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Added check to make sure file passed in with sample IDs is valid (used in SelectVariants) -- throws UserException. Corresponding test checks for UserException.

This commit is contained in:
Laura Gauthier 2014-04-04 15:38:50 -04:00
parent 06d78ba068
commit ff25b656e1
2 changed files with 55 additions and 1 deletions
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3
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair;
@ -280,7 +281,7 @@ public class SampleUtils {
samplesFromFiles.add(line);
}
} catch (FileNotFoundException e) {
// ignore exception
throw new UserException.CouldNotReadInputFile(file, e);
}
}
}

53
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SampleUtilsUnitTest.java 100644
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@ -0,0 +1,53 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* 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.sting.utils;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.io.IOUtils;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.util.*;
/**
* Testing framework for sample utilities class.
*
* @author gauthier
*/
public class SampleUtilsUnitTest extends BaseTest {
@Test(expectedExceptions=UserException.class)
public void testBadSampleFiles() throws Exception {
Set<File> sampleFiles = new HashSet<File>(0);
sampleFiles.add(new File("fileNotHere.samples"));
Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
}
}