From b51f4aae115dae5cf4e9d8cde0cc5598f866348d Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 Jan 2010 20:58:27 +0000
Subject: [PATCH] Updating the recalibrator to make use of StingSAMFileWriter.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2566 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../TableRecalibrationWalker.java             | 27 +++++++------------
 1 file changed, 9 insertions(+), 18 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index c45c8ab63..540d5d6cf 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.utils.cmdLine.*;
 import org.broadinstitute.sting.utils.*;
 
@@ -70,8 +71,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Argument(fullName="output_bam", shortName="outputBam", doc="output BAM file", required=true)
-    private String OUTPUT_BAM_FILE = null;
+    @Argument(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true)
+    private StingSAMFileWriter OUTPUT_BAM;
     @Argument(fullName="preserve_qscores_less_than", shortName="pQ",
         doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
     private int PRESERVE_QSCORES_LESS_THAN = 5;
@@ -79,9 +80,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private int SMOOTHING = 1;
     @Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default is 40")
     private int MAX_QUALITY_SCORE = 40;
-    @Argument(fullName="compression_level", shortName="compress", required = false, doc="Compression level parameter passed to SAMFileWriter, higher value means more compression at added cost in run time, default is 5")
-    private int COMPRESSION_LEVEL = 5;
-
+    
     /////////////////////////////
     // Debugging-only Arguments
     /////////////////////////////
@@ -96,8 +95,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
     private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
-    private static final String versionString = "v2.2.8"; // Major version, minor version, and build number
-    private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
+    private static final String versionString = "v2.2.9"; // Major version, minor version, and build number
     private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
     private static final long RANDOM_SEED = 1032861495;
 
@@ -247,14 +245,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             commandLineString += "smoothing = " + SMOOTHING;
             programRecord.setCommandLine( commandLineString );
             header.addProgramRecord( programRecord );
-        }
 
-        // Create the SAMFileWriter that we will be using to output the reads
-        if( OUTPUT_BAM_FILE != null ) {
-            final SAMFileWriterFactory factory = new SAMFileWriterFactory();
-            OUTPUT_BAM = factory.makeBAMWriter( header, true, new File(OUTPUT_BAM_FILE), COMPRESSION_LEVEL );
+            // write out the new header
+            OUTPUT_BAM.writeHeader( header );
         }
-
     }
 
     /**
@@ -353,7 +347,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      * @param key The list of Comparables that were calculated from the covariates
      * @return A recalibrated quality score as a byte
      */
-    private byte performSequentialQualityCalculation(final Object... key ) {
+    private byte performSequentialQualityCalculation( final Object... key ) {
 
         final byte qualFromRead = (byte)Integer.parseInt(key[1].toString());
         final Object[] readGroupCollapsedKey = new Object[1];
@@ -454,12 +448,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     }
 
     /**
-     * Close the output bam file
+     * Do nothing
      * @param output The SAMFileWriter that outputs the bam file
      */
     public void onTraversalDone(SAMFileWriter output) {
-        if( output != null ) {
-            output.close();
-        }
     }
 }