAMRecord> pair = createPair(header, readName, readLen, leftStart, rightStart, leftIsFirst, leftIsNegative);
+            List<GATKSAMRecord> pair = createPair(header, readName, readLen, leftStart, rightStart, leftIsFirst, leftIsNegative);
-            final SAMRecord left = pair.get(0);
+            final GATKSAMRecord left = pair.get(0);
-            final SAMRecord right = pair.get(1);
+            final GATKSAMRecord right = pair.get(1);
 
             pileupElements.add(new PileupElement(left, pos - leftStart));
 

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

@@ -188,15 +188,15 @@ public class ReadUtils {
      * This makes the following code a little nasty, since we can only detect if a base is in the adaptor, but not
      * if it overlaps the read.
      *
-     * @param rec
+     * @param read
      * @param basePos
      * @param adaptorLength
      * @return
      */
-    public static OverlapType readPairBaseOverlapType(final SAMRecord rec, long basePos, final int adaptorLength) {
+    public static OverlapType readPairBaseOverlapType(final SAMRecord read, long basePos, final int adaptorLength) {
         OverlapType state = OverlapType.NOT_OVERLAPPING;
 
-        Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(rec, adaptorLength);
+        Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(read, adaptorLength);
 
         if ( adaptorBoundaries != null ) { // we're not an unmapped pair -- cannot filter out
 
@@ -205,28 +205,28 @@ public class ReadUtils {
             if ( inAdapator ) { 
                 state = OverlapType.IN_ADAPTOR;
                 //System.out.printf("baseOverlapState: %50s negStrand=%b base=%d start=%d stop=%d, adaptorStart=%d adaptorEnd=%d isize=%d => %s%n",
-                //        rec.getReadName(), rec.getReadNegativeStrandFlag(), basePos, rec.getAlignmentStart(), rec.getAlignmentEnd(), adaptorBoundaries.first, adaptorBoundaries.second, rec.getInferredInsertSize(), state);
+                //        read.getReadName(), read.getReadNegativeStrandFlag(), basePos, read.getAlignmentStart(), read.getAlignmentEnd(), adaptorBoundaries.first, adaptorBoundaries.second, read.getInferredInsertSize(), state);
             }
         }
 
         return state;
     }
 
-    private static Pair<Integer, Integer> getAdaptorBoundaries(SAMRecord rec, int adaptorLength) {
+    private static Pair<Integer, Integer> getAdaptorBoundaries(SAMRecord read, int adaptorLength) {
-        int isize = rec.getInferredInsertSize();
+        int isize = read.getInferredInsertSize();
         if ( isize == 0 )
             return null; // don't worry about unmapped pairs
 
         int adaptorStart, adaptorEnd;
 
-        if ( rec.getReadNegativeStrandFlag() ) {
+        if ( read.getReadNegativeStrandFlag() ) {
             // we are on the negative strand, so our mate is on the positive strand
-            int mateStart = rec.getMateAlignmentStart();
+            int mateStart = read.getMateAlignmentStart();
             adaptorStart = mateStart - adaptorLength - 1;
             adaptorEnd = mateStart - 1;
         } else {
             // we are on the positive strand, so our mate is on the negative strand
-            int mateEnd = rec.getAlignmentStart() + isize - 1;
+            int mateEnd = read.getAlignmentStart() + isize - 1;
             adaptorStart = mateEnd + 1;
             adaptorEnd = mateEnd + adaptorLength;
         }
@@ -236,47 +236,47 @@ public class ReadUtils {
 
     /**
      *
-     * @param rec  original SAM record
+     * @param read  original SAM record
      * @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 GATKSAMRecord read, int adaptorLength) {
 
-        Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(rec, adaptorLength);
+        Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(read, adaptorLength);
-        GATKSAMRecord result = (GATKSAMRecord)rec;
+        GATKSAMRecord result = (GATKSAMRecord)read;
 
         if ( adaptorBoundaries != null ) {
-            if ( rec.getReadNegativeStrandFlag() && adaptorBoundaries.second >= rec.getAlignmentStart() && adaptorBoundaries.first < rec.getAlignmentEnd() )
+            if ( read.getReadNegativeStrandFlag() && adaptorBoundaries.second >= read.getAlignmentStart() && adaptorBoundaries.first < read.getAlignmentEnd() )
-                result = hardClipStartOfRead(rec, adaptorBoundaries.second);
+                result = hardClipStartOfRead(read, adaptorBoundaries.second);
-            else if ( !rec.getReadNegativeStrandFlag() && adaptorBoundaries.first <= rec.getAlignmentEnd() )
+            else if ( !read.getReadNegativeStrandFlag() && adaptorBoundaries.first <= read.getAlignmentEnd() )
-                result = hardClipEndOfRead(rec, adaptorBoundaries.first);
+                result = hardClipEndOfRead(read, adaptorBoundaries.first);
         }
 
         return result;
     }
 
     // return true if the read needs to be completely clipped
-    private static GATKSAMRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
+    private static GATKSAMRecord hardClipStartOfRead(GATKSAMRecord 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
-            //System.out.printf("Entire read needs to be clipped: %50s %n", rec.getReadName());
+            //System.out.printf("Entire read needs to be clipped: %50s %n", read.getReadName());
             return null;
         }
 
-        GATKSAMRecord rec;
+        GATKSAMRecord read;
         try {
-            rec = (GATKSAMRecord)oldRec.clone();
+            read = (GATKSAMRecord)oldRec.clone();
         } catch (Exception e) {
             return null;
         }
 
         //System.out.printf("Clipping start of read: %50s start=%d adaptorEnd=%d isize=%d %n",
-        //        rec.getReadName(), rec.getAlignmentStart(), stopPosition, rec.getInferredInsertSize());
+        //        read.getReadName(), read.getAlignmentStart(), stopPosition, read.getInferredInsertSize());
 
-        Cigar oldCigar = rec.getCigar();
+        Cigar oldCigar = read.getCigar();
         LinkedList<CigarElement> newCigarElements = new LinkedList<CigarElement>();
-        int currentPos = rec.getAlignmentStart();
+        int currentPos = read.getAlignmentStart();
         int basesToClip = 0;
         int basesAlreadyClipped = 0;
 
