From 78e94b5a84f4d074992f99fbc74d82ab07dd640c Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 12 Dec 2009 17:29:41 +0000
Subject: [PATCH] TableRecalibration now puts the full list of walker arguments
 into the PG tag of the bam file it creates. Thanks Matt and Eric. Also, the
 default nback for the HomopolymerCovariate is 8, down from 10.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2339 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/HomopolymerCovariate.java   |  2 +-
 .../RecalibrationArgumentCollection.java      |  2 +-
 .../TableRecalibrationWalker.java             | 22 ++++++++++++++-----
 3 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
index ecf82131d..0e9fb9306 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
@@ -40,7 +40,7 @@ import net.sf.samtools.SAMRecord;
 
 public class HomopolymerCovariate implements ExperimentalCovariate {
 
-    int numBack = 10;
+    int numBack = 8;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
     public void initialize( final RecalibrationArgumentCollection RAC ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
index 1266441f0..7a5c9cdc6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
@@ -58,7 +58,7 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "window_size_nqs", shortName="nqs", doc="The window size used by MinimumNQSCovariate for its calculation", required=false)
     public int WINDOW_SIZE = 5;
     @Argument(fullName = "homopolymer_nback", shortName="nback", doc="The number of previous bases to look at in HomopolymerCovariate", required=false)
-    public int HOMOPOLYMER_NBACK = 10;
+    public int HOMOPOLYMER_NBACK = 8;
 
     public boolean checkSolidRecalMode() {
         return ( SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO") ||
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 7e09f9d18..0d279315a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -6,8 +6,7 @@ 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.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
+import org.broadinstitute.sting.utils.cmdLine.*;
 import org.broadinstitute.sting.utils.*;
 
 import java.util.ArrayList;
@@ -16,6 +15,7 @@ import java.util.Random;
 import java.util.regex.Pattern;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.lang.reflect.Field;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -94,7 +94,7 @@ 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 = "v2.1.0"; // Major version, minor version, and build number
+    private static final String versionString = "v2.1.1"; // Major version, minor version, and build number
     private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
     private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
 
@@ -229,13 +229,25 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         // Take the header of the input SAM file and tweak it by adding in a new programRecord with the version number and list of covariates that were used
         SAMFileHeader header = getToolkit().getSAMFileHeader().clone();
         if( !NO_PG_TAG ) {
-            SAMProgramRecord programRecord = new SAMProgramRecord( "TableRecalibrationWalker" );
+            SAMProgramRecord programRecord = new SAMProgramRecord( "GATK TableRecalibration" );
             programRecord.setProgramVersion( versionString );
-            String commandLineString = "Covariates used: ";
+            String commandLineString = "Covariates used = [";
             for( Covariate cov : requestedCovariates ) {
                 commandLineString += cov.getClass().getSimpleName() + ", ";
             }
             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
+            Field[] fields = RAC.getClass().getFields();
+            for( Field field : fields ) {
+                ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
+                List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
+                for( ArgumentDefinition ad : adList ) {
+                    commandLineString += (ad.fullName + "=" + JVMUtils.getFieldValue(field, RAC) + ", ");
+                }
+            }
+            commandLineString += "pQ = " + PRESERVE_QSCORES_LESS_THAN + ", ";
+            commandLineString += "smoothing = " + SMOOTHING;
             programRecord.setCommandLine( commandLineString );
             header.addProgramRecord( programRecord );
         }