htsjdk.tribble.util.LittleEndianOutputStream Java Examples
The following examples show how to use
htsjdk.tribble.util.LittleEndianOutputStream.
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Example #1
| Source File: MatrixZoomData.java From JuiceboxLegacy with MIT License | 6 votes |
|
private void dumpPearsons(PrintWriter pw, LittleEndianOutputStream les, ExpectedValueFunction df) throws IOException {
BasicMatrix pearsons = getPearsons(df);
if (pearsons != null) {
int dim = pearsons.getRowDimension();
for (int i = 0; i < dim; i++) {
for (int j = 0; j < dim; j++) {
float output = pearsons.getEntry(i, j);
if (les != null) les.writeFloat(output);
else pw.print(output + " ");
}
if (les == null) pw.println();
}
pw.flush();
} else {
log.error("Pearson's not available at zoom " + zoom);
}
}
Example #2
| Source File: Preprocessor.java From Juicebox with MIT License | 6 votes |
|
private void writeZoomHeader(MatrixZoomDataPP zd, LittleEndianOutputStream los) throws IOException {
int numberOfBlocks = zd.blockNumbers.size();
los.writeString(zd.getUnit().toString()); // Unit
los.writeInt(zd.getZoom()); // zoom index, lowest res is zero
los.writeFloat((float) zd.getSum()); // sum
los.writeFloat((float) zd.getOccupiedCellCount());
los.writeFloat((float) zd.getPercent5());
los.writeFloat((float) zd.getPercent95());
los.writeInt(zd.getBinSize());
los.writeInt(zd.getBlockBinCount());
los.writeInt(zd.getBlockColumnCount());
los.writeInt(numberOfBlocks);
zd.blockIndexPosition = los.getWrittenCount();
// Placeholder for block index
for (int i = 0; i < numberOfBlocks; i++) {
los.writeInt(0);
los.writeLong(0L);
los.writeInt(0);
}
}
Example #3
| Source File: MultithreadedPreprocessor.java From Juicebox with MIT License | 6 votes |
|
@Override
// MatrixPP matrix, LittleEndianOutputStream los, Deflater compressor
protected Pair<Map<Long, List<IndexEntry>>, Long> writeMatrix(MatrixPP matrix, LittleEndianOutputStream[] localLos,
Deflater localCompressor, Map<String, IndexEntry> localMatrixPositions, int chromosomePairIndex, boolean doMultiThreadedBehavior) throws IOException {
Pair<Map<Long, List<IndexEntry>>, Long> localBlockIndexes = super.writeMatrix(matrix, localLos, localCompressor, localMatrixPositions, chromosomePairIndex, true);
chromosomePairBlockIndexes.put(chromosomePairIndex, localBlockIndexes.getFirst());
long size = localLos[0].getWrittenCount() - localBlockIndexes.getSecond();
matrixSizes.put(chromosomePairIndex, size);
localLos[0].close();
//System.out.print(".");
return localBlockIndexes;
}
Example #4
| Source File: ScratchPad.java From JuiceboxLegacy with MIT License | 5 votes |
|
public static void writeHeader(String path) throws IOException {
File f = new File(path);
FileOutputStream fos = new FileOutputStream(f);
BufferedOutputStream bos = new BufferedOutputStream(fos);
LittleEndianOutputStream los = new LittleEndianOutputStream(bos);
// Magic number - 4 bytes
los.writeByte('h');
los.writeByte('i');
los.writeByte('c');
los.writeByte(0);
// Version number
los.writeInt(1);
// Genome --
los.writeString("hg19");
// Chromosomes
los.writeString("14");
los.writeString("14");
// Resolution (bin size)
los.writeInt(5000);
// Statistics, other attributes
los.writeFloat(-0.004103539418429137f);
los.writeFloat(0.03536746241152287f);
los.writeInt(21458); // # rows, assuming square matrix
los.close();
bos.close();
fos.close();
}
Example #5
| Source File: AsciiToBinConverter.java From JuiceboxLegacy with MIT License | 5 votes |
|
/**
* @param inputPath
* @param outputFile
*/
public static void convert(String inputPath, String outputFile, List<Chromosome> chromosomes) throws IOException {
Map<String, Integer> chromosomeOrdinals = new HashMap<String, Integer>();
for (Chromosome c : chromosomes) {
chromosomeOrdinals.put(c.getName(), c.getIndex());
}