@@ -315,48 +315,48 @@ public class ReadUtils {
         }
 
         // copy over the unclipped bases
-        final byte[] bases = rec.getReadBases();
+        final byte[] bases = read.getReadBases();
-        final byte[] quals = rec.getBaseQualities();
+        final byte[] quals = read.getBaseQualities();
         int newLength = bases.length - basesToClip;
         byte[] newBases = new byte[newLength];
         byte[] newQuals = new byte[newLength];
         System.arraycopy(bases, basesToClip, newBases, 0, newLength);
         System.arraycopy(quals, basesToClip, newQuals, 0, newLength);
-        rec.setReadBases(newBases);
+        read.setReadBases(newBases);
-        rec.setBaseQualities(newQuals);
+        read.setBaseQualities(newQuals);
 
         // now add a CIGAR element for the clipped bases
         newCigarElements.addFirst(new CigarElement(basesToClip + basesAlreadyClipped, CigarOperator.H));
         Cigar newCigar = new Cigar(newCigarElements);
-        rec.setCigar(newCigar);
+        read.setCigar(newCigar);
 
         // adjust the start accordingly
-        rec.setAlignmentStart(stopPosition + 1);
+        read.setAlignmentStart(stopPosition + 1);
 
-        return rec;
+        return read;
     }
 
-    private static GATKSAMRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
+    private static GATKSAMRecord hardClipEndOfRead(GATKSAMRecord 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
-            //System.out.printf("Entire read needs to be clipped: %50s %n", rec.getReadName());
+            //System.out.printf("Entire read needs to be clipped: %50s %n", read.getReadName());
             return null;
         }
 
-        GATKSAMRecord rec;
+        GATKSAMRecord read;
         try {
-            rec = (GATKSAMRecord)oldRec.clone();
+            read = (GATKSAMRecord)oldRec.clone();
         } catch (Exception e) {
             return null;
         }
 
         //System.out.printf("Clipping end of read: %50s adaptorStart=%d end=%d isize=%d %n",
-        //        rec.getReadName(), startPosition, rec.getAlignmentEnd(), rec.getInferredInsertSize());
+        //        read.getReadName(), startPosition, read.getAlignmentEnd(), read.getInferredInsertSize());
 
-        Cigar oldCigar = rec.getCigar();
+        Cigar oldCigar = read.getCigar();
         LinkedList<CigarElement> newCigarElements = new LinkedList<CigarElement>();
-        int currentPos = rec.getAlignmentStart();
+        int currentPos = read.getAlignmentStart();
         int basesToKeep = 0;
         int basesAlreadyClipped = 0;
 
@@ -402,41 +402,41 @@ public class ReadUtils {
         }
 
         // copy over the unclipped bases
-        final byte[] bases = rec.getReadBases();
+        final byte[] bases = read.getReadBases();
-        final byte[] quals = rec.getBaseQualities();
+        final byte[] quals = read.getBaseQualities();
         byte[] newBases = new byte[basesToKeep];
         byte[] newQuals = new byte[basesToKeep];
         System.arraycopy(bases, 0, newBases, 0, basesToKeep);
         System.arraycopy(quals, 0, newQuals, 0, basesToKeep);
-        rec.setReadBases(newBases);
+        read.setReadBases(newBases);
-        rec.setBaseQualities(newQuals);
+        read.setBaseQualities(newQuals);
 
         // now add a CIGAR element for the clipped bases
         newCigarElements.add(new CigarElement((bases.length - basesToKeep) + basesAlreadyClipped, CigarOperator.H));
         Cigar newCigar = new Cigar(newCigarElements);
-        rec.setCigar(newCigar);
+        read.setCigar(newCigar);
 
         // adjust the stop accordingly
-        // rec.setAlignmentEnd(startPosition - 1);
+        // read.setAlignmentEnd(startPosition - 1);
 
-        return rec;
+        return read;
     }
 
     /**
      * Hard clips away (i.e.g, removes from the read) bases that were previously soft clipped.
      *
-     * @param rec
+     * @param read
      * @return
      */
-    @Requires("rec != null")
+    @Requires("read != null")
     @Ensures("result != null")
-    public static SAMRecord hardClipSoftClippedBases(SAMRecord rec) {
+    public static GATKSAMRecord hardClipSoftClippedBases(GATKSAMRecord read) {
-        List<CigarElement> cigarElts = rec.getCigar().getCigarElements();
+        List<CigarElement> cigarElts = read.getCigar().getCigarElements();
 
         if ( cigarElts.size() == 1 ) // can't be soft clipped, just return
-            return rec;
+            return read;
 
-        int keepStart = 0, keepEnd = rec.getReadLength() - 1;
+        int keepStart = 0, keepEnd = read.getReadLength() - 1;
         List<CigarElement> newCigarElements = new LinkedList<CigarElement>();
 
         for ( int i = 0; i < cigarElts.size(); i++ ) {
@@ -447,7 +447,7 @@ public class ReadUtils {
                     if ( i == 0 )
                         keepStart = l;
                     else
-                        keepEnd = rec.getReadLength() - l - 1;
+                        keepEnd = read.getReadLength() - l - 1;
                     newCigarElements.add(new CigarElement(l, CigarOperator.HARD_CLIP));
                     break;
 
@@ -477,54 +477,54 @@ public class ReadUtils {
         }
         mergedCigarElements.add(new CigarElement(currentOperatorLength, currentOperator));
 
-        return hardClipBases(rec, keepStart, keepEnd, mergedCigarElements);
+        return hardClipBases(read, keepStart, keepEnd, mergedCigarElements);
     }
 
