myseq-vcf/lib/io/FileReaders.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; }

const fs = require('fs');

const http = require('http');

const URL = require('url');

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

function bufferToArrayBufferSlice(buffer, bytes) {
  const bytesToRead = bytes === undefined ? buffer.byteLength : bytes;
  return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + bytesToRead);
}

class LocalFileReader extends AbstractFileReader {
  constructor(path) {
    super();

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

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

    this.handle = fs.openSync(path, 'r');
    this.size = fs.statSync(path).size;
  }

  bytes(start = 0, length) {
    return new Promise((resolve, reject) => {
      const lengthToRead = length === undefined ? this.size - start : length;
      const buffer = Buffer.alloc(lengthToRead);
      fs.read(this.handle, buffer, 0, lengthToRead, start, (err, read, buf) => {
        if (err) {
          reject(new Error(err));
        } else {
          resolve(bufferToArrayBufferSlice(buf, read));
        }
      });
    });
  }

}

class RemoteFileReader extends AbstractFileReader {
  constructor(url) {
    super();

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

    this.url = URL.parse(url);
  }

  bytes(start = 0, length) {
    const options = { ...this.url,
      method: 'GET'
    };

    if (start !== 0 || length !== undefined) {
      // Requesting only a portion of the file
      options.headers = {
        Range: length !== undefined ? `bytes=${start}-${start + (length - 1)}` : `bytes=${start}-`
      };
    }

    return new Promise((resolve, reject) => {
      const req = http.request(options, res => {
        const data = [];
        res.on('data', chunk => {
          data.push(chunk);
        }).on('end', () => {
          const buffer = Buffer.concat(data);
          resolve(bufferToArrayBufferSlice(buffer));
        });
      });
      req.on('error', e => {
        reject(new Error(`RemoteFileRequest failed: ${e.message}`));
      });
      req.end();
    });
  }

}

module.exports = {
  LocalFileReader,
  RemoteFileReader
};