From a12465b6d55e010f50d626f6fc5a036eb739b071 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Jan 2010 15:25:57 +0000
Subject: [PATCH] The recalFile argument is no longer added into the PG tag of
 a bam produced by TableRecalibration. Based on a request from the Sanger.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2625 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/RecalDataManager.java |  2 +-
 .../recalibration/TableRecalibrationWalker.java      | 12 +++++++-----
 .../variantoptimizer/AnalyzeAnnotationsWalker.java   |  2 --
 .../variantoptimizer/AnnotationDataManager.java      |  5 +----
 4 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index f3904810a..a17221614 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -57,7 +57,7 @@ public class RecalDataManager {
     private static boolean warnUserNullReadGroup = false;
     private static boolean warnUserNoColorSpace = false;
 
-    public static final String versionString = "v2.2.13"; // Major version, minor version, and build number
+    public static final String versionString = "v2.2.14"; // Major version, minor version, and build number
 
     RecalDataManager() {
     	data = new NestedHashMap();
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 d72d05c2b..54cd3b3d6 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -179,7 +179,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
                         // At this point all the covariates should have been found and initialized
                         if( requestedCovariates.size() < 2 ) {
-                            throw new StingException( "Malformed input recalibration file. Covariate names can't be found in file: " + RAC.RECAL_FILE );
+                            throw new StingException( "Malformed input recalibration csv file. Covariate names can't be found in file: " + RAC.RECAL_FILE );
                         }
 
                         final boolean createCollapsedTables = true;
@@ -226,15 +226,17 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             for( Covariate cov : requestedCovariates ) {
                 commandLineString += cov.getClass().getSimpleName() + ", ";
             }
-            commandLineString = commandLineString.substring(0, commandLineString.length() - 2); // trim off the trailing comma
+            commandLineString = commandLineString.substring( 0, commandLineString.length() - 2 ); // Trim off the trailing comma
             commandLineString += "] ";
-            // Add all of the arguments from the recalibraiton argument collection to the command line string
+            // Add all of the arguments from the recalibration argument collection to the command line string
             final Field[] fields = RAC.getClass().getFields();
             for( Field field : fields ) {
                 final ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
                 final List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
                 for( ArgumentDefinition ad : adList ) {
-                    commandLineString += (ad.fullName + "=" + JVMUtils.getFieldValue(field, RAC) + ", ");
+                    if( !ad.fullName.equalsIgnoreCase( "recalFile" ) && !ad.fullName.equalsIgnoreCase( "recal_file" ) ) { // recalFile argument is not added to the PG tag
+                        commandLineString += (ad.fullName + "=" + JVMUtils.getFieldValue(field, RAC) + ", ");
+                    }
                 }
             }
             commandLineString += "pQ = " + PRESERVE_QSCORES_LESS_THAN + ", ";
@@ -242,7 +244,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             programRecord.setCommandLine( commandLineString );
             header.addProgramRecord( programRecord );
 
-            // write out the new header
+            // Write out the new header
             OUTPUT_BAM.writeHeader( header );
         }
     }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
index c1389efdb..de2dbf4a6 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
@@ -3,11 +3,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.RODRecordList;
 import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.io.IOException;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
index d779373fd..9f85af89a 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
@@ -4,10 +4,7 @@ import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
 
-import java.util.HashMap;
-import java.util.TreeSet;
-import java.util.Map;
-import java.util.Iterator;
+import java.util.*;
 import java.io.PrintStream;
 import java.io.FileNotFoundException;