     /**
-     * Hard clips out the bases in rec, keeping the bases from keepStart to keepEnd, inclusive.  Note these
+     * Hard clips out the bases in read, keeping the bases from keepStart to keepEnd, inclusive.  Note these
      * are offsets, so they are 0 based
      *
-     * @param rec
+     * @param read
      * @param keepStart
      * @param keepEnd
      * @param newCigarElements
      * @return
      */
     @Requires({
-            "rec != null",
+            "read != null",
             "keepStart >= 0",
-            "keepEnd < rec.getReadLength()",
+            "keepEnd < read.getReadLength()",
-            "rec.getReadUnmappedFlag() || newCigarElements != null"})
+            "read.getReadUnmappedFlag() || newCigarElements != null"})
     @Ensures("result != null")
-    public static SAMRecord hardClipBases(SAMRecord rec, int keepStart, int keepEnd, List<CigarElement> newCigarElements) {
+    public static GATKSAMRecord hardClipBases(GATKSAMRecord read, int keepStart, int keepEnd, List<CigarElement> newCigarElements) {
         int newLength = keepEnd - keepStart + 1;
-        if ( newLength != rec.getReadLength() ) {
+        if ( newLength != read.getReadLength() ) {
             try {
-                rec = SimplifyingSAMFileWriter.simplifyRead((SAMRecord)rec.clone());
+                read = (GATKSAMRecord)read.clone();
                 // copy over the unclipped bases
-                final byte[] bases = rec.getReadBases();
+                final byte[] bases = read.getReadBases();
-                final byte[] quals = rec.getBaseQualities();
+                final byte[] quals = read.getBaseQualities();
                 byte[] newBases = new byte[newLength];
                 byte[] newQuals = new byte[newLength];
                 System.arraycopy(bases, keepStart, newBases, 0, newLength);
                 System.arraycopy(quals, keepStart, newQuals, 0, newLength);
-                rec.setReadBases(newBases);
+                read.setReadBases(newBases);
-                rec.setBaseQualities(newQuals);
+                read.setBaseQualities(newQuals);
 
                 // now add a CIGAR element for the clipped bases, if the read isn't unmapped
-                if ( ! rec.getReadUnmappedFlag() ) {
+                if ( ! read.getReadUnmappedFlag() ) {
                     Cigar newCigar = new Cigar(newCigarElements);
-                    rec.setCigar(newCigar);
+                    read.setCigar(newCigar);
                 }
             } catch ( CloneNotSupportedException e ) {
                 throw new ReviewedStingException("WTF, where did clone go?", e);
             }
         }
 
-        return rec;
+        return read;
     }
 
-    public static SAMRecord replaceSoftClipsWithMatches(SAMRecord read) {
+    public static GATKSAMRecord replaceSoftClipsWithMatches(GATKSAMRecord read) {
         List<CigarElement> newCigarElements = new ArrayList<CigarElement>();
 
         for ( CigarElement ce : read.getCigar().getCigarElements() ) {
@@ -561,15 +561,15 @@ public class ReadUtils {
 
     /**
      *
-     * @param rec  original SAM record
+     * @param read  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 GATKSAMRecord read) {
-        return hardClipAdaptorSequence(rec, DEFAULT_ADAPTOR_SIZE);
+        return hardClipAdaptorSequence(read, DEFAULT_ADAPTOR_SIZE);
     }
 
-    public static OverlapType readPairBaseOverlapType(final SAMRecord rec, long basePos) {
+    public static OverlapType readPairBaseOverlapType(final SAMRecord read, long basePos) {
-        return readPairBaseOverlapType(rec, basePos, DEFAULT_ADAPTOR_SIZE);
+        return readPairBaseOverlapType(read, basePos, DEFAULT_ADAPTOR_SIZE);
     }
 
     public static boolean is454Read(SAMRecord read) {
@@ -601,10 +601,10 @@ public class ReadUtils {
         readFlagNames.put(0x400, "Duplicate");
     }
 
-    public static String readFlagsAsString(SAMRecord rec) {
+    public static String readFlagsAsString(GATKSAMRecord read) {
         String flags = "";
         for (int flag : readFlagNames.keySet()) {
-            if ((rec.getFlags() & flag) != 0) {
+            if ((read.getFlags() & flag) != 0) {
                 flags += readFlagNames.get(flag) + " ";
             }
         }
@@ -618,7 +618,7 @@ public class ReadUtils {
      * @param reads
      * @return
      */
-    public final static List<SAMRecord> coordinateSortReads(List<SAMRecord> reads) {
+    public final static List<GATKSAMRecord> coordinateSortReads(List<GATKSAMRecord> reads) {
         final SAMRecordComparator comparer = new SAMRecordCoordinateComparator();
         Collections.sort(reads, comparer);
         return reads;
@@ -647,7 +647,7 @@ public class ReadUtils {
      * @param interval the interval
      * @return the overlap type as described by ReadAndIntervalOverlap enum (see above)
      */
-    public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(SAMRecord read, GenomeLoc interval) {
+    public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(GATKSAMRecord read, GenomeLoc interval) {
 
         int sStart = getRefCoordSoftUnclippedStart(read);
         int sStop = getRefCoordSoftUnclippedEnd(read);
@@ -685,7 +685,7 @@ public class ReadUtils {
     }
 
     @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
-    public static int getRefCoordSoftUnclippedStart(SAMRecord read) {
+    public static int getRefCoordSoftUnclippedStart(GATKSAMRecord read) {
         int start = read.getUnclippedStart();
         for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
             if (cigarElement.getOperator() == CigarOperator.HARD_CLIP)
@@ -697,7 +697,7 @@ public class ReadUtils {
     }
 
     @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
-    public static int getRefCoordSoftUnclippedEnd(SAMRecord read) {
+    public static int getRefCoordSoftUnclippedEnd(GATKSAMRecord read) {
         int stop = read.getUnclippedStart();
 
         if (readIsEntirelyInsertion(read))
@@ -716,7 +716,7 @@ public class ReadUtils {
         return (lastOperator == CigarOperator.HARD_CLIP) ? stop-1 : stop+shift-1 ;
     }
 
-    private static boolean readIsEntirelyInsertion(SAMRecord read) {
+    private static boolean readIsEntirelyInsertion(GATKSAMRecord read) {
         for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
             if (cigarElement.getOperator() != CigarOperator.INSERTION)
                 return false;
@@ -730,7 +730,7 @@ public class ReadUtils {
     }
 
     /**
-     * Pre-processes the results of getReadCoordinateForReferenceCoordinate(SAMRecord, int) in case it falls in
+     * Pre-processes the results of getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int) in case it falls in
      * a deletion following the typical clipping needs. If clipping the left tail (beginning of the read) returns
      * the base prior to the deletion. If clipping the right tail (end of the read) returns the base after the
      * deletion.
@@ -742,7 +742,7 @@ public class ReadUtils {
      */
     @Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"})
     @Ensures({"result >= 0", "result < read.getReadLength()"})
-    public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord, ClippingTail tail) {
+    public static int getReadCoordinateForReferenceCoordinate(GATKSAMRecord read, int refCoord, ClippingTail tail) {
         Pair<Integer, Boolean> result = getReadCoordinateForReferenceCoordinate(read, refCoord);
         int readCoord = result.getFirst();
 
