myseq-vcf/lib/features/VCFVariant.js

Query local or remote Tabix-indexed VCFs by genomic position

"use strict";

function _defineProperty(obj, key, value) { if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }

class VCFVariant {
  constructor(line, samples = [], isSynth = false) {
    _defineProperty(this, "_line", void 0);

    _defineProperty(this, "isSynth", void 0);

    _defineProperty(this, "contig", void 0);

    _defineProperty(this, "position", void 0);

    _defineProperty(this, "ref", void 0);

    _defineProperty(this, "alt", void 0);

    _defineProperty(this, "id", void 0);

    _defineProperty(this, "filter", void 0);

    _defineProperty(this, "_genotypes", void 0);

    this._line = line;
    this.isSynth = isSynth;

    const fields = this._line.split('\t', samples.length > 0 ? samples.length + 9 : 8);

    this.contig = fields[0]; // eslint-disable-line prefer-destructuring

    this.position = parseInt(fields[1], 10);
    const id = fields[2];
    this.id = id === '.' ? undefined : id.split(';');
    this.ref = fields[3].toUpperCase(); // eslint-disable-line prefer-destructuring

    this.alt = fields[4].split(',').map(allele => /^[ACGTN]+$/i.test(allele) ? allele.toUpperCase() : allele);
    const filter = fields[6];
    this.filter = filter === '.' || filter === '' ? undefined : filter.split(';'); // Parse genotypes

    this._genotypes = new Map();

    for (let s = 0; s < samples.length; s += 1) {
      // GT must be the first field for each sample
      const endOfGT = fields[s + 9].indexOf(':');
      const GT = endOfGT === -1 ? fields[s + 9] : fields[s + 9].substring(0, endOfGT); // Translate alleles, while ignoring the distinction bewteen '/' and '|'

      const stringGT = GT.split(/[/|]/).sort() // Reference allele should be first
      .map(allele => {
        if (allele === '.') {
          return '.';
        }

        if (allele === '0') {
          return this.ref;
        }

        return this.alt[parseInt(allele, 10) - 1];
      }).join('/');

      this._genotypes.set(samples[s], stringGT);
    }
  }

  toString() {
    return `${this.contig}:g.${this.position}${this.ref}>${this.alt.join(',')}`;
  }

  isBiAllelic() {
    return this.alt.length === 1;
  }

  isPASS() {
    return this.filter ? this.filter.length === 1 && this.filter[0] === 'PASS' : false;
  }

  isFILTER() {
    return this.filter ? this.filter.length >= 1 && this.filter[0] !== 'PASS' : false;
  }
  /**
   * If no sample is specified, return the 1st genotype
   */


  genotype(sample) {
    return sample === undefined ? this._genotypes.values().next().value : this._genotypes.get(sample);
  }

}

module.exports = VCFVariant;