florin-chelaru

import org.umd.assemblytest.readcoverage.samfile as sam

# Parse a file into a SamFile instance
samfile = sam.SamFile.read('../../../../../../tutorial/read_coverage/influenza-A.sam')

# In the background, the SamFile class partitions the alignments in the file
# by reference sequence, and organizes them in an IntervalTree, used for quick
# retrieval of overlaps.

# Compute the coverage of reference sequence '1' within the interval 1-100, and

florin-chelaru

/**
 * Created with JetBrains PhpStorm.
 * User: florin
 * Date: 4/4/13
 * Time: 7:22 PM
 * To change this template use File | Settings | File Templates.
 */
BarcodePlot.prototype = new BaseChart();

BarcodePlot.prototype.constructor = BarcodePlot;

florin-chelaru

/**
 * Created with JetBrains PhpStorm.
 * User: florin
 * Date: 4/10/13
 * Time: 10:43 AM
 * To change this template use File | Settings | File Templates.
 */

BarcodePlotHandler.prototype = new ChartTypeHandler({
  dataTypeHandler: new BarcodeDataHandler(),

florin-chelaru

/**
 * Created by Llewellyn
 * User: florin
 * Date: 8/2/13
 * Time: 
 * To change this template use File | Settings | File Templates.
 */

ExonExpressionTrack.prototype = new LineTrack();
ExonExpressionTrack.prototype.constructor = ExonExpressionTrack;

florin-chelaru

/**
 * 
 * User: florin
 * Date: 8/2/13
 * Time:
 * Created by Llewellyn
 */

ExonExpressionTrackHandler.prototype = new TrackTypeHandler({
  dataTypeHandler: new ProbeDataHandler(),

florin-chelaru

/**
 * Created by Florin Chelaru ( florinc [at] umd [dot] edu )
 * Date: 11/14/13
 * Time: 11:55 PM
 */

// goog.provide('epiviz.plugins.charts.ScatterPlot');

/**
 * @param {string} id

florin-chelaru

/**
 * Created by Florin Chelaru ( florinc [at] umd [dot] edu )
 * Date: 11/14/13
 * Time: 11:55 PM
 */

//goog.provide('epiviz.plugins.charts.ScatterPlotType');

goog.require('epiviz.ui.charts.Chart');

florin-chelaru

/**
 * Created by Florin Chelaru ( florinc [at] umd [dot] edu )
 * Date: 10/9/13
 * Time: 11:13 AM
 */

/**
 * Overrides the default configuration settings for EpiViz
 */
epiviz.EpiViz.SETTINGS = {

florin-chelaru

/**
 * Created by Florin Chelaru ( florinc [at] umd [dot] edu )
 * Date: 4/8/14
 * Time: 9:13 AM
 */

/**
 * Overrides the default configuration settings for EpiViz
 *
 * Settings specific to measuring performance

florin-chelaru

epiviz.EpiViz.SETTINGS.chartTypes.push('epiviz.plugins.charts.MyTrackType');