PrintReads writes a header when used with -BQSR

protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java

@@ -220,6 +220,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                         " -R " + hg18Reference +
                         " -I " + privateTestDir + "HiSeq.1mb.1RG.bam" +
                         " -nct " + nct +
+                        " --no_pg_tag" +
                         " -BQSR " + privateTestDir + "HiSeq.20mb.1RG.table" +
                         params.args +
                         " -o %s",
@@ -234,6 +235,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                         " -R " + hg18Reference +
                         " -I " + HiSeqBam +
                         " -L " + HiSeqInterval +
+                        " --no_pg_tag" +
                         " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.highMaxCycle.table" +
                         " -o /dev/null",
                 0,
@@ -248,6 +250,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                         " -R " + hg18Reference +
                         " -I " + HiSeqBam +
                         " -L " + HiSeqInterval +
+                        " --no_pg_tag" +
                         " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
                         " -o /dev/null",
                 0,

public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java

@@ -28,15 +28,19 @@ package org.broadinstitute.sting.gatk.walkers.readutils;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -97,7 +101,7 @@ import java.util.*;
 public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> implements NanoSchedulable {
 
     @Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
-    SAMFileWriter out;
+    StingSAMFileWriter out;
 
     @Argument(fullName = "readGroup", shortName = "readGroup", doc="Exclude all reads with this read group from the output", required = false)
     String readGroup = null;
@@ -137,18 +141,27 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
      */
     @Argument(fullName="simplify", shortName="s", doc="Simplify all reads.", required=false)
     public boolean simplifyReads = false;
-    
+
+    @Hidden
+    @Argument(fullName = "no_pg_tag", shortName = "npt", doc ="", required = false)
+    private boolean NO_PG_TAG = false;
 
     List<ReadTransformer> readTransformers = Collections.emptyList();
     private TreeSet<String> samplesToChoose = new TreeSet<String>();
     private boolean SAMPLES_SPECIFIED = false;
+
+    public static final String PROGRAM_RECORD_NAME = "GATK PrintReads";   // The name that will go in the @PG tag
     
     Random random;
 
+
     /**
      * The initialize function.
      */
     public void initialize() {
+        final boolean keep_records = true;
+        final GenomeAnalysisEngine toolkit = getToolkit();
+
         if  ( platform != null )
             platform = platform.toUpperCase();
 
@@ -167,9 +180,14 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
         if(!samplesToChoose.isEmpty()) {
             SAMPLES_SPECIFIED = true;
         }
-        
+
         random = GenomeAnalysisEngine.getRandomGenerator();
 
+        final boolean preSorted = true;
+        if (getToolkit() != null && getToolkit().getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) {
+            Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
+        }
+
     }
 
     /**

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

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -61,12 +62,12 @@ import java.util.List;
 /**
  * @author aaron
  *         <p/>
- *         Class ArtificialSAMFileWriter
+ *         Class ArtificialStingSAMFileWriter
  *         <p/>
  * generates a fake samwriter, that you can get the output reads
  * from when you're done.  
  */
-public class ArtificialSAMFileWriter implements SAMFileWriter {
+public class ArtificialStingSAMFileWriter implements StingSAMFileWriter {
 
     // are we closed
     private boolean closed = false;
@@ -106,4 +107,16 @@ public class ArtificialSAMFileWriter implements SAMFileWriter {
     public List<SAMRecord> getRecords() {
         return records;
     }
+
+    @Override
+    public void writeHeader(SAMFileHeader header) {
+    }
+
+    @Override
+    public void setPresorted(boolean presorted) {
+    }
+
+    @Override
+    public void setMaxRecordsInRam(int maxRecordsInRam) {
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java

@@ -75,6 +75,7 @@ public class PrintReadsIntegrationTest extends WalkerTest {
                         " -R " + params.reference +
                         " -I " + privateTestDir + params.bam +
                         params.args +
+                        " --no_pg_tag" +
                         " -o %s",
                 Arrays.asList(params.md5));
         executeTest("testPrintReads-"+params.args, spec).getFirst();

public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java

@@ -30,7 +30,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter;
+import org.broadinstitute.sting.utils.sam.ArtificialStingSAMFileWriter;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.annotations.BeforeMethod;
@@ -85,7 +85,7 @@ public class PrintReadsUnitTest extends BaseTest {
     //private ReferenceContext ref = new ReferenceContext()
 
     org.broadinstitute.sting.gatk.walkers.readutils.PrintReads walker;
-    ArtificialSAMFileWriter writer;
+    ArtificialStingSAMFileWriter writer;
 
     @BeforeMethod
     public void before() {
@@ -93,8 +93,7 @@ public class PrintReadsUnitTest extends BaseTest {
         readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
 
         walker = new org.broadinstitute.sting.gatk.walkers.readutils.PrintReads();
-        writer = new ArtificialSAMFileWriter();
+        writer = new ArtificialStingSAMFileWriter();
-        walker.out = writer;
         walker.initialize();
     }
 
@@ -121,7 +120,4 @@ public class PrintReadsUnitTest extends BaseTest {
         assertTrue(ret == rec);
         assertTrue(ret.getReadName().equals(rec.getReadName()));
     }
-
-
-    
 }

public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java

@@ -65,14 +65,14 @@ import java.util.List;
 /**
  * @author aaron
  *         <p/>
- *         Class ArtificialSAMFileWriter
+ *         Class ArtificialStingSAMFileWriter
  *         <p/>
- *         Test out the ArtificialSAMFileWriter class
+ *         Test out the ArtificialStingSAMFileWriter class
  */
 public class ArtificialSAMFileWriterUnitTest extends BaseTest {
 
     /** the artificial sam writer */
-    private ArtificialSAMFileWriter writer;
+    private ArtificialStingSAMFileWriter writer;
     private SAMFileHeader header;
     private final int startChr = 1;
     private final int numChr = 2;
@@ -80,7 +80,7 @@ public class ArtificialSAMFileWriterUnitTest extends BaseTest {
 
     @BeforeMethod
     public void before() {
-        writer = new ArtificialSAMFileWriter();
+        writer = new ArtificialStingSAMFileWriter();
         header = ArtificialSAMUtils.createArtificialSamHeader(numChr, startChr, chrSize);
     }