@@ -760,7 +760,7 @@ public class ReadUtils {
      * Pair(int readCoord, boolean fallsInsideDeletion) so you can choose which readCoordinate to use when faced with
      * a deletion.
      *
-     * SUGGESTION: Use getReadCoordinateForReferenceCoordinate(SAMRecord, int, ClippingTail) instead to get a
+     * SUGGESTION: Use getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int, ClippingTail) instead to get a
      * pre-processed result according to normal clipping needs. Or you can use this function and tailor the
      * behavior to your needs.
      *
@@ -770,7 +770,7 @@ public class ReadUtils {
      */
     @Requires({"refCoord >= getRefCoordSoftUnclippedStart(read)", "refCoord <= getRefCoordSoftUnclippedEnd(read)"})
     @Ensures({"result.getFirst() >= 0", "result.getFirst() < read.getReadLength()"})
-    public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
+    public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(GATKSAMRecord read, int refCoord) {
         int readBases = 0;
         int refBases = 0;
         boolean fallsInsideDeletion = false;
@@ -851,13 +851,13 @@ public class ReadUtils {
         return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion);
     }
 
-    public static SAMRecord unclipSoftClippedBases(SAMRecord rec) {
+    public static GATKSAMRecord unclipSoftClippedBases(GATKSAMRecord read) {
-        int newReadStart = rec.getAlignmentStart();
+        int newReadStart = read.getAlignmentStart();
-        int newReadEnd = rec.getAlignmentEnd();
+        int newReadEnd = read.getAlignmentEnd();
-        List<CigarElement> newCigarElements = new ArrayList<CigarElement>(rec.getCigar().getCigarElements().size());
+        List<CigarElement> newCigarElements = new ArrayList<CigarElement>(read.getCigar().getCigarElements().size());
         int heldOver = -1;
         boolean sSeen = false;
-        for ( CigarElement e : rec.getCigar().getCigarElements() ) {
+        for ( CigarElement e : read.getCigar().getCigarElements() ) {
             if ( e.getOperator().equals(CigarOperator.S) ) {
                 newCigarElements.add(new CigarElement(e.getLength(),CigarOperator.M));
                 if ( sSeen ) {
@@ -872,7 +872,7 @@ public class ReadUtils {
         }
         // merge duplicate operators together
         int idx = 0;
-        List<CigarElement> finalCigarElements = new ArrayList<CigarElement>(rec.getCigar().getCigarElements().size());
+        List<CigarElement> finalCigarElements = new ArrayList<CigarElement>(read.getCigar().getCigarElements().size());
         while ( idx < newCigarElements.size() -1 ) {
             if ( newCigarElements.get(idx).getOperator().equals(newCigarElements.get(idx+1).getOperator()) ) {
                 int combSize = newCigarElements.get(idx).getLength();
@@ -889,10 +889,10 @@ public class ReadUtils {
             idx++;
         }
 
-        rec.setCigar(new Cigar(finalCigarElements));
+        read.setCigar(new Cigar(finalCigarElements));
-        rec.setAlignmentStart(newReadStart);
+        read.setAlignmentStart(newReadStart);
 
-        return rec;
+        return read;
     }
 
     /**
@@ -905,7 +905,7 @@ public class ReadUtils {
 
     @Requires({"read1 != null", "read2 != null"})
     @Ensures("result == 0 || result == 1 || result == -1")
-    public static int compareSAMRecords(SAMRecord read1, SAMRecord read2) {
+    public static int compareSAMRecords(GATKSAMRecord read1, GATKSAMRecord read2) {
         AlignmentStartComparator comp = new AlignmentStartComparator();
         return comp.compare(read1, read2);
     }

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java

@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 /**
@@ -38,7 +37,7 @@ public class AllLocusViewUnitTest extends LocusViewTemplate {
      * @param reads
      */
     @Override
-    protected void testReadsInContext( LocusView view, List<GenomeLoc> range, List<SAMRecord> reads ) {
+    protected void testReadsInContext( LocusView view, List<GenomeLoc> range, List<GATKSAMRecord> reads ) {
         AllLocusView allLocusView = (AllLocusView)view;
 
         // TODO: Should skip over loci not in the given range.
@@ -52,7 +51,7 @@ public class AllLocusViewUnitTest extends LocusViewTemplate {
             Assert.assertEquals(locusContext.getLocation(), site, "Locus context location is incorrect");
             int expectedReadsAtSite = 0;
 
-            for( SAMRecord read: reads ) {
+            for( GATKSAMRecord read: reads ) {
                 if(genomeLocParser.createGenomeLoc(read).containsP(locusContext.getLocation())) {
                     Assert.assertTrue(locusContext.getReads().contains(read),"Target locus context does not contain reads");
                     expectedReadsAtSite++;

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java

@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 /**
@@ -41,7 +41,7 @@ public class CoveredLocusViewUnitTest extends LocusViewTemplate {
      * @param reads
      */
     @Override
-    protected void testReadsInContext( LocusView view, List<GenomeLoc> range, List<SAMRecord> reads ) {
+    protected void testReadsInContext( LocusView view, List<GenomeLoc> range, List<GATKSAMRecord> reads ) {
         CoveredLocusView coveredLocusView = (CoveredLocusView)view;
 
         // TODO: Should skip over loci not in the given range.
@@ -53,7 +53,7 @@ public class CoveredLocusViewUnitTest extends LocusViewTemplate {
             GenomeLoc site = genomeLocParser.createGenomeLoc("chr1",i);
 
             int expectedReadsAtSite = 0;
-            for( SAMRecord read: reads ) {
+            for( GATKSAMRecord read: reads ) {
                 if( genomeLocParser.createGenomeLoc(read).containsP(site) )
                     expectedReadsAtSite++;
             }
@@ -67,7 +67,7 @@ public class CoveredLocusViewUnitTest extends LocusViewTemplate {
             Assert.assertEquals(locusContext.getLocation(), site, "Target locus context location is incorrect");
             Assert.assertEquals(locusContext.getReads().size(), expectedReadsAtSite, "Found wrong number of reads at site");
 
