@gmod/jbrowse/src/JBrowse/Store/SeqFeature/IndexedFasta/File.js

JBrowse - client-side genome browser

define( [
            'dojo/_base/declare',
            'JBrowse/Model/SimpleFeature'
        ],
        function(
            declare,
            SimpleFeature
            ) {

return declare( null,
{
    constructor: function( args ) {
        this.store = args.store;
        this.data  = args.data;
        this.fai   = args.fai;

        this.chunkSizeLimit = args.chunkSizeLimit || 500000;
    },

    init: function( args ) {
        var bam = this;
        var successCallback = args.success || function() {};
        var failCallback = args.failure || function(e) { console.error(e, e.stack); };

        this._readFAI( dojo.hitch( this, function() {
            successCallback();
        }), failCallback );
    },

    _readFAI: function( successCallback, failCallback ) {
        this.fai.fetch( dojo.hitch( this, function(text) {
            if (!text.byteLength) {
                failCallback("No data read from FASTA index (FAI) file");
                return;
            }


            var buf = "";
            var bytes = new Uint8Array(text);
            var length = bytes.length;
            for (var i = 0; i < length; i++) {
                buf += String.fromCharCode(bytes[i]);
            }
            buf.split(/\r?\n/).forEach( dojo.hitch( this, function ( line ) {
                var row = line.split('\t');
                if(row[0]=="") return;

                this.store.index[row[0]] = {
                    name: row[0],
                    length: +row[1],
                    start: 0,
                    end: +row[1],
                    offset: +row[2],
                    linelen: +row[3],
                    linebytelen: +row[4]
                };
            }) );

            successCallback(  );
        }), failCallback );
    },

    fetch: function(chr, min, max, featCallback, endCallback, errorCallback ) {
        errorCallback = errorCallback || function(e) { console.error(e); };
        var refname = chr;
        if( ! this.store.browser.compareReferenceNames( chr, refname ) )
            refname = chr;
        var refindex = this.store.index[refname];
        var s = Math.max(0,min);
        var offset = this._fai_offset(refindex, s);
        var readlen = this._fai_offset(refindex, max) - offset;



        this.data.read(offset, readlen,
            function (data) {
                var buf = "";
                var bytes = new Uint8Array(data);
                var length = bytes.length;
                for (var i = 0; i < length; i++) {
                    buf += String.fromCharCode(bytes[i]);
                }
                buf=buf.replace(/\s+/g, '');
                featCallback(
                    new SimpleFeature({
                      data: {
                          start:    s,
                          end:      max,
                          residues: buf,
                          seq_id:   refname,
                          name:     refname
                      }
                    })
                );
                endCallback();
            },
            function (err) {
                errorCallback(err)
            }
        );
    },

    _fai_offset: function(idx, pos) {
        return idx.offset + idx.linebytelen * Math.floor(pos / idx.linelen) + pos % idx.linelen;
    }


});


});