@Override
public synchronized void printStats(final PrintStream out) {
messageChunkWriter.printStats(out);
out.println(
"Number of bits/base "
+ (messageChunkWriter.getTotalBytesWritten() * 8.0f) / (float) sequenceBasesWritten);
}
@Override
public synchronized void appendEntry(final Reads.ReadEntry.Builder entryBuilder)
throws IOException {
collectionBuilder.addReads(entryBuilder.build());
messageChunkWriter.writeAsNeeded(collectionBuilder);
barcodeIndex = -1;
}
public ReadsWriterImpl(final OutputStream output) {
collectionBuilder = Reads.ReadCollection.newBuilder();
messageChunkWriter = new MessageChunksWriter(output);
messageChunkWriter.setParser(new ReadProtobuffCollectionHandler());
readIndex = 0;
}
@Override
public void setNumEntriesPerChunk(final int numEntriesPerChunk) {
messageChunkWriter.setNumEntriesPerChunk(numEntriesPerChunk);
}
/**
* Append an entry with a specific read index.
*
* @param readIndex Index of the read that will be written
* @throws IOException If an error occurs while writing the file.
*/
@Override
public synchronized void appendEntry(final int readIndex) throws IOException {
Reads.ReadEntry.Builder entryBuilder = Reads.ReadEntry.newBuilder();
entryBuilder.setReadIndex(readIndex);
// set current read index to enable interleaving calls to appendEntry(readIndex)/appendEntry().
this.readIndex = readIndex;
if (barcodeIndex != -1) {
entryBuilder.setBarcodeIndex(barcodeIndex);
}
if (description != null) {
entryBuilder.setDescription(description.toString());
description = null;
}
if (identifier != null) {
entryBuilder.setReadIdentifier(identifier.toString());
identifier = null;
}
if (sequence != null) {
entryBuilder.setSequence(encodeSequence(sequence));
sequence = null;
}
entryBuilder.setReadLength(previousReadLength);
if (pairSequence != null) {
entryBuilder.setSequencePair(encodeSequence(pairSequence));
pairSequence = null;
entryBuilder.setReadLengthPair(previousReadLength);
}
if (qualityScores != null) {
entryBuilder.setQualityScores(ByteString.copyFrom(qualityScores));
qualityScores = null;
}
if (qualityScoresPair != null) {
entryBuilder.setQualityScoresPair(ByteString.copyFrom(qualityScoresPair));
qualityScoresPair = null;
}
if (firstRead == true && keyValuePairs != null) {
// Append meta data on the very first read of each file. This is used instead of a separate
// header file.
for (Object keyObject : keyValuePairs.keySet()) {
String key = keyObject.toString();
String value = keyValuePairs.get(key).toString();
entryBuilder.addMetaData(Reads.MetaData.newBuilder().setKey(key).setValue(value));
}
firstRead = false;
}
if (codec != null) {
if (collectionBuilder.getReadsCount() == 0) {
codec.newChunk();
}
Reads.ReadEntry.Builder result = codec.encode(entryBuilder);
if (result != null) {
entryBuilder = result;
}
}
collectionBuilder.addReads(entryBuilder.build());
messageChunkWriter.writeAsNeeded(collectionBuilder);
barcodeIndex = -1;
}
/** {@inheritDoc} */
@Override
public void close() throws IOException {
messageChunkWriter.close(collectionBuilder);
}