Naughty Platypus Memorabilia

    fqreader

    0.0.2 • Public • Published

    fqreader

    fqreader reads FASTQ files.

    installation

    $ npm install fqreader

    usage

    call it like this

    var fqreader = require("fqreader");
    fqreader.read(filename, function(data) {
      console.log(data.id);
      console.log(data.seq);
      console.log("+");
      process.stdout.write(data.qual + "\n"); // to avoid %% -> %. or use consolog (https://github.com/shinout/consolog)
    });

    or like this

    var fqreader = require("fqreader");
    fqreader.read(filename, 
      data: function(data) {
        console.log("on data", data);
      },
      end: function() {
        console.log("on end");
      }
    });

    fqreader.read(fastqfile, params)

    Reads file with its name fastqfile as fastq format.

    fastqfile is a filename or a readable stream like process.stdin.

    if fastqfile is "-", then it reads from processs.stdin.

    params is required, must be an object or a function.

    params.data is called for each fastq unit with data.

    • data.id : sequence id
    • data.seq : sequence
    • data.qual : quality values

    params.end is called after the file is read through.

    other values in params is used for fs.createReadStream(fastqfile, params)

    for example, highWaterMark can be useful for performancd tuning.

    this.pause() and this.resume()

    are callable in "data" function

    var fqreader = require("fqreader");
    fqreader.read(filename, 
      data: function(data) {
        this.pause();
     
        var _this = this
        setTimeout(function() {
          _this.resume();
        }, 10);
      }
     
    });

    Install

    npm i fqreader

    DownloadsWeekly Downloads

    4

    Version

    0.0.2

    License

    none

    Last publish

    Collaborators

    • shinout