Merge pull request #253 from broadinstitute/md_bad_compress

Check that -compress arguments are within range 0-9

public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java

@@ -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 )
+            if ( compressionLevel != null ) {
-                stub.setCompressionLevel(compressionLevel);
+                stub.setCompressionLevel(ReadUtils.validateCompressionLevel(compressionLevel));
-            if ( indexOnTheFly )
+            } if ( indexOnTheFly )
                 stub.setIndexOnTheFly(indexOnTheFly);
             if ( generateMD5 )
                 stub.setGenerateMD5(generateMD5);

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -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?
      *

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -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);
+    }
 }