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Merge pull request #253 from broadinstitute/md_bad_compress 

Check that -compress arguments are within range 0-9
This commit is contained in:
MauricioCarneiro 2013-05-31 12:40:01 -07:00
parent a96f48bc39 4b206a3540
commit 749f53d60e
3 changed files with 28 additions and 3 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -30,6 +30,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.io.OutputStream;
import java.lang.annotation.Annotation;
@ -132,9 +133,9 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
if (writerFileName != null && writerFileName.asFile() != null ) {
stub = new SAMFileWriterStub(engine, writerFileName.asFile());
if ( compressionLevel != null )
stub.setCompressionLevel(compressionLevel);
if ( indexOnTheFly )
if ( compressionLevel != null ) {
stub.setCompressionLevel(ReadUtils.validateCompressionLevel(compressionLevel));
} if ( indexOnTheFly )
stub.setIndexOnTheFly(indexOnTheFly);
if ( generateMD5 )
stub.setGenerateMD5(generateMD5);

8
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.util.*;
@ -152,11 +153,18 @@ public class ReadUtils {
* @return a SAMFileWriter with the compression level if it is a bam.
*/
public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) {
validateCompressionLevel(compression);
if (file.endsWith(".bam"))
return new SAMFileWriterFactory().makeBAMWriter(header, presorted, new File(file), compression);
return new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, new File(file));
}
public static int validateCompressionLevel(final int requestedCompressionLevel) {
if ( requestedCompressionLevel < 0 || requestedCompressionLevel > 9 )
throw new UserException.BadArgumentValue("compress", "Compression level must be 0-9 but got " + requestedCompressionLevel);
return requestedCompressionLevel;
}
/**
* is this base inside the adaptor of the read?
*

16
public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
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@ -174,4 +174,20 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
1, Arrays.asList("ecf27a776cdfc771defab1c5d19de9ab"));
executeTest("testUserReadFilterAppliedBeforeWalker", spec);
}
@Test
public void testNegativeCompress() {
testBadCompressArgument(-1);
}
@Test
public void testTooBigCompress() {
testBadCompressArgument(100);
}
private void testBadCompressArgument(final int compress) {
WalkerTestSpec spec = new WalkerTestSpec("-T PrintReads -R " + b37KGReference + " -I private/testdata/NA12878.1_10mb_2_10mb.bam -o %s -compress " + compress,
1, UserException.class);
executeTest("badCompress " + compress, spec);
}
}