Find a coding sequence in a contig

find-coding-range.js

module.exports = function findCodingRange (codingSeq, contig, reverse) {
  let codingLength = codingSeq.length
    , start = 0
    , end = 0
    , selector = 12
    , fail = false

  start = contig.indexOf(codingSeq.substring(0, selector))
  end = contig.indexOf(codingSeq.substring(codingLength - selector, codingLength)) + selector

  if (start < 0 && end <= selector) fail = true
  if (start === -1) start = 0
  if (end <= selector) end = contig.length

  if (fail && !reverse) {
    return findCodingRange(reverseCompliment(codingSeq), contig, true)
  } else {
    return { start, end, fail }
  }

  function reverseCompliment (sequence) {
    let reverse = sequence.split('').reverse().join('')

    return reverse.replace(/[ACTG]/g, (base) => {
      return 'ACTG'.charAt('TGAC'.indexOf(base))
    })
  }
}