ReadsTrack

• The ReadsTrack represents short sequence reads from modern deep sequencing hardware
• Rendering occurs in one of three zoom-dependent modes: depth, box and sequence (see screenshots).

Screenshots

When zoomed out, reads are presented in a histogram form that shows read depth. Individual reads cannot be discerned at this level (zoom >= 10:1).

At moderate zoom levels, the individual reads themselves are shown as boxes. This occurs when zoom is >= 1:1 and < 10:1.

When zoomed in closer than 1:1, individual reads are shown with colour coding to represent base calls. If space is available, the individual letters will also be printed.

Configuration Options

		// Defaults shown
		var params = {
		
			// Config options inherited from BaseTrack
			id           : Ext.id(),          // a unique ID for the track, if not provided then one will be automatically assigned
			name         : 'Track',           // the name of the track, used in the track selector tree and as the track title
			path         : '',                // path used to position the track in the track selector tree, eg /All Tracks/My Track
			minHeight    : 40,                // the minimum height of the track (if resizable)
			maxHeight    : 1000,              // the maximum height of the track (if resizable)
			height       : 40,                // the height of the track when it is first created
			resizable    : true,              // allow the track to be vertically resized by the user
			showControls : false,             // show the track's controls when it is first created
			cls          : 'AJ_track',        // class name to apply to the div that contains the track
			iconCls      : 'silk_bricks',     // class name to use for the track's icon

			// Config options inherited from BrowserTrack
			enableMenu   : true,              // enable the custom right-click context menu
			autoResize   : false,             // automatically resize the track to fit its content
			autoScroll   : true,              // ???
			minCache     : 100,               // the minimum size that a cache is allowed to shrink to
			cache        : 3 * screen.width,  // number of pixels (width) to cache in the browser by default
			maxCache     : 20 * screen.width, // the maximum size that a cache is allowed to grow to
			scaler       : 0.5,               // default starting position of the scaler control (must be between 0.0 and 1.0)
			dragMode     : 'browse',          // default dragMode for the track

			// Config options inherited from DataTrack
			datasource    : '',               // URL to the track's data provider
			requestMethod : 'POST',           // HTTP request method to use
			requestParams : null,             // name : value pairs to send with all requests (object)			

			// Config options specific to ModelsTrack
			single        : false,            // show only one strand
			clsAbove      : 'AJ_above',       // class name to apply to the div that contains the watson strand
			clsBelow      : 'AJ_below',       // class name to apply to the div that contains the crick strand
			slider        : 0.5,              // default starting position of the slider control (must be between 0.0 and 1.0)
			boxHeight     : 10,               // default box height for the models
			boxHeightMax  : 24,               // maximum box height for the models (height is modified when dragging in 'scale' mode)
			boxHeightMin  : 1,                // minimum box height for the models
			boxBlingLimit : 6                 // minimum height at which labels and arrows will be shown
		};
	

Zoom Categories

		//Zoom policies
		var policies = [
			{ index:0, min:1/100 , max:1/1    , bases:1   , pixels:100, cache:1000     },
			{ index:1, min:1/1   , max:10/1   , bases:1   , pixels:1  , cache:10000    },
			{ index:2, min:10/1  , max:100/1  , bases:10  , pixels:1  , cache:100000   },
			{ index:3, min:100/1 , max:1000/1 , bases:100 , pixels:1  , cache:1000000  },
			{ index:4, min:1000/1, max:10000/1, bases:1000, pixels:1  , cache:10000000 }
		];	
	

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