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removed comments and uneeded imports

This commit is contained in:
Yossi Farjoun 2012-12-15 12:31:37 -05:00
parent 19dd2d628a
commit 6da2338ea7
1 changed files with 16 additions and 17 deletions
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33
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -23,14 +23,17 @@
*/
package org.broadinstitute.sting.gatk.datasources.reads;
import org.broad.tribble.util.SeekableBufferedStream;
import org.broad.tribble.util.SeekableFileStream;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.FileChannel;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@ -65,6 +68,9 @@ public class GATKBAMIndex {
private final File mFile;
//TODO: figure out a good value for this buffer size
private final int BUFFERED_STREAM_BUFFER_SIZE=1024;
/**
* Number of sequences stored in this index.
*/
@ -75,9 +81,8 @@ public class GATKBAMIndex {
*/
private final long[] sequenceStartCache;
private FileInputStream fileStream;
private FileChannel fileChannel;
private BufferedInputStream bufferedStream;
private SeekableFileStream fileStream;
private SeekableBufferedStream bufferedStream;
public GATKBAMIndex(final File file) {
mFile = file;
@ -297,9 +302,8 @@ public class GATKBAMIndex {
private void openIndexFile() {
try {
fileStream = new FileInputStream(mFile);
fileChannel = fileStream.getChannel();
bufferedStream = new BufferedInputStream(fileStream);
fileStream = new SeekableFileStream(mFile);
bufferedStream = new SeekableBufferedStream(fileStream);
}
catch (IOException exc) {
throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc);
@ -308,7 +312,6 @@ public class GATKBAMIndex {
private void closeIndexFile() {
try {
fileChannel.close();
bufferedStream.close();
fileStream.close();
}
@ -399,10 +402,10 @@ public class GATKBAMIndex {
try {
//try to skip forward the requested amount.
long remainingCount = count - bufferedStream.skip(count);
long skipped = bufferedStream.skip(count);
if( remainingCount > 0 ) { //if not enough data in buffer, reset buffer
seek(position() + remainingCount);
if( skipped != count ) { //if not managed to skip the requested amount
throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile);
}
}
catch(IOException ex) {
@ -413,8 +416,7 @@ public class GATKBAMIndex {
private void seek(final long position) {
try {
//to seek a new position, move the fileChannel, and reposition the bufferedStream
fileChannel.position(position);
bufferedStream = new BufferedInputStream(fileStream);
bufferedStream.seek(position);
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to reposition of file channel of index file " + mFile);
@ -427,10 +429,7 @@ public class GATKBAMIndex {
*/
private long position() {
try {
// It's a little complicated to figure out the position from a bufferedStream because it could be
// connected to a stream for which it makes no sense. Since we are on a file, this is OK.
final int bufferRemaining = bufferedStream.available() - fileStream.available();
return fileChannel.position() - bufferRemaining;
return bufferedStream.position();
}
catch (IOException exc) {
throw new ReviewedStingException("Unable to read position from index file " + mFile, exc);