-            for( SAMRecord read: reads ) {
+            for( GATKSAMRecord read: reads ) {
                 if(genomeLocParser.createGenomeLoc(read).containsP(locusContext.getLocation()))
                     Assert.assertTrue(locusContext.getReads().contains(read),"Target locus context does not contain reads");
             }

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java

@@ -13,6 +13,7 @@ import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -55,12 +56,12 @@ public abstract class LocusViewTemplate extends BaseTest {
 
         LocusView view = createView(dataProvider);
 
-        testReadsInContext(view, shard.getGenomeLocs(), Collections.<SAMRecord>emptyList());
+        testReadsInContext(view, shard.getGenomeLocs(), Collections.<GATKSAMRecord>emptyList());
     }
 
     @Test
     public void singleReadTest() {
-        SAMRecord read = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
@@ -76,7 +77,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readCoveringFirstPartTest() {
-        SAMRecord read = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -90,7 +91,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readCoveringLastPartTest() {
-        SAMRecord read = buildSAMRecord("chr1", 6, 10);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -104,7 +105,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readCoveringMiddleTest() {
-        SAMRecord read = buildSAMRecord("chr1", 3, 7);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 3, 7);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -118,7 +119,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readAndLocusOverlapAtLastBase() {
-        SAMRecord read = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 5, 5)));
@@ -132,7 +133,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readOverlappingStartTest() {
-        SAMRecord read = buildSAMRecord("chr1", 1, 10);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
@@ -146,7 +147,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readOverlappingEndTest() {
-        SAMRecord read = buildSAMRecord("chr1", 6, 15);
+        GATKSAMRecord read = buildSAMRecord("read1","chr1", 6, 15);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -160,8 +161,8 @@ public abstract class LocusViewTemplate extends BaseTest {
 
     @Test
     public void readsSpanningTest() {
-        SAMRecord read1 = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read1 = buildSAMRecord("read1","chr1", 1, 5);
-        SAMRecord read2 = buildSAMRecord("chr1", 6, 10);
+        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -170,17 +171,17 @@ public abstract class LocusViewTemplate extends BaseTest {
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
 
-        List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
+        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
         Collections.addAll(expectedReads, read1, read2);
         testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
     }
 
     @Test
     public void duplicateReadsTest() {
-        SAMRecord read1 = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read1 = buildSAMRecord("read1","chr1", 1, 5);
-        SAMRecord read2 = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 1, 5);
-        SAMRecord read3 = buildSAMRecord("chr1", 6, 10);
+        GATKSAMRecord read3 = buildSAMRecord("read3","chr1", 6, 10);
-        SAMRecord read4 = buildSAMRecord("chr1", 6, 10);
+        GATKSAMRecord read4 = buildSAMRecord("read4","chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -189,17 +190,17 @@ public abstract class LocusViewTemplate extends BaseTest {
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
 
-        List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
+        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
         Collections.addAll(expectedReads, read1, read2, read3, read4);
         testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
     }
 
     @Test
     public void cascadingReadsWithinBoundsTest() {
-        SAMRecord read1 = buildSAMRecord("chr1", 2, 6);
+        GATKSAMRecord read1 = buildSAMRecord("read1","chr1", 2, 6);
-        SAMRecord read2 = buildSAMRecord("chr1", 3, 7);
+        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 3, 7);
-        SAMRecord read3 = buildSAMRecord("chr1", 4, 8);
+        GATKSAMRecord read3 = buildSAMRecord("read3","chr1", 4, 8);
-        SAMRecord read4 = buildSAMRecord("chr1", 5, 9);
+        GATKSAMRecord read4 = buildSAMRecord("read4","chr1", 5, 9);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -208,19 +209,19 @@ public abstract class LocusViewTemplate extends BaseTest {
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
 
-        List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
+        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
         Collections.addAll(expectedReads, read1, read2, read3, read4);
         testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
     }
 
     @Test
     public void cascadingReadsAtBoundsTest() {
-        SAMRecord read1 = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read1 = buildSAMRecord("read1","chr1", 1, 5);
-        SAMRecord read2 = buildSAMRecord("chr1", 2, 6);
+        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 2, 6);
-        SAMRecord read3 = buildSAMRecord("chr1", 3, 7);
+        GATKSAMRecord read3 = buildSAMRecord("read3","chr1", 3, 7);
-        SAMRecord read4 = buildSAMRecord("chr1", 4, 8);
+        GATKSAMRecord read4 = buildSAMRecord("read4","chr1", 4, 8);
-        SAMRecord read5 = buildSAMRecord("chr1", 5, 9);
+        GATKSAMRecord read5 = buildSAMRecord("read5","chr1", 5, 9);
-        SAMRecord read6 = buildSAMRecord("chr1", 6, 10);
+        GATKSAMRecord read6 = buildSAMRecord("read6","chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
@@ -229,25 +230,25 @@ public abstract class LocusViewTemplate extends BaseTest {
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
 
-        List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
+        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
         Collections.addAll(expectedReads, read1, read2, read3, read4, read5, read6);
         testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
     }
 
     @Test
     public void cascadingReadsOverlappingBoundsTest() {
-        SAMRecord read01 = buildSAMRecord("chr1", 1, 5);
+        GATKSAMRecord read01 = buildSAMRecord("read1","chr1", 1, 5);
-        SAMRecord read02 = buildSAMRecord("chr1", 2, 6);
+        GATKSAMRecord read02 = buildSAMRecord("read2","chr1", 2, 6);
-        SAMRecord read03 = buildSAMRecord("chr1", 3, 7);
+        GATKSAMRecord read03 = buildSAMRecord("read3","chr1", 3, 7);
-        SAMRecord read04 = buildSAMRecord("chr1", 4, 8);
+        GATKSAMRecord read04 = buildSAMRecord("read4","chr1", 4, 8);
-        SAMRecord read05 = buildSAMRecord("chr1", 5, 9);
+        GATKSAMRecord read05 = buildSAMRecord("read5","chr1", 5, 9);
-        SAMRecord read06 = buildSAMRecord("chr1", 6, 10);
+        GATKSAMRecord read06 = buildSAMRecord("read6","chr1", 6, 10);
-        SAMRecord read07 = buildSAMRecord("chr1", 7, 11);
+        GATKSAMRecord read07 = buildSAMRecord("read7","chr1", 7, 11);
-        SAMRecord read08 = buildSAMRecord("chr1", 8, 12);
+        GATKSAMRecord read08 = buildSAMRecord("read8","chr1", 8, 12);
-        SAMRecord read09 = buildSAMRecord("chr1", 9, 13);
+        GATKSAMRecord read09 = buildSAMRecord("read9","chr1", 9, 13);
-        SAMRecord read10 = buildSAMRecord("chr1", 10, 14);
+        GATKSAMRecord read10 = buildSAMRecord("read10","chr1", 10, 14);
-        SAMRecord read11 = buildSAMRecord("chr1", 11, 15);
+        GATKSAMRecord read11 = buildSAMRecord("read11","chr1", 11, 15);
-        SAMRecord read12 = buildSAMRecord("chr1", 12, 16);
+        GATKSAMRecord read12 = buildSAMRecord("read12","chr1", 12, 16);
         SAMRecordIterator iterator = new SAMRecordIterator(read01, read02, read03, read04, read05, read06,
                                                            read07, read08, read09, read10, read11, read12);
 
