htsjdk.tribble.util.LittleEndianOutputStream Java Examples

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);
    }
}
 

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);
        }

    }
 

@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;
}
 

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();

    }
 

/**
 * @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();

    }
}
 

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);
    }
}
 

/**
 * @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();

    }
}
 

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);
    }