From a36951f11abf2050a6d0acfdd2e46c114fd19cd4 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 14 Aug 2010 18:36:28 +0000
Subject: [PATCH] @output and @input arguments for table recalibration for use
 with Q

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4037 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/recalibration/TableRecalibrationWalker.java   | 8 ++++----
 1 file changed, 4 insertions(+), 4 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 1c4a7d69c..b3d3ab4fd 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -78,13 +78,13 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     /////////////////////////////
     @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
 
-    @Argument(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file")
-    public String RECAL_FILE = "output.recal_data.csv";
+    @Input(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file")
+    public File RECAL_FILE = new File("output.recal_data.csv");
 
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Argument(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true)
+    @Output(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true)
     private StingSAMFileWriter OUTPUT_BAM = null;
     @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)
@@ -159,7 +159,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         boolean sawEOF = false;
         try {
-            for ( String line : new XReadLines(new File( RECAL_FILE )) ) {
+            for ( String line : new XReadLines(RECAL_FILE) ) {
                 lineNumber++;
                 if ( EOF_MARKER.equals(line) ) {
                     sawEOF = true;