@@ -257,7 +258,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
 
-        List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
+        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
         Collections.addAll(expectedReads, read01, read02, read03, read04, read05, read06,
                            read07, read08, read09, read10, read11, read12);
         testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
@@ -277,7 +278,7 @@ public abstract class LocusViewTemplate extends BaseTest {
      * @param bounds
      * @param reads
      */
-    protected abstract void testReadsInContext(LocusView view, List<GenomeLoc> bounds, List<SAMRecord> reads);
+    protected abstract void testReadsInContext(LocusView view, List<GenomeLoc> bounds, List<GATKSAMRecord> reads);
 
     /**
      * Fake a reference sequence file.  Essentially, seek a header with a bunch of dummy data.
@@ -321,12 +322,13 @@ public abstract class LocusViewTemplate extends BaseTest {
      *
      * @return New SAM Record
      */
-    protected SAMRecord buildSAMRecord(String contig, int alignmentStart, int alignmentEnd) {
+    protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
         SAMFileHeader header = new SAMFileHeader();
         header.setSequenceDictionary(sequenceSourceFile.getSequenceDictionary());
 
-        SAMRecord record = new SAMRecord(header);
+        GATKSAMRecord record = new GATKSAMRecord(header);
 
+        record.setReadName(readName);
         record.setReferenceIndex(sequenceSourceFile.getSequenceDictionary().getSequenceIndex(contig));
         record.setAlignmentStart(alignmentStart);
         Cigar cigar = new Cigar();

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java

@@ -25,13 +25,10 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
 import com.google.caliper.Param;
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
@@ -41,9 +38,9 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker;
 import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
-import java.lang.reflect.Field;
 import java.util.Collections;
 
 /**
@@ -126,7 +123,7 @@ class CountBasesInReadPerformanceWalker extends ReadWalker<Integer,Long> {
     private long Gs;
     private long Ts;
 
-    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
         for(byte base: read.getReadBases()) {
             switch(base) {
                 case 'A': As++; break;

public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java

@@ -7,6 +7,7 @@ import net.sf.samtools.util.CloseableIterator;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.ReadProperties;
@@ -38,8 +39,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
     }
 
     private final LocusIteratorByState makeLTBS(List<SAMRecord> reads, ReadProperties readAttributes) {
-        return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()),
+        return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()), readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
-                readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
     }
 
     @Test
@@ -212,12 +212,12 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
             Assert.assertEquals(alignmentContext.getLocation().getStart(),currentLocus,"Current locus returned by alignment context is incorrect");
 
             if(currentLocus == firstLocus) {
-                List<SAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
+                List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
                 Assert.assertEquals(readsAtLocus.size(),1,"Wrong number of reads at locus " + currentLocus);
                 Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at locus " + currentLocus);
             }
             else if(currentLocus == secondLocus) {
-                List<SAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
+                List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
                 Assert.assertEquals(readsAtLocus.size(),2,"Wrong number of reads at locus " + currentLocus);
                 Assert.assertSame(readsAtLocus.get(0),indelOnlyRead,"indelOnlyRead absent from pileup at locus " + currentLocus);
                 Assert.assertSame(readsAtLocus.get(1),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at locus " + currentLocus);
@@ -265,7 +265,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         Assert.assertTrue(li.hasNext(),"Missing first locus at " + firstLocus);
         AlignmentContext alignmentContext = li.next();
         Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect locus at this position; should be " + firstLocus);
-        List<SAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
+        List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
         Assert.assertEquals(readsAtLocus.size(),1,"Wrong number of reads at locus " + firstLocus);
         Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at locus " + firstLocus);
 

public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java

@@ -10,6 +10,8 @@ import net.sf.samtools.SAMFileHeader;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
+
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -94,8 +96,8 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
         walker.out = writer;
 
         SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
-        SAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
+        GATKSAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
-        SAMRecord ret = walker.map(bases, rec,null);
+        SAMRecord ret = walker.map(bases, rec, null);
         assertTrue(ret == rec);
         assertTrue(ret.getReadName().equals(rec.getReadName()));
     }

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

@@ -32,7 +32,7 @@ public class ReadUtilsUnitTest extends BaseTest {
         reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
     }
 
-    private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
+    private void testReadBasesAndQuals(GATKSAMRecord read, int expectedStart, int expectedStop) {
         SAMRecord clipped = ReadUtils.hardClipBases(read, expectedStart, expectedStop - 1, null);
         String expectedBases = BASES.substring(expectedStart, expectedStop);
         String expectedQuals = QUALS.substring(expectedStart, expectedStop);

public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java

@@ -26,9 +26,9 @@
 package org.broadinstitute.sting.utils.clipreads;
 
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -44,7 +44,7 @@ public class ReadClipperUnitTest extends BaseTest {
 
     // TODO: Add error messages on failed tests
 
-    SAMRecord read, expected;
+    GATKSAMRecord read, expected;
     ReadClipper readClipper;
     final static String BASES = "ACTG";
     final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63
@@ -65,7 +65,7 @@ public class ReadClipperUnitTest extends BaseTest {
         logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
 
         //Clip whole read
-        Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(0,0), new SAMRecord(read.getHeader()));
+        Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(0,0), new GATKSAMRecord(read.getHeader()));
         //clip 1 base
         expected = readClipper.hardClipBothEndsByReferenceCoordinates(0,3);
         Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes());
@@ -79,7 +79,7 @@ public class ReadClipperUnitTest extends BaseTest {
         logger.warn("Executing testHardClipByReadCoordinates");
 