AsciiPairIterator iter = null;
BufferedOutputStream bos = null;
try {
bos = new BufferedOutputStream(new FileOutputStream(outputFile));
LittleEndianOutputStream les = new LittleEndianOutputStream(bos);
iter = new AsciiPairIterator(inputPath, chromosomeOrdinals
);
while (iter.hasNext()) {
AlignmentPair pair = iter.next();
les.writeBoolean(pair.getStrand1());
les.writeInt(pair.getChr1());
les.writeInt(pair.getPos1());
les.writeInt(pair.getFrag1());
les.writeBoolean(pair.getStrand2());
les.writeInt(pair.getChr2());
les.writeInt(pair.getPos2());
les.writeInt(pair.getFrag2());
}
les.flush();
bos.flush();
} finally {
if (iter != null) iter.close();
if (bos != null) bos.close();
}
}
Example #6
| Source File: Preprocessor.java From Juicebox with MIT License | 5 votes |
|
protected void updateIndexPositions(List<IndexEntry> blockIndex, LittleEndianOutputStream[] losArray, boolean doRestore,
File outputFile, long currentPosition, long blockIndexPosition) throws IOException {
// Temporarily close output stream. Remember position
long losPos = 0;
if (doRestore) {
losPos = losArray[0].getWrittenCount();
losArray[0].close();
}
RandomAccessFile raf = null;
try {
raf = new RandomAccessFile(outputFile, "rw");
// Block indices
long pos = blockIndexPosition;
raf.getChannel().position(pos);
// Write as little endian
BufferedByteWriter buffer = new BufferedByteWriter();
for (IndexEntry aBlockIndex : blockIndex) {
buffer.putInt(aBlockIndex.id);
buffer.putLong(aBlockIndex.position + currentPosition);
buffer.putInt(aBlockIndex.size);
}
raf.write(buffer.getBytes());
} finally {
if (raf != null) raf.close();
}
if (doRestore) {
FileOutputStream fos = new FileOutputStream(outputFile, true);
fos.getChannel().position(losPos);
losArray[0] = new LittleEndianOutputStream(new BufferedOutputStream(fos, HiCGlobals.bufferSize));
losArray[0].setWrittenCount(losPos);
}
}
Example #7
| Source File: AsciiToBinConverter.java From Juicebox with MIT License | 5 votes |
|
/**
* @param inputPath
* @param outputFile
* @param chromosomeHandler
*/
public static void convert(String inputPath, String outputFile, ChromosomeHandler chromosomeHandler) throws IOException {
Map<String, Integer> chromosomeOrdinals = new HashMap<>();
for (Chromosome c : chromosomeHandler.getChromosomeArray()) {
chromosomeOrdinals.put(c.getName(), c.getIndex());
}
AsciiPairIterator iter = null;
BufferedOutputStream bos = null;
try {
bos = new BufferedOutputStream(new FileOutputStream(outputFile));
LittleEndianOutputStream les = new LittleEndianOutputStream(bos);
iter = new AsciiPairIterator(inputPath, chromosomeOrdinals, chromosomeHandler);
while (iter.hasNext()) {
AlignmentPair pair = iter.next();
les.writeBoolean(pair.getStrand1());
les.writeInt(pair.getChr1());
les.writeInt(pair.getPos1());
les.writeInt(pair.getFrag1());
les.writeBoolean(pair.getStrand2());
les.writeInt(pair.getChr2());
les.writeInt(pair.getPos2());
les.writeInt(pair.getFrag2());
}
les.flush();
bos.flush();
} finally {
if (iter != null) iter.close();
if (bos != null) bos.close();
}
}
Example #8
| Source File: Pearsons.java From Juicebox with MIT License | 5 votes |
|
private void writeHeader(LittleEndianOutputStream les, int dim, float lower, float upper) throws IOException {
// Magic number - 4 bytes
les.writeByte('h');
les.writeByte('i');
les.writeByte('c');
les.writeByte(0);
// Version number
les.writeInt(1);
// Genome --
les.writeString(dataset.getGenomeId());
// Chromosomes
les.writeString(chromosome1.getName());
les.writeString(chromosome1.getName());
// Resolution (bin size)
les.writeInt(binSize);
// Statistics, other attributes
les.writeFloat(lower); // this is supposed to be lower quartile
les.writeFloat(upper); // this is supposed to be upper quartile
les.writeInt(dim); // # rows
les.writeInt(dim); // # cols
les.writeInt(BLOCK_TILE);
}
