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Check for empty BAM lists in command line input

This commit is contained in:
Laura Gauthier 2014-02-12 10:20:28 -05:00
parent 7095a60c8e
commit 29bb3d4dc1
2 changed files with 32 additions and 4 deletions
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17
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -497,19 +497,27 @@ public class GenomeAnalysisEngine {
}
/**
* Verifies that the supplied set of reads files mesh with what the walker says it requires,
* and also makes sure that there were no duplicate SAM files specified on the command line.
* Verifies that the supplied set of reads files mesh with what the walker says it requires;
* also makes sure that list of SAM files specified on the command line is not empty and contains
* no duplicates.
*/
protected void validateSuppliedReads() {
GATKArgumentCollection arguments = this.getArguments();
final Boolean samFilesArePresent = (arguments.samFiles != null && !arguments.samFiles.isEmpty());
// Check what the walker says is required against what was provided on the command line.
if (WalkerManager.isRequired(walker, DataSource.READS) && (arguments.samFiles == null || arguments.samFiles.size() == 0))
if (WalkerManager.isRequired(walker, DataSource.READS) && !samFilesArePresent)
throw new ArgumentException("Walker requires reads but none were provided.");
// Check what the walker says is allowed against what was provided on the command line.
if ((arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker, DataSource.READS))
if (samFilesArePresent && !WalkerManager.isAllowed(walker, DataSource.READS))
throw new ArgumentException("Walker does not allow reads but reads were provided.");
//Make sure SAM list specified by the user (if necessary) is not empty
if(WalkerManager.isRequired(walker, DataSource.READS) && samFilesArePresent && samReaderIDs.isEmpty() ) {
throw new UserException("The list of input files does not contain any BAM files.");
}
// Make sure no SAM files were specified multiple times by the user.
checkForDuplicateSamFiles();
}
@ -535,6 +543,7 @@ public class GenomeAnalysisEngine {
throw new UserException("The following BAM files appear multiple times in the list of input files: " +
duplicateSamFiles + " BAM files may be specified at most once.");
}
}
/**

19
public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
View File

@ -28,9 +28,11 @@ package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.ArgumentException;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
import org.broadinstitute.sting.gatk.walkers.readutils.PrintReads;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@ -51,6 +53,23 @@ import java.util.*;
*/
public class GenomeAnalysisEngineUnitTest extends BaseTest {
@Test(expectedExceptions=UserException.class)
public void testEmptySamFileListHandling() throws Exception {
GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
testEngine.setWalker(new CountReads()); //generalizable to any walker requiring reads
//supply command line args so validateSuppliedReads() knows whether reads were passed in
GATKArgumentCollection testArgs = new GATKArgumentCollection();
testArgs.samFiles.add("empty.list");
testEngine.setArguments(testArgs);
//represents the empty list of samFiles read in from empty.list by CommandLineExecutable
Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
testEngine.setSAMFileIDs(samFiles);
testEngine.validateSuppliedReads();
}
@Test(expectedExceptions=UserException.class)
public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();