hic-straw/src/binary.js

Utilities for reading .files (contact matrix files)

// TODO -- big endian

const BinaryParser = function (dataView, littleEndian) {

    this.littleEndian = littleEndian !== undefined ? littleEndian : true
    this.position = 0;
    this.view = dataView;
    this.length = dataView.byteLength;
}

BinaryParser.prototype.available = function () {
    return this.length - this.position;
}

BinaryParser.prototype.remLength = function () {
    return this.length - this.position;
}

BinaryParser.prototype.hasNext = function () {
    return this.position < this.length - 1;
}

BinaryParser.prototype.getByte = function () {
    var retValue = this.view.getUint8(this.position, this.littleEndian);
    this.position++;
    return retValue;
}

BinaryParser.prototype.getShort = function () {

    var retValue = this.view.getInt16(this.position, this.littleEndian);
    this.position += 2
    return retValue;
}

BinaryParser.prototype.getUShort = function () {

    // var byte1 = this.getByte(),
    //     byte2 = this.getByte(),
    //     retValue = ((byte2 << 24 >>> 16) + (byte1 << 24 >>> 24));
    //     return retValue;

    //
    var retValue = this.view.getUint16(this.position, this.littleEndian);
    this.position += 2
    return retValue;
}


BinaryParser.prototype.getInt = function () {

    var retValue = this.view.getInt32(this.position, this.littleEndian);
    this.position += 4;
    return retValue;
}


BinaryParser.prototype.getUInt = function () {
    var retValue = this.view.getUint32(this.position, this.littleEndian);
    this.position += 4;
    return retValue;
}

BinaryParser.prototype.getLong = function () {

    // DataView doesn't support long. So we'll try manually

    var b = [];
    b[0] = this.view.getUint8(this.position);
    b[1] = this.view.getUint8(this.position + 1);
    b[2] = this.view.getUint8(this.position + 2);
    b[3] = this.view.getUint8(this.position + 3);
    b[4] = this.view.getUint8(this.position + 4);
    b[5] = this.view.getUint8(this.position + 5);
    b[6] = this.view.getUint8(this.position + 6);
    b[7] = this.view.getUint8(this.position + 7);

    var value = 0;
    if (this.littleEndian) {
        for (var i = b.length - 1; i >= 0; i--) {
            value = (value * 256) + b[i];
        }
    } else {
        for (var i = 0; i < b.length; i++) {
            value = (value * 256) + b[i];
        }
    }


    this.position += 8;
    return value;
}

BinaryParser.prototype.getString = function (len) {

    var s = "";
    var c;
    while ((c = this.view.getUint8(this.position++)) != 0) {
        s += String.fromCharCode(c);
        if (len && s.length == len) break;
    }
    return s;
}

BinaryParser.prototype.getFixedLengthString = function (len) {

    var s = "";
    var i;
    var c;
    for (i = 0; i < len; i++) {
        c = this.view.getUint8(this.position++);
        if (c > 0) {
            s += String.fromCharCode(c);
        }
    }
    return s;
}

BinaryParser.prototype.getFixedLengthTrimmedString = function (len) {

    var s = "";
    var i;
    var c;
    for (i = 0; i < len; i++) {
        c = this.view.getUint8(this.position++);
        if (c > 32) {
            s += String.fromCharCode(c);
        }
    }
    return s;
}

BinaryParser.prototype.getFloat = function () {

    var retValue = this.view.getFloat32(this.position, this.littleEndian);
    this.position += 4;
    return retValue;


}

BinaryParser.prototype.getDouble = function () {

    var retValue = this.view.getFloat64(this.position, this.littleEndian);
    this.position += 8;
    return retValue;
}

BinaryParser.prototype.skip = function (n) {

    this.position += n;
    return this.position;
}


/**
 * Return a bgzip (bam and tabix) virtual pointer
 * TODO -- why isn't 8th byte used ?
 * @returns {*}
 */
BinaryParser.prototype.getVPointer = function () {

    var position = this.position,
        offset = (this.view.getUint8(position + 1) << 8) | (this.view.getUint8(position)),
        byte6 = ((this.view.getUint8(position + 6) & 0xff) * 0x100000000),
        byte5 = ((this.view.getUint8(position + 5) & 0xff) * 0x1000000),
        byte4 = ((this.view.getUint8(position + 4) & 0xff) * 0x10000),
        byte3 = ((this.view.getUint8(position + 3) & 0xff) * 0x100),
        byte2 = ((this.view.getUint8(position + 2) & 0xff)),
        block = byte6 + byte5 + byte4 + byte3 + byte2;
    this.position += 8;

    //       if (block == 0 && offset == 0) {
    //           return null;
    //       } else {
    return new VPointer(block, offset);
    //       }
}


function VPointer(block, offset) {
    this.block = block;
    this.offset = offset;
}

VPointer.prototype.isLessThan = function (vp) {
    return this.block < vp.block ||
        (this.block === vp.block && this.offset < vp.offset);
}

VPointer.prototype.isGreaterThan = function (vp) {
    return this.block > vp.block ||
        (this.block === vp.block && this.offset > vp.offset);
}

VPointer.prototype.print = function () {
    return "" + this.block + ":" + this.offset;
}


export default BinaryParser;