The GATK engine now ensures that incoming GATKSAMRecords have GATKSAMReadGroupRecord objects in their header

-- Update SAMDataSource so that the merged header contains GATKSAMReadGroupRecord
-- Now getting the NGSPlatform for a GATKSAMRecord is actually efficient, instead of computing the NGS platform over and over from the PL string
-- Updated a few places in the code where the input argument is actually a GATKSAMRecord, not a SAMRecord for type safety

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -44,6 +44,7 @@ import org.broadinstitute.sting.utils.SimpleTimer;
 import org.broadinstitute.sting.utils.baq.ReadTransformingIterator;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
 
 import java.io.File;
@@ -894,9 +895,11 @@ public class SAMDataSource {
             long lastTick = timer.currentTime();
             for(final SAMReaderID readerID: readerIDs) {
                 final ReaderInitializer init = new ReaderInitializer(readerID).call();
+
                 if (removeProgramRecords) {
                     init.reader.getFileHeader().setProgramRecords(new ArrayList<SAMProgramRecord>());
                 }
+
                 if (threadAllocation.getNumIOThreads() > 0) {
                     inputStreams.put(init.readerID, init.blockInputStream); // get from initializer
                 }
@@ -916,6 +919,13 @@ public class SAMDataSource {
             for(SAMFileReader reader: readers.values())
                 headers.add(reader.getFileHeader());
             headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,headers,true);
+
+            // update all read groups to GATKSAMRecordReadGroups
+            final List<SAMReadGroupRecord> gatkReadGroups = new LinkedList<SAMReadGroupRecord>();
+            for ( final SAMReadGroupRecord rg : headerMerger.getMergedHeader().getReadGroups() ) {
+                gatkReadGroups.add(new GATKSAMReadGroupRecord(rg));
+            }
+            headerMerger.getMergedHeader().setReadGroups(gatkReadGroups);
         }
 
         final private void printReaderPerformance(final int nExecutedTotal,

public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
@@ -37,6 +38,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 public class Platform454Filter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
-        return (ReadUtils.is454Read(rec));
+        return (ReadUtils.is454Read((GATKSAMRecord)rec));
     }
 }

public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
@@ -41,7 +42,7 @@ public class PlatformFilter extends ReadFilter {
 
     public boolean filterOut(SAMRecord rec) {
         for ( String name : PLFilterNames )
-            if ( ReadUtils.isPlatformRead(rec, name.toUpperCase() ))
+            if ( ReadUtils.isPlatformRead((GATKSAMRecord)rec, name.toUpperCase() ))
                 return true;
         return false;
     }

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

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.variant.variantcontext.Allele;
 
@@ -421,7 +422,7 @@ public class HaplotypeIndelErrorModel {
         double[][] haplotypeLikehoodMatrix = new double[haplotypesInVC.size()][haplotypesInVC.size()];
         double readLikelihoods[][] = new double[pileup.getReads().size()][haplotypesInVC.size()];
         int i=0;
-        for (SAMRecord read : pileup.getReads()) {
+        for (GATKSAMRecord read : pileup.getReads()) {
             if(ReadUtils.is454Read(read)) {
                 continue;
             }

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

@@ -529,7 +529,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         sawReadInCurrentInterval = false;
     }
 
-    private boolean doNotTryToClean(SAMRecord read) {
+    private boolean doNotTryToClean(GATKSAMRecord read) {
         return read.getReadUnmappedFlag() ||
                 read.getNotPrimaryAlignmentFlag() ||
                 read.getReadFailsVendorQualityCheckFlag() ||
@@ -835,7 +835,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         // TODO -- get rid of this try block when Picard does the right thing for reads aligned off the end of the reference
                         try {
                             if ( read.getAttribute(SAMTag.NM.name()) != null )
-                                read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, leftmostIndex-1));
+                                read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, leftmostIndex - 1));
                             if ( read.getAttribute(SAMTag.UQ.name()) != null )
                                 read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, leftmostIndex-1));
                         } catch (Exception e) {

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

@@ -24,8 +24,7 @@
 
 package org.broadinstitute.sting.utils;
 
-import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import net.sf.samtools.SAMRecord;
 
 /**
  * A canonical, master list of the standard NGS platforms.  These values
@@ -64,25 +63,15 @@ public enum NGSPlatform {
     }
 
