apr144-bam/src/virtualOffset.ts

Parser for BAM and BAM index (bai) files

export default class VirtualOffset {
  public blockPosition: number
  public dataPosition: number
  constructor(blockPosition: number, dataPosition: number) {
    this.blockPosition = blockPosition // < offset of the compressed data block
    this.dataPosition = dataPosition // < offset into the uncompressed data
  }

  toString() {
    return `${this.blockPosition}:${this.dataPosition}`
  }

  compareTo(b: VirtualOffset) {
    return (
      this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition
    )
  }

  static min(...args: VirtualOffset[]) {
    let min
    let i = 0
    for (; !min; i += 1) {
      min = args[i]
    }
    for (; i < args.length; i += 1) {
      if (min.compareTo(args[i]) > 0) {
        min = args[i]
      }
    }
    return min
  }
}
export function fromBytes(bytes: Buffer, offset = 0, bigendian = false) {
  if (bigendian) {
    throw new Error('big-endian virtual file offsets not implemented')
  }

  return new VirtualOffset(
    bytes[offset + 7] * 0x10000000000 +
      bytes[offset + 6] * 0x100000000 +
      bytes[offset + 5] * 0x1000000 +
      bytes[offset + 4] * 0x10000 +
      bytes[offset + 3] * 0x100 +
      bytes[offset + 2],
    (bytes[offset + 1] << 8) | bytes[offset],
  )
}