alignment.js/helpers/bam.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/

"use strict";

Object.defineProperty(exports, "__esModule", {
  value: true
});
exports["default"] = void 0;

function asyncGeneratorStep(gen, resolve, reject, _next, _throw, key, arg) { try { var info = gen[key](arg); var value = info.value; } catch (error) { reject(error); return; } if (info.done) { resolve(value); } else { Promise.resolve(value).then(_next, _throw); } }

function _asyncToGenerator(fn) { return function () { var self = this, args = arguments; return new Promise(function (resolve, reject) { var gen = fn.apply(self, args); function _next(value) { asyncGeneratorStep(gen, resolve, reject, _next, _throw, "next", value); } function _throw(err) { asyncGeneratorStep(gen, resolve, reject, _next, _throw, "throw", err); } _next(undefined); }); }; }

function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }

function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }

function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }

var BAMReader = /*#__PURE__*/function () {
  function BAMReader(bam_file) {
    _classCallCheck(this, BAMReader);

    this.bam_file = bam_file;
  }

  _createClass(BAMReader, [{
    key: "bamToFasta",
    value: function bamToFasta(bam_record, window_start, window_end) {
      var query = bam_record.getReadBases(),
          cigar_information = bam_record.cigar().split(/(\d+|[A-Z])/).filter(function (x) {
        return x;
      }),
          number_of_cigar_pairs = cigar_information.length / 2;
      var alignment = "",
          position = 0,
          action,
          stride,
          match,
          insertion,
          deletion;

      for (var i = 0; i < number_of_cigar_pairs; i++) {
        stride = +cigar_information[2 * i];
        action = cigar_information[2 * i + 1];
        match = action == "M";
        insertion = action == "I";
        deletion = action == "D";

        if (match || insertion) {
          if (match) {
            alignment += query.slice(position, position + stride);
          }

          position += stride;
        } else if (deletion) {
          if (alignment.length > 0 || i < number_of_cigar_pairs) {
            alignment += "-".repeat(stride);
          }
        }
      }

      var reference_start = bam_record.get("start"),
          reference_end = bam_record.get("end"),
          left_pad_amount = Math.max(0, reference_start - window_start),
          left_pad = "-".repeat(left_pad_amount),
          right_pad_amount = Math.max(0, window_end - reference_end),
          right_pad = "-".repeat(right_pad_amount),
          left_trim_amount = Math.max(0, window_start - reference_start),
          right_trim_amount = Math.max(0, reference_end - window_end),
          full_length = alignment.length,
          inner_fasta = alignment.slice(left_trim_amount, full_length - right_trim_amount);
      var fasta_record = {
        header: bam_record.get("name"),
        seq: left_pad + inner_fasta + right_pad
      };
      return fasta_record;
    }
  }, {
    key: "fasta_window",
    value: function () {
      var _fasta_window = _asyncToGenerator( /*#__PURE__*/regeneratorRuntime.mark(function _callee(start_site, end_site) {
        var _this = this;

        var header, reference;
        return regeneratorRuntime.wrap(function _callee$(_context) {
          while (1) {
            switch (_context.prev = _context.next) {
              case 0:
                _context.next = 2;
                return this.bam_file.getHeader();

              case 2:
                header = _context.sent;
                reference = header[1].data[0].value;
                _context.next = 6;
                return this.bam_file.getRecordsForRange(reference, start_site, end_site).then(function (records) {
                  var fasta = records.map(function (bam_record) {
                    return _this.bamToFasta(bam_record, start_site, end_site);
                  });
                  fasta.number_of_sequences = fasta.length;
                  fasta.number_of_sites = fasta[0].seq.length;
                  return fasta;
                });

              case 6:
                return _context.abrupt("return", _context.sent);

              case 7:
              case "end":
                return _context.stop();
            }
          }
        }, _callee, this);
      }));

      function fasta_window(_x, _x2) {
        return _fasta_window.apply(this, arguments);
      }

      return fasta_window;
    }()
  }]);

  return BAMReader;
}();

var _default = BAMReader;
exports["default"] = _default;