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Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices 

GATKBAMIndex would allow an extremely confusing BufferUnderflowException to be
thrown when a BAM index file was truncated or corrupt. Now, a UserException is
thrown in this situation instructing the user to re-index the BAM.

Added a unit test for this case as well.
This commit is contained in:
David Roazen 2012-03-08 12:52:11 -05:00
parent c04853eae6
commit 32dee7ed9b
2 changed files with 26 additions and 1 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
View File

@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.io.FileInputStream;
@ -349,7 +350,18 @@ public class GATKBAMIndex {
private void read(final ByteBuffer buffer) {
try {
fileChannel.read(buffer);
int bytesExpected = buffer.limit();
int bytesRead = fileChannel.read(buffer);
// We have a rigid expectation here to read in exactly the number of bytes we've limited
// our buffer to -- if we read in fewer bytes than this, or encounter EOF (-1), the index
// must be truncated or otherwise corrupt:
if ( bytesRead < bytesExpected ) {
throw new UserException.MalformedFile(mFile, String.format("Premature end-of-file while reading BAM index file %s. " +
"It's likely that this file is truncated or corrupt -- " +
"Please try re-indexing the corresponding BAM file.",
mFile));
}
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile);

13
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@ -91,4 +92,16 @@ public class GATKBAMIndexUnitTest extends BaseTest {
Assert.assertEquals(bamIndex.getLevelSize(5),37448-4681+1);
}
@Test( expectedExceptions = UserException.MalformedFile.class )
public void testDetectTruncatedBamIndexWordBoundary() {
GATKBAMIndex index = new GATKBAMIndex(new File(validationDataLocation + "truncated_at_word_boundary.bai"));
index.readReferenceSequence(0);
}
@Test( expectedExceptions = UserException.MalformedFile.class )
public void testDetectTruncatedBamIndexNonWordBoundary() {
GATKBAMIndex index = new GATKBAMIndex(new File(validationDataLocation + "truncated_at_non_word_boundary.bai"));
index.readReferenceSequence(0);
}
}