src/main/data/bam.js
function fetchAlignments(remoteFile: RemoteFile,
                         refName: string,
                         idxRange: ContigInterval<number>,
                         contained: boolean,
                         chunks: Chunk[]): Q.Promise<SamRead[]> {

  var numRequests = 0,
      alignments = [],
      deferred = Q.defer();

  function fetch(chunks: Chunk[]) {
    if (chunks.length === 0) {
      deferred.resolve(alignments);
      return;
    }

    // Never fetch more than 128k at a time -- this reduces contention on the
    // main thread and can avoid sending unnecessary bytes over the network.
    var chunk = chunks[0],
        chunk_beg = chunk.chunk_beg.coffset,
        chunk_end = chunk.chunk_end.coffset;
    var bytesToFetch = Math.min(kMaxFetch, (chunk_end + 65536) - chunk_beg);
    remoteFile.getBytes(chunk_beg, bytesToFetch).then(buffer => {
      numRequests++;
      deferred.notify({numRequests});
      var cacheKey = {
        filename: remoteFile.url,
        initialOffset: chunk_beg
      };
      var blocks = utils.inflateConcatenatedGzip(buffer, chunk_end - chunk_beg, cacheKey);

      // If the chunk hasn't been exhausted, resume it at an appropriate place.
      // The last block needs to be re-read, since it may not have been exhausted.
      var lastBlock = blocks[blocks.length - 1],
          lastByte = chunk_beg + lastBlock.offset - 1,
          newChunk = null;
      if (blocks.length > 1 && lastByte < chunk_end) {
        newChunk = {
          chunk_beg: new VirtualOffset(lastByte + 1, 0),
          chunk_end: chunk.chunk_end
        };
      }

      var buffers = blocks.map(x => x.buffer);
      buffers[0] = buffers[0].slice(chunk.chunk_beg.uoffset);
      var decomp = utils.concatArrayBuffers(buffers);
      if (decomp.byteLength > 0) {
        var {shouldAbort, nextOffset} =
            readAlignmentsToEnd(decomp, refName, idxRange, contained,
                                chunk.chunk_beg, blocks, alignments);
        if (shouldAbort) {
          deferred.resolve(alignments);
          return;
        }
        if (newChunk) {
          newChunk.chunk_beg = nextOffset;
        }
      } else {
        newChunk = null;  // This is most likely EOF
      }
      fetch((newChunk !== null ? [newChunk] : []).concat(_.rest(chunks)));
    });
  }

  fetch(chunks);
  return deferred.promise;
}
function fetchAlignments(remoteFile: RemoteFile,
                         refName: string,
                         idxRange: ContigInterval<number>,
                         contained: boolean,
                         chunks: Chunk[]): Q.Promise<SamRead[]> {

  var numRequests = 0,
      alignments = [],
      deferred = Q.defer();

  function fetch(chunks: Chunk[]) {
    if (chunks.length === 0) {
      deferred.resolve(alignments);
      return;
    }

    // Never fetch more than 128k at a time -- this reduces contention on the
    // main thread and can avoid sending unnecessary bytes over the network.
    var chunk = chunks[0],
        chunk_beg = chunk.chunk_beg.coffset,
        chunk_end = chunk.chunk_end.coffset;
    var bytesToFetch = Math.min(kMaxFetch, (chunk_end + 65536) - chunk_beg);
    remoteFile.getBytes(chunk_beg, bytesToFetch).then(buffer => {
      numRequests++;
      deferred.notify({numRequests});
      var cacheKey = {
        filename: remoteFile.url,
        initialOffset: chunk_beg
      };
      var blocks = utils.inflateConcatenatedGzip(buffer, chunk_end - chunk_beg, cacheKey);

      // If the chunk hasn't been exhausted, resume it at an appropriate place.
      // The last block needs to be re-read, since it may not have been exhausted.
      var lastBlock = blocks[blocks.length - 1],
          lastByte = chunk_beg + lastBlock.offset - 1,
          newChunk = null;
      if (blocks.length > 1 && lastByte < chunk_end) {
        newChunk = {
          chunk_beg: new VirtualOffset(lastByte + 1, 0),
          chunk_end: chunk.chunk_end
        };
      }

      var buffers = blocks.map(x => x.buffer);
      buffers[0] = buffers[0].slice(chunk.chunk_beg.uoffset);
      var decomp = utils.concatArrayBuffers(buffers);
      if (decomp.byteLength > 0) {
        var {shouldAbort, nextOffset} =
            readAlignmentsToEnd(decomp, refName, idxRange, contained,
                                chunk.chunk_beg, blocks, alignments);
        if (shouldAbort) {
          deferred.resolve(alignments);
          return;
        }
        if (newChunk) {
          newChunk.chunk_beg = nextOffset;
        }
      } else {
        newChunk = null;  // This is most likely EOF
      }
      fetch((newChunk !== null ? [newChunk] : []).concat(_.rest(chunks)));
    });
  }

  fetch(chunks);
  return deferred.promise;
}
Fetch alignments from the remote source at the locations specified by Chunks. This can potentially result in many network requests. The returned promise is fulfilled once it can be proved that no more alignments need to be fetched.