Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java

@@ -256,7 +256,6 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
         // todo -- rework the whole NO_PG_TAG thing
         final boolean preSorted = true;
         final boolean indexOnTheFly = true;
-        final boolean generateMD5 = true;
         final boolean keep_records = true;
         final SAMFileHeader.SortOrder sortOrder = SAMFileHeader.SortOrder.coordinate;
         if (nwayout) {
@@ -267,7 +266,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
             writerToUse = out;
             out.setPresorted(false);
             if (!NO_PG_TAG) {
-                Utils.setupWriter(out, toolkit, !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
+                Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
             }
         }
     }

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

@@ -687,23 +687,69 @@ public class Utils {
             array[i] = value;
     }
 
-    public static void setupWriter(StingSAMFileWriter writer, GenomeAnalysisEngine toolkit, boolean preSorted, boolean KEEP_ALL_PG_RECORDS, Object walker, String PROGRAM_RECORD_NAME) {
+    /**
-        final SAMProgramRecord programRecord = createProgramRecord(toolkit, walker, PROGRAM_RECORD_NAME);
+     * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets
-
+     * up the writer with the header and presorted status.
-        SAMFileHeader header = toolkit.getSAMFileHeader();
+     *
+     * @param toolkit             the engine
+     * @param originalHeader      original header
+     * @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already existing in this BAM file
+     * @param programRecord       the program record for this program
+     */
+    public static SAMFileHeader setupWriter(GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean KEEP_ALL_PG_RECORDS, SAMProgramRecord programRecord) {
+        SAMFileHeader header = originalHeader.clone();
         List<SAMProgramRecord> oldRecords = header.getProgramRecords();
         List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
         for ( SAMProgramRecord record : oldRecords )
-            if ( !record.getId().startsWith(PROGRAM_RECORD_NAME) || KEEP_ALL_PG_RECORDS )
+            if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS )
                 newRecords.add(record);
 
         newRecords.add(programRecord);
         header.setProgramRecords(newRecords);
+        return header;
+    }
 
+    /**
+    * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and returns
+    * the new header to be added to the BAM writer.
+    *
+    * @param toolkit             the engine
+    * @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already existing in this BAM file
+    * @param walker              the walker object (so we can extract the command line)
+    * @param PROGRAM_RECORD_NAME the name for the PG tag
+    * @return a pre-filled header for the bam writer
+    */
+    public static SAMFileHeader setupWriter(GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean KEEP_ALL_PG_RECORDS, Object walker, String PROGRAM_RECORD_NAME) {
+        final SAMProgramRecord programRecord = createProgramRecord(toolkit, walker, PROGRAM_RECORD_NAME);
+        return setupWriter(toolkit, originalHeader, KEEP_ALL_PG_RECORDS, programRecord);
+    }
+
+    /**
+     * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets
+     * up the writer with the header and presorted status.
+     *
+     * @param writer              BAM file writer
+     * @param toolkit             the engine
+     * @param preSorted           whether or not the writer can assume reads are going to be added are already sorted
+     * @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already existing in this BAM file
+     * @param walker              the walker object (so we can extract the command line)
+     * @param PROGRAM_RECORD_NAME the name for the PG tag
+     */
+    public static void setupWriter(StingSAMFileWriter writer, GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean preSorted, boolean KEEP_ALL_PG_RECORDS, Object walker, String PROGRAM_RECORD_NAME) {
+        SAMFileHeader header = setupWriter(toolkit, originalHeader, KEEP_ALL_PG_RECORDS, walker, PROGRAM_RECORD_NAME);
         writer.writeHeader(header);
         writer.setPresorted(preSorted);
     }
-    
+
+
+    /**
+     * Creates a program record (@PG) tag
+     *
+     * @param toolkit             the engine
+     * @param walker              the walker object (so we can extract the command line)
+     * @param PROGRAM_RECORD_NAME the name for the PG tag
+     * @return a program record for the tool
+     */
     public static SAMProgramRecord createProgramRecord(GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) {
         final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
         final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
@@ -858,4 +904,5 @@ public class Utils {
         }
         return subLists;
     }
+
 }

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

@@ -28,11 +28,14 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
@@ -138,21 +141,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
     private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted,
                            boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) {
         File f = new File(outName);
-        SAMFileHeader header = toolkit.getSAMFileHeader(id).clone();
+        SAMFileHeader header = Utils.setupWriter(toolkit, toolkit.getSAMFileHeader(id), KEEP_ALL_PG_RECORDS, programRecord);
-        header.setSortOrder(order);
-
-        if ( programRecord != null )  {
-            // --->> add program record
-            List<SAMProgramRecord> oldRecords = header.getProgramRecords();
-            List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
-            for ( SAMProgramRecord record : oldRecords ) {
-                if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS )
-                    newRecords.add(record);
-            }
-            newRecords.add(programRecord);
-            header.setProgramRecords(newRecords);
-            // <-- add program record ends here
-        }
         SAMFileWriterFactory factory = new SAMFileWriterFactory();
         factory.setCreateIndex(indexOnTheFly);
         factory.setCreateMd5File(generateMD5);