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Proper function call in BCF2Decoder to validateReadBytes

This commit is contained in:
Mark DePristo 2012-08-17 10:14:19 -04:00
parent 67ebd65512
commit de3be45806
1 changed files with 37 additions and 11 deletions
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48
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
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@ -82,7 +82,7 @@ public final class BCF2Decoder {
public void skipNextBlock(final int blockSizeInBytes, final InputStream stream) { public void skipNextBlock(final int blockSizeInBytes, final InputStream stream) {
try { try {
final int bytesRead = (int)stream.skip(blockSizeInBytes); final int bytesRead = (int)stream.skip(blockSizeInBytes);
validateReadBytes(bytesRead, blockSizeInBytes); validateReadBytes(bytesRead, 1, blockSizeInBytes);
} catch ( IOException e ) { } catch ( IOException e ) {
throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e); throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e);
} }
@ -316,17 +316,37 @@ public final class BCF2Decoder {
} }
/** /**
* Read all bytes for a BCF record block into a byte[], and return it
* *
* @param inputStream * Is smart about reading from the stream multiple times to fill the buffer, if necessary
* @return *
* @param blockSizeInBytes number of bytes to read
* @param inputStream the stream to read from
* @return a non-null byte[] containing exactly blockSizeInBytes bytes from the inputStream
*/ */
private final static byte[] readRecordBytes(final int blockSizeInBytes, final InputStream inputStream) { @Requires({"blockSizeInBytes >= 0", "inputStream != null"})
@Ensures("result != null")
private static byte[] readRecordBytes(final int blockSizeInBytes, final InputStream inputStream) {
assert blockSizeInBytes >= 0; assert blockSizeInBytes >= 0;
final byte[] record = new byte[blockSizeInBytes]; final byte[] record = new byte[blockSizeInBytes];
try { try {
final int bytesRead = inputStream.read(record); int bytesRead = 0;
validateReadBytes(bytesRead, blockSizeInBytes); int nReadAttempts = 0; // keep track of how many times we've read
// because we might not read enough bytes from the file in a single go, do it in a loop until we get EOF
while ( bytesRead < blockSizeInBytes ) {
final int read1 = inputStream.read(record, bytesRead, blockSizeInBytes - bytesRead);
if ( read1 == -1 )
validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes);
else
bytesRead += read1;
}
if ( nReadAttempts > 1 ) // TODO -- remove me
logger.warn("Required multiple read attempts to actually get the entire BCF2 block, unexpected behavior");
validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes);
} catch ( IOException e ) { } catch ( IOException e ) {
throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e); throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e);
} }
@ -334,14 +354,20 @@ public final class BCF2Decoder {
return record; return record;
} }
private final static void validateReadBytes(final int actuallyRead, final int expected) { /**
* Make sure we read the right number of bytes, or throw an error
*
* @param actuallyRead
* @param nReadAttempts
* @param expected
*/
private static void validateReadBytes(final int actuallyRead, final int nReadAttempts, final int expected) {
assert expected >= 0; assert expected >= 0;
if ( actuallyRead < expected ) { if ( actuallyRead < expected ) {
throw new UserException.MalformedBCF2(String.format("Failed to read next complete record: %s", throw new UserException.MalformedBCF2(
actuallyRead == -1 ? String.format("Failed to read next complete record: expected %d bytes but read only %d after %d iterations",
"premature end of input stream" : expected, actuallyRead, nReadAttempts));
String.format("expected %d bytes but read only %d", expected, actuallyRead)));
} }
} }