myseq-vcf/lib/io/TabixIndexedFile.test.js

Query local or remote Tabix-indexed VCFs by genomic position

"use strict";

/* eslint-disable no-underscore-dangle */
const chai = require('chai');

const chaiAsPromised = require('chai-as-promised');

const {
  LocalFileReader
} = require('./FileReaders');

const TabixIndexedFile = require('./TabixIndexedFile');

chai.use(chaiAsPromised);
const {
  expect
} = chai;
describe('TabixIndexedFile', () => {
  function getTestFile(vcfPath = './test-data/single_sample.vcf.gz', idxPath = `${vcfPath}.tbi`) {
    return new TabixIndexedFile(new LocalFileReader(vcfPath), new LocalFileReader(idxPath));
  }

  it('should load tabix index', () => {
    const indexedFile = getTestFile();
    return indexedFile._contigs.then(contigs => {
      expect(contigs.size).to.equal(1);
    });
  });
  it('should reject on invalid index file', () => {
    const indexedFile = getTestFile('./test-data/single_sample.vcf.gz', './test-data/single_sample.vcf.gz');
    return expect(indexedFile._contigs).to.be.rejected;
  });
  it('should return requested records', () => {
    const indexedFile = getTestFile();
    return indexedFile.records('chr1', 1, 200).then(records => {
      expect(records).to.deep.equal(['chr1\t100\trs1\tA\tT\t100.0\tPASS\tAC=1;AN=2\tGT\t0/1']);
    });
  });
  it('should return zero length array for empty region', () => {
    const indexedFile = getTestFile();
    return indexedFile.records('chr1', 102, 102).then(records => {
      expect(records).to.have.lengthOf(0);
    });
  }); // TODO: Test filtering on structural variants

  it('should return header lines', () => {
    const indexedFile = getTestFile();
    return indexedFile.header().then(header => {
      expect(header).to.have.lengthOf(7);
    });
  });
});