From a301ba1977817cab5b6cb1cc10bd306ee394a8ac Mon Sep 17 00:00:00 2001
From: Pierre Lindenbaum <plindenbaum@yahoo.fr>
Date: Fri, 23 Sep 2016 11:17:24 +0200
Subject: [PATCH] Add read group identifier to column names

If two SAMReadGroupRecords share the same sample name, the output will contain duplicate column headers.
This PR fix the problem.
---
 .../diagnostics/ReadLengthDistribution.java   |  2 +-
 ...ReadLengthDistributionIntegrationTest.java | 42 +++++++++++++++++++
 2 files changed, 43 insertions(+), 1 deletion(-)
 create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistributionIntegrationTest.java

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
index 098d4d4ba..1e7e48c5a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
@@ -163,7 +163,7 @@ public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
         }
         else{
             for (SAMReadGroupRecord rg : readGroups)
-                tableReport.addColumn(rg.getSample());
+                tableReport.addColumn(rg.getSample() + "[rg:" + rg.getReadGroupId() +"]");
             int rowIndex = 0;
             for (Integer length : table.keySet()){
                 tableReport.set(rowIndex,0,length);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistributionIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistributionIntegrationTest.java
new file mode 100644
index 000000000..e25b1be8c
--- /dev/null
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistributionIntegrationTest.java
@@ -0,0 +1,42 @@
+/*
+* Copyright 2012-2016 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.diagnostics;
+
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class ReadLengthDistributionIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testReadLengthDistributionMultiSample() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T ReadLengthDistribution -R " + b37KGReference + " -I " + privateTestDir + "testReadPos.snippet.bam -rf NotPrimaryAlignment -rf UnmappedRead -rf FailsVendorQualityCheck -rf DuplicateRead -o %s", 1,
+                Arrays.asList("9f0551e7116c7c8a56d6f7f756d02795"));
+        executeTest("test ReadLengthDistribution with a bame with multiple read groups", spec);
+    }
+}