// TODO: get rid of this; move all methods into SamRead.
getFull(): Object {
if (this._full) return this._full;
var jb = new jBinary(this.buffer, bamTypes.TYPE_SET);
var full = jb.read(bamTypes.ThickAlignment, 0);
this._full = full;
return full;
}
function extractFeaturesFromBlock(buffer, dataRange, block): ChrIdBedRow[] {
var blockOffset = block.offset - dataRange.start,
blockLimit = blockOffset + block.size,
// TODO: where does the +2 come from? (I copied it from dalliance)
blockBuffer = buffer.slice(blockOffset + 2, blockLimit);
// TODO: only inflate if necessary
var inflatedBuffer = pako.inflateRaw(new Uint8Array(blockBuffer));
var jb = new jBinary(inflatedBuffer, bbi.TYPE_SET);
// TODO: parse only one BedEntry at a time & use an iterator.
return jb.read('BedBlock');
}
this.indexCache[contig] = this.getSlice(start, stop).then(buffer => {
var jb = new jBinary(buffer, bamTypes.TYPE_SET);
return jb.read('BaiIndex');
});