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chose smaller buffer size for the bufferedStream

This commit is contained in:
Yossi Farjoun 2012-12-15 13:01:38 -05:00
parent 6da2338ea7
commit ea704d688f
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -69,7 +69,7 @@ public class GATKBAMIndex {
private final File mFile; private final File mFile;
//TODO: figure out a good value for this buffer size //TODO: figure out a good value for this buffer size
private final int BUFFERED_STREAM_BUFFER_SIZE=1024; private final int BUFFERED_STREAM_BUFFER_SIZE=8192;
/** /**
* Number of sequences stored in this index. * Number of sequences stored in this index.
@ -303,7 +303,7 @@ public class GATKBAMIndex {
private void openIndexFile() { private void openIndexFile() {
try { try {
fileStream = new SeekableFileStream(mFile); fileStream = new SeekableFileStream(mFile);
bufferedStream = new SeekableBufferedStream(fileStream); bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
} }
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);