     /**
-     * Convenience constructor -- calculates the NGSPlatfrom from a SAMRecord.
+     * Convenience get -- get the NGSPlatfrom from a SAMRecord.
-     * Note you should not use this function if you have a GATKSAMRecord -- use the
-     * accessor method instead.
      *
-     * @param read
+     * Just gets the platform from the GATKReadGroupRecord associated with this read.
+     *
+     * @param read a GATKSAMRecord
      * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
      */
-    public static final NGSPlatform fromRead(SAMRecord read) {
+    public static NGSPlatform fromRead(GATKSAMRecord read) {
-        return fromReadGroup(read.getReadGroup());
+        return read.getReadGroup().getNGSPlatform();
-    }
-
-    /**
-     * Returns the NGSPlatform corresponding to the PL tag in the read group
-     * @param rg
-     * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
-     */
-    public static final NGSPlatform fromReadGroup(SAMReadGroupRecord rg) {
-        if ( rg == null ) return UNKNOWN;
-        return fromReadGroupPL(rg.getPlatform());
     }
 
     /**
@@ -90,7 +79,7 @@ public enum NGSPlatform {
      * @param plFromRG -- the PL field (or equivalent) in a ReadGroup object
      * @return an NGSPlatform object matching the PL field of the header, or UNKNOWN if there was no match
      */
-    public static final NGSPlatform fromReadGroupPL(final String plFromRG) {
+    public static NGSPlatform fromReadGroupPL(final String plFromRG) {
         if ( plFromRG == null ) return UNKNOWN;
 
         // todo -- algorithm could be implemented more efficiently, as the list of all
@@ -113,7 +102,7 @@ public enum NGSPlatform {
      * @param platform the read group string that describes the platform used
      * @return true if the platform is known (i.e. it's in the list and is not UNKNOWN)
      */
-    public static final boolean isKnown (final String platform) {
+    public static final boolean isKnown(final String platform) {
         return fromReadGroupPL(platform) != UNKNOWN;
     }
 }

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

@@ -12,9 +12,6 @@ import org.broadinstitute.sting.utils.NGSPlatform;
  *
  */
 public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
-
-    public static final String LANE_TAG = "LN";
-    
     // the SAMReadGroupRecord data we're caching
     private String mSample = null;
     private String mPlatform = null;
@@ -33,46 +30,14 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
         super(record.getReadGroupId(), record);
     }
 
-    public GATKSAMReadGroupRecord(SAMReadGroupRecord record, NGSPlatform pl) {
+    /**
-        super(record.getReadGroupId(), record);
+     * Get the NGSPlatform enum telling us the platform of this read group
-        setPlatform(pl.getDefaultPlatform());
+     *
-        mNGSPlatform = pl;
+     * This function call is caching, so subsequent calls to it are free, while
-        retrievedPlatform = retrievedNGSPlatform = true;
+     * the first time it's called there's a bit of work to resolve the enum
-    }
+     *
-
+     * @return an NGSPlatform enum value
-    ///////////////////////////////////////////////////////////////////////////////
+     */
-    // *** The following methods are overloaded to cache the appropriate data ***//
-    ///////////////////////////////////////////////////////////////////////////////
-
-    public String getSample() {
-        if ( !retrievedSample ) {
-            mSample = super.getSample();
-            retrievedSample = true;
-        }
-        return mSample;
-    }
-
-    public void setSample(String s) {
-        super.setSample(s);
-        mSample = s;
-        retrievedSample = true;
-    }
-
-    public String getPlatform() {
-        if ( !retrievedPlatform ) {
-            mPlatform = super.getPlatform();
-            retrievedPlatform = true;
-        }
-        return mPlatform;
-    }
-
-    public void setPlatform(String s) {
-        super.setPlatform(s);
-        mPlatform = s;
-        retrievedPlatform = true;
-        retrievedNGSPlatform = false; // recalculate the NGSPlatform
-    }
-
     public NGSPlatform getNGSPlatform() {
         if ( ! retrievedNGSPlatform ) {
             mNGSPlatform = NGSPlatform.fromReadGroupPL(getPlatform());
@@ -82,11 +47,40 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
         return mNGSPlatform;
     }
 
-    public String getLane() {
+    ///////////////////////////////////////////////////////////////////////////////
-        return this.getAttribute(LANE_TAG);
+    // *** The following methods are overloaded to cache the appropriate data ***//
+    ///////////////////////////////////////////////////////////////////////////////
+
+    @Override
+    public String getSample() {
+        if ( !retrievedSample ) {
+            mSample = super.getSample();
+            retrievedSample = true;
+        }
+        return mSample;
     }
 
