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Merge pull request #1488 from broadinstitute/rhl_dup_col_rld 

Add read group identifier to column names
This commit is contained in:
Ron Levine 2016-10-11 18:40:40 -04:00 committed by GitHub
parent 967b4f4ae8 a301ba1977
commit a72be69062
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);
}
}