         //Clip whole read
-        Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new SAMRecord(read.getHeader()));
+        Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader()));
 
         //clip 1 base at start
         expected = readClipper.hardClipByReadCoordinates(0,0);
@@ -112,7 +112,7 @@ public class ReadClipperUnitTest extends BaseTest {
         logger.warn("Executing testHardClipByReferenceCoordinates");
 
         //Clip whole read
-        Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(1,4), new SAMRecord(read.getHeader()));
+        Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(1,4), new GATKSAMRecord(read.getHeader()));
 
         //clip 1 base at start
         expected = readClipper.hardClipByReferenceCoordinates(-1,1);
@@ -145,7 +145,7 @@ public class ReadClipperUnitTest extends BaseTest {
         logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail");
 
         //Clip whole read
-        Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new SAMRecord(read.getHeader()));
+        Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new GATKSAMRecord(read.getHeader()));
 
         //clip 1 base at start
         expected = readClipper.hardClipByReferenceCoordinatesLeftTail(1);
@@ -166,7 +166,7 @@ public class ReadClipperUnitTest extends BaseTest {
         logger.warn("Executing testHardClipByReferenceCoordinatesRightTail");
 
         //Clip whole read
-        Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new SAMRecord(read.getHeader()));
+        Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new GATKSAMRecord(read.getHeader()));
 
         //clip 1 base at end
         expected = readClipper.hardClipByReferenceCoordinatesRightTail(3);
@@ -188,7 +188,7 @@ public class ReadClipperUnitTest extends BaseTest {
 
 
         //Clip whole read
-        Assert.assertEquals(readClipper.hardClipLowQualEnds((byte)64), new SAMRecord(read.getHeader()));
+        Assert.assertEquals(readClipper.hardClipLowQualEnds((byte)64), new GATKSAMRecord(read.getHeader()));
 
         //clip 1 base at start
         expected = readClipper.hardClipLowQualEnds((byte)34);

public/java/test/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java

@@ -25,12 +25,12 @@
 package org.broadinstitute.sting.utils.fragments;
 
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.DataProvider;
@@ -52,16 +52,16 @@ public class FragmentUtilsUnitTest extends BaseTest {
                                   boolean leftIsFirst, boolean leftIsNegative) {
             super(FragmentUtilsTest.class, String.format("%s-leftIsFirst:%b-leftIsNegative:%b", name, leftIsFirst, leftIsNegative));
 
-            List<SAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", readLen, leftStart, rightStart, leftIsFirst, leftIsNegative);
+            List<GATKSAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", readLen, leftStart, rightStart, leftIsFirst, leftIsNegative);
-            SAMRecord left = pair.get(0);
+            GATKSAMRecord left = pair.get(0);
-            SAMRecord right = pair.get(1);
+            GATKSAMRecord right = pair.get(1);
 
             for ( int pos = leftStart; pos < rightStart + readLen; pos++) {
                 boolean posCoveredByLeft = pos >= left.getAlignmentStart() && pos <= left.getAlignmentEnd();
                 boolean posCoveredByRight = pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd();
 
                 if ( posCoveredByLeft || posCoveredByRight ) {
-                    List<SAMRecord> reads = new ArrayList<SAMRecord>();
+                    List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>();
                     List<Integer> offsets = new ArrayList<Integer>();
 
                     if ( posCoveredByLeft ) {
@@ -89,9 +89,9 @@ public class FragmentUtilsUnitTest extends BaseTest {
     private class TestState {
         int expectedSingletons, expectedPairs;
         ReadBackedPileup pileup;
-        List<SAMRecord> rawReads;
+        List<GATKSAMRecord> rawReads;
 
-        private TestState(final int expectedSingletons, final int expectedPairs, final ReadBackedPileup pileup, final List<SAMRecord> rawReads) {
+        private TestState(final int expectedSingletons, final int expectedPairs, final ReadBackedPileup pileup, final List<GATKSAMRecord> rawReads) {
             this.expectedSingletons = expectedSingletons;
             this.expectedPairs = expectedPairs;
             this.pileup = pileup;
@@ -131,7 +131,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
     @Test(enabled = true, dataProvider = "fragmentUtilsTest")
     public void testAsListOfReadsFromPileup(FragmentUtilsTest test) {
         for ( TestState testState : test.statesForPileup ) {
-            FragmentCollection<SAMRecord> fp = FragmentUtils.create(testState.pileup.getReads());
+            FragmentCollection<GATKSAMRecord> fp = FragmentUtils.create(testState.pileup.getReads());
             Assert.assertEquals(fp.getOverlappingPairs().size(), testState.expectedPairs);
             Assert.assertEquals(fp.getSingletonReads().size(), testState.expectedSingletons);
         }
@@ -140,7 +140,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
     @Test(enabled = true, dataProvider = "fragmentUtilsTest")
     public void testAsListOfReads(FragmentUtilsTest test) {
         for ( TestState testState : test.statesForReads ) {
-            FragmentCollection<SAMRecord> fp = FragmentUtils.create(testState.rawReads);
+            FragmentCollection<GATKSAMRecord> fp = FragmentUtils.create(testState.rawReads);
             Assert.assertEquals(fp.getOverlappingPairs().size(), testState.expectedPairs);
             Assert.assertEquals(fp.getSingletonReads().size(), testState.expectedSingletons);
         }
@@ -148,10 +148,10 @@ public class FragmentUtilsUnitTest extends BaseTest {
 
     @Test(enabled = true, expectedExceptions = IllegalArgumentException.class)
     public void testOutOfOrder() {
-        final List<SAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", 100, 1, 50, true, true);
+        final List<GATKSAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", 100, 1, 50, true, true);
-        final SAMRecord left = pair.get(0);
+        final GATKSAMRecord left = pair.get(0);
-        final SAMRecord right = pair.get(1);
+        final GATKSAMRecord right = pair.get(1);
-        final List<SAMRecord> reads = Arrays.asList(right, left); // OUT OF ORDER!
+        final List<GATKSAMRecord> reads = Arrays.asList(right, left); // OUT OF ORDER!
         final List<Integer> offsets = Arrays.asList(0, 50);
         final ReadBackedPileup pileup = new ReadBackedPileupImpl(null, reads, offsets);
         FragmentUtils.create(pileup); // should throw exception

public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java

@@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.pileup;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 
@@ -50,27 +50,25 @@ public class ReadBackedPileupUnitTest {
         header.addReadGroup(readGroupOne);
         header.addReadGroup(readGroupTwo);
 
