Package htsjdk.tribble.util

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

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            // Get zoom level information
            if(isLowToHigh){
                reductionLevel = lbdis.readInt();
                reserved = lbdis.readInt();
                dataOffset = lbdis.readLong();
                indexOffset = lbdis.readLong();
            }
            else {
                reductionLevel = bdis.readInt();
                reserved = bdis.readInt();
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            // Get zoom level information
            if(isLowToHigh){
                reductionLevel = lbdis.readInt();
                reserved = lbdis.readInt();
                dataOffset = lbdis.readLong();
                indexOffset = lbdis.readLong();
            }
            else {
                reductionLevel = bdis.readInt();
                reserved = bdis.readInt();
                dataOffset = bdis.readLong();
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        SeekableStream ss = null;
        try {
            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();
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            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);
            }

        } finally {
            if (ss != null) ss.close();
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                // Get mChromosome B+ header information
                blockSize = lbdis.readInt();
                keySize = lbdis.readInt();
                valSize = lbdis.readInt();
                itemCount = lbdis.readLong();
                reserved = lbdis.readLong();
            }
            else {
                bdis = new DataInputStream(new ByteArrayInputStream(buffer));
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                // Get mChromosome B+ header information
                blockSize = lbdis.readInt();
                keySize = lbdis.readInt();
                valSize = lbdis.readInt();
                itemCount = lbdis.readLong();
                reserved = lbdis.readLong();
            }
            else {
                bdis = new DataInputStream(new ByteArrayInputStream(buffer));

                // check for a valid B+ Tree Header
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        assertEquals("Binary test file", lis.readString());
        assertEquals(Float.MAX_VALUE, lis.readFloat());
        assertEquals(Byte.MAX_VALUE, lis.readByte());
        assertEquals(Short.MAX_VALUE, lis.readShort());
        assertEquals(Integer.MAX_VALUE, lis.readInt());
        assertEquals(Long.MAX_VALUE, lis.readLong());
        assertEquals(Double.MAX_VALUE, lis.readDouble());
        lis.close();
    }

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                    thisNode.insertItem(leafItem);
               }
               else {
                   // get the child node pointed to in the node item
                   if(isLowToHigh)
                        childOffset =  lbdis.readLong();
                   else
                        childOffset =  bdis.readLong();

                   childNode = readBPTreeNode(this.fis, childOffset, thisNode, isLowToHigh);
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            else
                bdis = new DataInputStream(new ByteArrayInputStream(buffer));

            // Get TotalSummaryBlcok information
            if(isLowToHigh){
                basesCovered = lbdis.readLong();
                minVal = lbdis.readFloat();
                maxVal = lbdis.readFloat();
                sumData = lbdis.readFloat();
                sumSquares = lbdis.readFloat();
            }
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           if(magic != RPTREE_MAGIC_LTH)
               return false;

           // Get mChromosome B+ header information
           blockSize = lbdis.readInt();
           itemCount = lbdis.readLong();
           startChromID = lbdis.readInt();
           startBase = lbdis.readInt();
           endChromID = lbdis.readInt();
           endBase = lbdis.readInt();
           endFileOffset = lbdis.readLong();
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