Package htsjdk.tribble.util

Examples of htsjdk.tribble.util.LittleEndianInputStream.readInt()

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                bdis = new DataInputStream(new ByteArrayInputStream(buffer));

            // Get zoom level information
            if(isLowToHigh){
                reductionLevel = lbdis.readInt();
                reserved = lbdis.readInt();
                dataOffset = lbdis.readLong();
                indexOffset = lbdis.readLong();
            }
            else {
                reductionLevel = bdis.readInt();
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            ss = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
            LittleEndianInputStream is = new LittleEndianInputStream(new BufferedInputStream(ss));

            long indexPosition = is.readLong();
            trackLine = is.readString();
            nTimePoints = is.readInt();
            times = new int[nTimePoints];
            for (int t = 0; t < nTimePoints; t++) {
                times[t] = is.readInt();
            }
            signalsPath = is.readString();
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            long indexPosition = is.readLong();
            trackLine = is.readString();
            nTimePoints = is.readInt();
            times = new int[nTimePoints];
            for (int t = 0; t < nTimePoints; t++) {
                times[t] = is.readInt();
            }
            signalsPath = is.readString();
            timeSignalsPath = new String[nTimePoints];
            for (int t = 0; t < nTimePoints; t++) {
                timeSignalsPath[t] = is.readString();
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            chrIndex = new HashMap<String, Long>();

            ss.seek(indexPosition);
            is = new LittleEndianInputStream(new BufferedInputStream(ss));
            int nChrs = is.readInt();
            for (int i = 0; i < nChrs; i++) {
                String chr = is.readString();
                long pos = is.readLong();
                chrIndex.put(chr, pos);
            }
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                IGVSeekableBufferedStream bufferedStream = new IGVSeekableBufferedStream(ss, bufferSize);
                bufferedStream.seek(chrPos);

                reader = new LittleEndianInputStream(bufferedStream);
                int nBytes = reader.readInt();

                byte[] compressedBytes = new byte[nBytes];
                bufferedStream.readFully(compressedBytes);

                byte[] bytes = compressionUtils.decompress(compressedBytes);
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                if (!chrRecorded.equals(chr)) {
                    throw new RuntimeException("Error paring peak file: " + path +
                            "<br>Expected: " + chr + "  found: " + chrRecorded);
                }

                int nDataPoints = reader.readInt();
                for (int n = 0; n < nDataPoints; n++) {
                    int start = reader.readInt();
                    int end = reader.readInt();
                    float combinedScore = reader.readFloat();
                    float[] timePointScores = new float[nTimePoints];
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                            "<br>Expected: " + chr + "  found: " + chrRecorded);
                }

                int nDataPoints = reader.readInt();
                for (int n = 0; n < nDataPoints; n++) {
                    int start = reader.readInt();
                    int end = reader.readInt();
                    float combinedScore = reader.readFloat();
                    float[] timePointScores = new float[nTimePoints];
                    for (int i = 0; i < nTimePoints; i++) {
                        timePointScores[i] = reader.readFloat();
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                }

                int nDataPoints = reader.readInt();
                for (int n = 0; n < nDataPoints; n++) {
                    int start = reader.readInt();
                    int end = reader.readInt();
                    float combinedScore = reader.readFloat();
                    float[] timePointScores = new float[nTimePoints];
                    for (int i = 0; i < nTimePoints; i++) {
                        timePointScores[i] = reader.readFloat();
                    }
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            // decode header
            if(isLowToHigh){
                lbdis = new LittleEndianInputStream(new ByteArrayInputStream(buffer));

                // check for a valid B+ Tree Header
                magic = lbdis.readInt();

                if(magic != BPTREE_MAGIC_LTH)
                    return false;

                // Get mChromosome B+ header information
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                if(magic != BPTREE_MAGIC_LTH)
                    return false;

                // Get mChromosome B+ header information
                blockSize = lbdis.readInt();
                keySize = lbdis.readInt();
                valSize = lbdis.readInt();
                itemCount = lbdis.readLong();
                reserved = lbdis.readLong();
            }
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