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florin-chelaru

console.log('New worker started');

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

/**
 * 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

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

#!/bin/bash

function showHelp {
    printf "\nUsage: $1 [OPTION]... [IGNORES]...\n"
    printf "Valid options:\n"
    printf "  -h\tThis help message\n"
    printf "  -d\tTarget directory\n"
    printf "  -o\tOutput file\n"
    printf "  -i=[list of dirs to ignore] (must be the last option in the command)\n"
    printf "\n"

florin-chelaru

#!/bin/bash

function ceil {
    echo "$1" | awk 'function ceil(v) { return (v == int(v)) ? v : int(v)+1 } { printf "%d", ceil($1) } '
}

input=$1
filename=$(basename $input)
linecount=$(wc -l $input | cut -f1 -d' ')

florin-chelaru

#!/bin/bash

# input is a file containing a list of paths (generated with extract_all_paths.sh)
input=$1

# get the id of the task, generated by GridEngine
taskId=$SGE_TASK_ID

# the number of files to be processed in one run
batchSize=$2

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@transition-speed: 0.5s;
@light-gray: #ddd;
@medium-gray: #808080;
@dark-gray: #494949;
@transparent-light-gray: rgba(0, 0, 0, 0.025);
@transparent-gray: rgba(0, 0, 0, 0.05);
@transparent-dark-gray: rgba(0, 0, 0, 0.075);
@item-max-height: 120px;