-    public void setLane(String lane) {
+    @Override
-        this.setAttribute(LANE_TAG, lane);
+    public void setSample(String s) {
+        super.setSample(s);
+        mSample = s;
+        retrievedSample = true;
+    }
+
+    @Override
+    public String getPlatform() {
+        if ( !retrievedPlatform ) {
+            mPlatform = super.getPlatform();
+            retrievedPlatform = true;
+        }
+        return mPlatform;
+    }
+
+    @Override
+    public void setPlatform(String s) {
+        super.setPlatform(s);
+        mPlatform = s;
+        retrievedPlatform = true;
+        retrievedNGSPlatform = false; // recalculate the NGSPlatform
     }
 }

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

@@ -25,9 +25,9 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.recalibration.EventType;
 import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.recalibration.EventType;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -141,16 +141,26 @@ public class GATKSAMRecord extends BAMRecord {
         mReadString = s;
     }
 
+    /**
+     * Get the GATKSAMReadGroupRecord of this read
+     * @return a non-null GATKSAMReadGroupRecord
+     */
     @Override
     public GATKSAMReadGroupRecord getReadGroup() {
-        if ( !retrievedReadGroup ) {
+        if ( ! retrievedReadGroup ) {
-            SAMReadGroupRecord tempReadGroup = super.getReadGroup();
+            mReadGroup = (GATKSAMReadGroupRecord)super.getReadGroup();
-            mReadGroup = (tempReadGroup == null ? null : new GATKSAMReadGroupRecord(tempReadGroup));
             retrievedReadGroup = true;
         }
         return mReadGroup;
     }
 
+    public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
+        mReadGroup = readGroup;
+        retrievedReadGroup = true;
+        setAttribute("RG", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils!
+    }
+
+
     @Override
     public int hashCode() {
         return super.hashCode();
@@ -259,12 +269,6 @@ public class GATKSAMRecord extends BAMRecord {
         return getReadGroup().getNGSPlatform();
     }
 
-    public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
-        mReadGroup = readGroup;
-        retrievedReadGroup = true;
-        setAttribute("RG", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils!
-    }
-
     ///////////////////////////////////////////////////////////////////////////////
     // *** ReduceReads functions                                              ***//
     ///////////////////////////////////////////////////////////////////////////////

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

@@ -226,7 +226,7 @@ public class ReadUtils {
      * @param read the read to test
      * @return checks the read group tag PL for the default 454 tag
      */
-    public static boolean is454Read(SAMRecord read) {
+    public static boolean is454Read(GATKSAMRecord read) {
         return NGSPlatform.fromRead(read) == NGSPlatform.LS454;
     }
 
@@ -236,7 +236,7 @@ public class ReadUtils {
      * @param read the read to test
      * @return checks the read group tag PL for the default ion tag
      */
-    public static boolean isIonRead(SAMRecord read) {
+    public static boolean isIonRead(GATKSAMRecord read) {
         return NGSPlatform.fromRead(read) == NGSPlatform.ION_TORRENT;
     }
 
@@ -246,7 +246,7 @@ public class ReadUtils {
      * @param read the read to test
      * @return checks the read group tag PL for the default SOLiD tag
      */
-    public static boolean isSOLiDRead(SAMRecord read) {
+    public static boolean isSOLiDRead(GATKSAMRecord read) {
         return NGSPlatform.fromRead(read) == NGSPlatform.SOLID;
     }
 
@@ -256,7 +256,7 @@ public class ReadUtils {
      * @param read the read to test
      * @return checks the read group tag PL for the default SLX tag
      */
-    public static boolean isIlluminaRead(SAMRecord read) {
+    public static boolean isIlluminaRead(GATKSAMRecord read) {
         return NGSPlatform.fromRead(read) == NGSPlatform.ILLUMINA;
     }
 
@@ -268,7 +268,7 @@ public class ReadUtils {
      * @param name the upper-cased platform name to test
      * @return whether or not name == PL tag in the read group of read
      */
-    public static boolean isPlatformRead(SAMRecord read, String name) {
+    public static boolean isPlatformRead(GATKSAMRecord read, String name) {
 
         SAMReadGroupRecord readGroup = read.getReadGroup();
         if (readGroup != null) {