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Merge pull request #202 from broadinstitute/yf_remove_getlength_from_every_GATKBAMIndex_read 

GATKBAMIndex calls buffer.length() on every read.
This commit is contained in:
Mark DePristo 2013-04-30 06:24:34 -07:00
parent a3a2ec5a1c 73fcacbf1b
commit 6ea2bceb55
1 changed files with 10 additions and 6 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -25,16 +25,17 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.Bin;
import net.sf.samtools.GATKBin;
import net.sf.samtools.GATKChunk;
import net.sf.samtools.LinearIndex;
import net.sf.samtools.seekablestream.SeekableBufferedStream; import net.sf.samtools.seekablestream.SeekableBufferedStream;
import net.sf.samtools.seekablestream.SeekableFileStream; import net.sf.samtools.seekablestream.SeekableFileStream;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*; import java.io.File;
import java.io.IOException;
import java.nio.ByteBuffer; import java.nio.ByteBuffer;
import java.nio.ByteOrder; import java.nio.ByteOrder;
import java.util.ArrayList; import java.util.ArrayList;
@ -86,6 +87,7 @@ public class GATKBAMIndex {
private SeekableFileStream fileStream; private SeekableFileStream fileStream;
private SeekableBufferedStream bufferedStream; private SeekableBufferedStream bufferedStream;
private long fileLength;
public GATKBAMIndex(final File file) { public GATKBAMIndex(final File file) {
mFile = file; mFile = file;
@ -307,6 +309,7 @@ public class GATKBAMIndex {
try { try {
fileStream = new SeekableFileStream(mFile); fileStream = new SeekableFileStream(mFile);
bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE); bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
fileLength=bufferedStream.length();
} }
catch (IOException exc) { catch (IOException exc) {
throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc); throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc);
@ -317,6 +320,7 @@ public class GATKBAMIndex {
try { try {
bufferedStream.close(); bufferedStream.close();
fileStream.close(); fileStream.close();
fileLength = -1;
} }
catch (IOException exc) { catch (IOException exc) {
throw new ReviewedStingException("Unable to close index file " + mFile, exc); throw new ReviewedStingException("Unable to close index file " + mFile, exc);
@ -368,7 +372,7 @@ public class GATKBAMIndex {
// We have a rigid expectation here to read in exactly the number of bytes we've limited // We have a rigid expectation here to read in exactly the number of bytes we've limited
// our buffer to -- if there isn't enough data in the file, the index // our buffer to -- if there isn't enough data in the file, the index
// must be truncated or otherwise corrupt: // must be truncated or otherwise corrupt:
if(bytesRequested > bufferedStream.length() - bufferedStream.position()){ if(bytesRequested > fileLength - bufferedStream.position()){
throw new UserException.MalformedFile(mFile, String.format("Premature end-of-file while reading BAM index file %s. " + 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 -- " + "It's likely that this file is truncated or corrupt -- " +
"Please try re-indexing the corresponding BAM file.", "Please try re-indexing the corresponding BAM file.",