Package htsjdk.tribble.util

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

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           // 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();
           itemsPerSlot = lbdis.readInt();
           reserved = lbdis.readInt();
       }
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           blockSize = lbdis.readInt();
           itemCount = lbdis.readLong();
           startChromID = lbdis.readInt();
           startBase = lbdis.readInt();
           endChromID = lbdis.readInt();
           endBase = lbdis.readInt();
           endFileOffset = lbdis.readLong();
           itemsPerSlot = lbdis.readInt();
           reserved = lbdis.readInt();
       }
       else {
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           startChromID = lbdis.readInt();
           startBase = lbdis.readInt();
           endChromID = lbdis.readInt();
           endBase = lbdis.readInt();
           endFileOffset = lbdis.readLong();
           itemsPerSlot = lbdis.readInt();
           reserved = lbdis.readInt();
       }
       else {
           bdis = new DataInputStream(new ByteArrayInputStream(buffer));
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           startBase = lbdis.readInt();
           endChromID = lbdis.readInt();
           endBase = lbdis.readInt();
           endFileOffset = lbdis.readLong();
           itemsPerSlot = lbdis.readInt();
           reserved = lbdis.readInt();
       }
       else {
           bdis = new DataInputStream(new ByteArrayInputStream(buffer));

           // check for a valid B+ Tree Header
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            fis.readFully(buffer);

            // decode header - or fail
            if(this.isLowToHigh) {
                LittleEndianInputStream lbdis = new LittleEndianInputStream(new ByteArrayInputStream(buffer));
                zoomRecordCount = lbdis.readInt();
            }
            else {
                DataInputStream bdis = new DataInputStream(new ByteArrayInputStream(buffer));
                zoomRecordCount = bdis.readInt();
            }
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            int startBase, endBase;
            for (int item = 0; item < itemCount; ++item) {

                // always extract the bounding rectangle
                if (isLowToHigh) {
                    startChromID = lbdis.readInt();
                    startBase = lbdis.readInt();
                    endChromID = lbdis.readInt();
                    endBase = lbdis.readInt();
                } else {
                    startChromID = bdis.readInt();
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            for (int item = 0; item < itemCount; ++item) {

                // always extract the bounding rectangle
                if (isLowToHigh) {
                    startChromID = lbdis.readInt();
                    startBase = lbdis.readInt();
                    endChromID = lbdis.readInt();
                    endBase = lbdis.readInt();
                } else {
                    startChromID = bdis.readInt();
                    startBase = bdis.readInt();
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                // always extract the bounding rectangle
                if (isLowToHigh) {
                    startChromID = lbdis.readInt();
                    startBase = lbdis.readInt();
                    endChromID = lbdis.readInt();
                    endBase = lbdis.readInt();
                } else {
                    startChromID = bdis.readInt();
                    startBase = bdis.readInt();
                    endChromID = bdis.readInt();
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                // always extract the bounding rectangle
                if (isLowToHigh) {
                    startChromID = lbdis.readInt();
                    startBase = lbdis.readInt();
                    endChromID = lbdis.readInt();
                    endBase = lbdis.readInt();
                } else {
                    startChromID = bdis.readInt();
                    startBase = bdis.readInt();
                    endChromID = bdis.readInt();
                    endBase = bdis.readInt();
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