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Fix for bug GSA-314: Detect -XL and -L incompatibility. An ArgumentException is 

now thrown if the combination of -L and -XL intervals specified on the command 
line results in an empty interval set after set subtraction. 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5571 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-04-04 18:41:55 +00:00
parent 798fb6a7a2
commit a5acb0b7a6
2 changed files with 33 additions and 2 deletions
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18
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -118,6 +118,14 @@ public class GenomeAnalysisEngine {
*/
private GenomeLocSortedSet intervals = null;
/**
* Explicitly assign the interval set to use for this traversal (for unit testing purposes)
* @param intervals set of intervals to use for this traversal
*/
public void setIntervals( GenomeLocSortedSet intervals ) {
this.intervals = intervals;
}
/**
* Collection of inputs used by the engine.
*/
@ -395,6 +403,16 @@ public class GenomeAnalysisEngine {
if(intervals != null && getIntervals().contains(GenomeLoc.UNMAPPED))
throw new ArgumentException("Interval list specifies unmapped region. Only read walkers may include the unmapped region.");
}
// If intervals is non-null and empty at this point, it means that the list of intervals to process
// was filtered down to an empty set (eg., the user specified something like -L chr1 -XL chr1). Since
// this was very likely unintentional, the user should be informed of this. Note that this is different
// from the case where intervals == null, which indicates either that there were no interval arguments,
// or that -L all was specified.
if ( intervals != null && intervals.isEmpty() ) {
throw new ArgumentException("The given combination of -L and -XL options results in an empty set. " +
"No intervals to process.");
}
}
/**

17
java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
View File

@ -24,12 +24,13 @@
package org.broadinstitute.sting.gatk;
import org.testng.annotations.Test;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.ArgumentException;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.testng.annotations.Test;
import java.io.File;
import java.util.ArrayList;
@ -66,4 +67,16 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
testEngine.setSAMFileIDs(samFiles);
testEngine.checkForDuplicateSamFiles();
}
@Test(expectedExceptions=ArgumentException.class)
public void testEmptyIntervalSetHandling() throws Exception {
GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
WalkerManager walkerManager = new WalkerManager();
testEngine.setWalker(walkerManager.createByName("PrintReadsWalker"));
testEngine.setIntervals(new GenomeLocSortedSet(null));
testEngine.validateSuppliedIntervals();
}
}