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Enable on the fly indexing of BCF2

This commit is contained in:
Mark DePristo 2012-05-10 12:56:22 -04:00
parent 81ab0dd051
commit 27b51d4dea
1 changed files with 14 additions and 17 deletions
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31
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/IndexingVCFWriter.java
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@ -43,11 +43,11 @@ import java.io.*;
* this class writes VCF files * this class writes VCF files
*/ */
public abstract class IndexingVCFWriter implements VCFWriter { public abstract class IndexingVCFWriter implements VCFWriter {
final private String name; private final String name;
private final SAMSequenceDictionary refDict; private final SAMSequenceDictionary refDict;
private OutputStream outputStream; private OutputStream outputStream;
private PositionalStream positionalStream = null; private PositionalOutputStream positionalOutputStream = null;
private DynamicIndexCreator indexer = null; private DynamicIndexCreator indexer = null;
private LittleEndianOutputStream idxStream = null; private LittleEndianOutputStream idxStream = null;
@ -65,13 +65,13 @@ public abstract class IndexingVCFWriter implements VCFWriter {
//System.out.println("Creating index on the fly for " + location); //System.out.println("Creating index on the fly for " + location);
indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
indexer.initialize(location, indexer.defaultBinSize()); indexer.initialize(location, indexer.defaultBinSize());
positionalStream = new PositionalStream(output); positionalOutputStream = new PositionalOutputStream(output);
outputStream = positionalStream; outputStream = positionalOutputStream;
} catch ( IOException ex ) { } catch ( IOException ex ) {
// No matter what we keep going, since we don't care if we can't create the index file // No matter what we keep going, since we don't care if we can't create the index file
idxStream = null; idxStream = null;
indexer = null; indexer = null;
positionalStream = null; positionalOutputStream = null;
} }
} }
} }
@ -95,7 +95,7 @@ public abstract class IndexingVCFWriter implements VCFWriter {
// try to close the index stream (keep it separate to help debugging efforts) // try to close the index stream (keep it separate to help debugging efforts)
if ( indexer != null ) { if ( indexer != null ) {
try { try {
Index index = indexer.finalizeIndex(positionalStream.getPosition()); Index index = indexer.finalizeIndex(positionalOutputStream.getPosition());
IndexDictionaryUtils.setIndexSequenceDictionary(index, refDict); IndexDictionaryUtils.setIndexSequenceDictionary(index, refDict);
index.write(idxStream); index.write(idxStream);
idxStream.close(); idxStream.close();
@ -113,7 +113,7 @@ public abstract class IndexingVCFWriter implements VCFWriter {
public void add(VariantContext vc) { public void add(VariantContext vc) {
// if we are doing on the fly indexing, add the record ***before*** we write any bytes // if we are doing on the fly indexing, add the record ***before*** we write any bytes
if ( indexer != null ) if ( indexer != null )
indexer.addFeature(vc, positionalStream.getPosition()); indexer.addFeature(vc, positionalOutputStream.getPosition());
} }
/** /**
@ -141,30 +141,27 @@ public abstract class IndexingVCFWriter implements VCFWriter {
} }
} }
class PositionalStream extends OutputStream { final class PositionalOutputStream extends OutputStream {
OutputStream out = null; private final OutputStream out;
private long position = 0; private long position = 0;
public PositionalStream(OutputStream out) { public PositionalOutputStream(final OutputStream out) {
this.out = out; this.out = out;
} }
public void write(final byte[] bytes) throws IOException { public final void write(final byte[] bytes) throws IOException {
write(bytes, 0, bytes.length); write(bytes, 0, bytes.length);
} }
public void write(final byte[] bytes, int startIndex, int numBytes) throws IOException { public final void write(final byte[] bytes, final int startIndex, final int numBytes) throws IOException {
//System.out.println("write: " + bytes + " " + numBytes);
position += numBytes; position += numBytes;
out.write(bytes, startIndex, numBytes); out.write(bytes, startIndex, numBytes);
} }
public void write(int c) throws IOException { public final void write(int c) throws IOException {
System.out.println("write byte: " + c);
//System.out.printf("Position %d for %c\n", position, (char)c);
position++; position++;
out.write(c); out.write(c);
} }
public long getPosition() { return position; } public final long getPosition() { return position; }
} }