-        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
+        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
         read1.setAttribute("RG",readGroupOne.getId());
-        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
+        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
         read2.setAttribute("RG",readGroupTwo.getId());
-        SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
+        GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
         read3.setAttribute("RG",readGroupOne.getId());
-        SAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
+        GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
         read4.setAttribute("RG",readGroupTwo.getId());
-        SAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,10);
+        GATKSAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,10);
         read5.setAttribute("RG",readGroupTwo.getId());
-        SAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header,"read6",0,1,10);
+        GATKSAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header,"read6",0,1,10);
         read6.setAttribute("RG",readGroupOne.getId());
-        SAMRecord read7 = ArtificialSAMUtils.createArtificialRead(header,"read7",0,1,10);
+        GATKSAMRecord read7 = ArtificialSAMUtils.createArtificialRead(header,"read7",0,1,10);
         read7.setAttribute("RG",readGroupOne.getId());
 
-        ReadBackedPileup pileup = new ReadBackedPileupImpl(null,
+        ReadBackedPileup pileup = new ReadBackedPileupImpl(null, Arrays.asList(read1,read2,read3,read4,read5,read6,read7), Arrays.asList(1,1,1,1,1,1,1));
-                                                           Arrays.asList(read1,read2,read3,read4,read5,read6,read7),
-                                                           Arrays.asList(1,1,1,1,1,1,1));
 
         ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
-        List<SAMRecord> rg1Reads = rg1Pileup.getReads();
+        List<GATKSAMRecord> rg1Reads = rg1Pileup.getReads();
         Assert.assertEquals(rg1Reads.size(), 4, "Wrong number of reads in read group rg1");
         Assert.assertEquals(rg1Reads.get(0), read1, "Read " + read1.getReadName() + " should be in rg1 but isn't");
         Assert.assertEquals(rg1Reads.get(1), read3, "Read " + read3.getReadName() + " should be in rg1 but isn't");
@@ -78,7 +76,7 @@ public class ReadBackedPileupUnitTest {
         Assert.assertEquals(rg1Reads.get(3), read7, "Read " + read7.getReadName() + " should be in rg1 but isn't");
 
         ReadBackedPileup rg2Pileup = pileup.getPileupForReadGroup("rg2");
-        List<SAMRecord> rg2Reads = rg2Pileup.getReads();        
+        List<GATKSAMRecord> rg2Reads = rg2Pileup.getReads();        
         Assert.assertEquals(rg2Reads.size(), 3, "Wrong number of reads in read group rg2");
         Assert.assertEquals(rg2Reads.get(0), read2, "Read " + read2.getReadName() + " should be in rg2 but isn't");
         Assert.assertEquals(rg2Reads.get(1), read4, "Read " + read4.getReadName() + " should be in rg2 but isn't");
@@ -92,16 +90,16 @@ public class ReadBackedPileupUnitTest {
     public void testSplitByNullReadGroups() {
         SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
 
-        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
+        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
-        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
+        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
-        SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
+        GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
 
         ReadBackedPileup pileup = new ReadBackedPileupImpl(null,
                                                            Arrays.asList(read1,read2,read3),
                                                            Arrays.asList(1,1,1));
 
         ReadBackedPileup nullRgPileup = pileup.getPileupForReadGroup(null);
-        List<SAMRecord> nullRgReads = nullRgPileup.getReads();
+        List<GATKSAMRecord> nullRgReads = nullRgPileup.getReads();
         Assert.assertEquals(nullRgPileup.getNumberOfElements(), 3, "Wrong number of reads in null read group");
         Assert.assertEquals(nullRgReads.get(0), read1, "Read " + read1.getReadName() + " should be in null rg but isn't");
         Assert.assertEquals(nullRgReads.get(1), read2, "Read " + read2.getReadName() + " should be in null rg but isn't");
@@ -125,13 +123,13 @@ public class ReadBackedPileupUnitTest {
         header.addReadGroup(readGroupOne);
         header.addReadGroup(readGroupTwo);
 
-        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
+        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
         read1.setAttribute("RG",readGroupOne.getId());
-        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
+        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
         read2.setAttribute("RG",readGroupTwo.getId());
-        SAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
+        GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
         read3.setAttribute("RG",readGroupOne.getId());
-        SAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
+        GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
         read4.setAttribute("RG",readGroupTwo.getId());
 
         ReadBackedPileupImpl sample1Pileup = new ReadBackedPileupImpl(null,
@@ -147,14 +145,14 @@ public class ReadBackedPileupUnitTest {
         ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null,sampleToPileupMap);
 
         ReadBackedPileup rg1Pileup = compositePileup.getPileupForReadGroup("rg1");
-        List<SAMRecord> rg1Reads = rg1Pileup.getReads();
+        List<GATKSAMRecord> rg1Reads = rg1Pileup.getReads();
 
         Assert.assertEquals(rg1Reads.size(), 2, "Wrong number of reads in read group rg1");
         Assert.assertEquals(rg1Reads.get(0), read1, "Read " + read1.getReadName() + " should be in rg1 but isn't");
         Assert.assertEquals(rg1Reads.get(1), read3, "Read " + read3.getReadName() + " should be in rg1 but isn't");
 
         ReadBackedPileup rg2Pileup = compositePileup.getPileupForReadGroup("rg2");
-        List<SAMRecord> rg2Reads = rg2Pileup.getReads();
+        List<GATKSAMRecord> rg2Reads = rg2Pileup.getReads();
 
         Assert.assertEquals(rg1Reads.size(), 2, "Wrong number of reads in read group rg2");
         Assert.assertEquals(rg2Reads.get(0), read2, "Read " + read2.getReadName() + " should be in rg2 but isn't");
@@ -175,9 +173,9 @@ public class ReadBackedPileupUnitTest {
         header.addReadGroup(readGroupOne);
         header.addReadGroup(readGroupTwo);
 
-        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
+        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
         read1.setAttribute("RG",readGroupOne.getId());
-        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
+        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
         read2.setAttribute("RG",readGroupTwo.getId());
 
         Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();