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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.
This commit is contained in:
Pierre Lindenbaum 2016-09-23 11:17:24 +02:00 committed by Ron Levine
parent 967b4f4ae8
commit a301ba1977
2 changed files with 43 additions and 1 deletions
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2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
View File

@ -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);

42
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistributionIntegrationTest.java 100644
View File

@ -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);
}
}