I tried to convert a base64 string generated from pdf file using FileReader.readAsDataURL() to its original format.
In NodeJS I did it like this and it was able generated the pdf to its initial state.
filebuffer = "data:application/pdf;base64,JVBERi0xLjQKJSDi48/..........."
let base64file = fileBuffer.split(';base64,').pop();
fs.writeFileSync('download.pdf',base64file,{encoding:'base64'},function(err){
    if(err === null){
        console.log("file created");
        return;
    }
    else{
        console.log(err);
        return;
    }
})
But i tried to do it in HTML + Javascript in this way.But in this way , pdf was empty/no letter wasn't in it
let stringval = "data:application/pdf;base64,JVBERi0xLjQKJSDi48/..........."
let encodedString = stringval.split(';base64,').pop();
let data = atob(encodedString);
let blob = new Blob([data]);
// //if you need a literal File object
let file = new File([blob], "filename");
link.href = URL.createObjectURL(file);
link.download = 'filename';
I was Capturing file and converting to base64 string in this way:
captureFile: function () {
event.preventDefault();
const file = event.target.files[0];
$("#labelinput1").html(file.name);
const reader = new window.FileReader();
reader.readAsDataURL(file);
reader.onloadend = () => {
  var x = reader.result.toString();
  App.buffer2 = x;
  console.log("buffer", App.buffer);
};}
Then after clicking a button , I added the buffer to IPFS node
addfile: async function () {
if (App.buffer2 === null) return;
App.node = await window.Ipfs.create()
App.node.add(App.buffer2, function (errx, resipfs) {
      if (errx === null) {
        console.log(resipfs[0].hash);
        App.buffer2 = null;
        return App.showInfo(resipfs[0].hash);
      }
      else {
        return App.showError(errx.message.toString() + errx.stack.toString());
      }
    });
}
using the IPFS HASH i can get back the base64 encoded string , I retrieved this string in this way:
ipfsfiledownload: async function () {
var filebuffer = await App.node.cat(hashtext);
var stringval = filebuffer.toString();
//convert this string to main file
}
I used Truffle Petshop and write those functions in top of it. Here is a IPFS hash QmfSefUiwjV44hpfnHyUngGATyHm9M4vN3PzF1mpe59Nn1.  you can try out this Hash value in nodejs with this code
const IPFS = require('ipfs');
const fs = require('fs');
const main = async() => {
    const node = await IPFS.create()
    var fileBuffer = await 
    node.cat('QmfSefUiwjV44hpfnHyUngGATyHm9M4vN3PzF1mpe59Nn1')
    fileBuffer = fileBuffer.toString()
    let base64file = fileBuffer.split(';base64,').pop();
    fs.writeFileSync('download.pdf',base64file, {encoding:'base64'},function(err){
        if(err === null){
            console.log("file created");
            return;
        }
        else{
            console.log(err);
            return;
        }
    })
}
main()
You can find the full code here. What I am doing wrong and how to solve it?