From b28f63a9484b2f12c1ff3ec8803117e2c1c6d014 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Sep 2010 22:13:50 +0000
Subject: [PATCH] Base recalibrator now uses -o and deprecates -outputBam

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4189 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/TableRecalibrationWalker.java      | 12 +++++-------
 .../RecalibrationWalkersIntegrationTest.java         | 10 +++++-----
 2 files changed, 10 insertions(+), 12 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 ebf18aa90..715a1f177 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -82,13 +82,14 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     @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");
 
-    @Output
-    private PrintStream out;
-
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Output(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true)
+    @Argument(fullName="output_bam", shortName="outputBam", doc="Please use --out instead", required=false)
+    @Deprecated
+    protected String outbam;
+
+    @Output(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)
@@ -501,10 +502,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
         if( output != null ) {
             output.addAlignment(read);
-        } else {
-            out.println(read.format());
         }
-
         return output;
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index eb5c60d67..57abd4c4b 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -69,7 +69,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " -I " + bam +
                                 ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
                                     ? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) +
-                                " -outputBam %s" +
+                                " -o %s" +
                                 " --no_pg_tag" +
                                 " --solid_recal_mode SET_Q_ZERO" +
                                 " -recalFile " + paramsFile,
@@ -120,7 +120,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " -I " + bam +
                                 ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
                                     ? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) +
-                                " -outputBam %s" +
+                                " -o %s" +
                                 " --no_pg_tag" +
                                 " -maxQ 70" +
                                 " --solid_recal_mode SET_Q_ZERO" +
@@ -175,7 +175,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                         "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
-                                " -outputBam %s" +
+                                " -o %s" +
                                 " --no_pg_tag" +
                                 " -U" +
                                 " -L 1:10,000,000-20,000,000" +
@@ -289,7 +289,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " -T TableRecalibration" +
                                 " -I " + bam +
                                 " -L 1:10,100,000-10,300,000" +
-                                " -outputBam %s" +
+                                " -o %s" +
                                 " --no_pg_tag" +
                                 " --solid_recal_mode SET_Q_ZERO" +
                                 " --default_read_group DefaultReadGroup" +
@@ -343,7 +343,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                         "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
-                                " -outputBam %s" +
+                                " -o %s" +
                                 " --no_pg_tag" +
                                 " --solid_recal_mode DO_NOTHING" +
                                 " -recalFile " + paramsFile +