In this page http://www.html5rocks.com/en/tutorials/file/dndfiles/ if you scroll down to example \"Example: Slicing a file. Try it!\" you will see uses of readAsBin
This is my solution.
var reader = new FileReader();
reader.readAsBinaryString(fileData);
reader.onload = function(e) {
  if (reader.result) reader.content = reader.result;
  var base64Data = btoa(reader.content);
  //...
}
//extend FileReader
if (!FileReader.prototype.readAsBinaryString) {
    FileReader.prototype.readAsBinaryString = function (fileData) {
       var binary = "";
       var pt = this;
       var reader = new FileReader();      
       reader.onload = function (e) {
           var bytes = new Uint8Array(reader.result);
           var length = bytes.byteLength;
           for (var i = 0; i < length; i++) {
               binary += String.fromCharCode(bytes[i]);
           }
        //pt.result  - readonly so assign binary
        pt.content = binary;
        $(pt).trigger('onload');
    }
    reader.readAsArrayBuffer(fileData);
    }
}