Colin Diesh cmdcolin

CoffeeScript Family (& Friends)

CoffeeScript Unfancy JavaScript
CoffeeScript II: The Wrath of Khan Rewrite of the CS compiler

Family (share genes with CoffeeScript)

Coco A CoffeeScript dialect that aims to be more radical and practical, also acts as a test bed for features that get imported in CoffeeScript.
- LiveScript is a fork of Coco that is much more compatible with CoffeeScript, more functional, and with more features.
IcedCoffeeScript A CoffeeScript dialect that adds support for await and defer keywords which simplify async control flow.

Firefox bullshit removal

Updated: Just use qutebrowser (and disable javascript). The web is done for.

I'm having a problem with my layer file not properly interning my widget template strings resulting in separate requests for each template file:

I have set up a simple example repo with an application containing two widgets (App & Widget). My goal is to build my entire application (JS & HTML) into one file. Here's my build profile:

var profile = {
    basePath: '../src/',
    action: 'release',
    optimize: 'closure',
    selectorEngine: 'acme',

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

Bioconductor Shiny Example #4

Example Shiny App showing an example of being embedded in a larger, non-Shiny workflow.

This is an example Shiny app featuring some basic analysis of Ovarian Cancer gene expression data collected on the Affymetrix U133A platform. We filter the available genes and samples down to a much smaller matrix to make reproducibility simpler for a broader audience. The R code involved in sampling the data is available in this Gist as an R-Markdown file, and the sampled data are available in this Gist as Rds files.

To run the application, install shiny (install.packages("shiny")) then run the following command:

library(shiny)

	// Adapted from http://stackoverflow.com/questions/563198/how-do-you-detect-where-two-line-segments-intersect/1968345#1968345
	var eps = 0.0000001;
	function between(a, b, c) {
	return a-eps <= b && b <= c+eps;
	}
	function segment_intersection(x1,y1,x2,y2, x3,y3,x4,y4) {
	var x=((x1y2-y1x2)(x3-x4)-(x1-x2)(x3y4-y3x4)) /
	((x1-x2)(y3-y4)-(y1-y2)(x3-x4));
	var y=((x1y2-y1x2)(y3-y4)-(y1-y2)(x3y4-y3x4)) /
	((x1-x2)(y3-y4)-(y1-y2)(x3-x4));

	#include <stdio.h>
	#include <string.h>
	#include <stdlib.h>
	#include <htslib/sam.h>

	int main(int argc, char *argv[]){

	samFile *fp_in = hts_open(argv[1],"r"); //open bam file
	bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header
	bam1_t *aln = bam_init1(); //initialize an alignment

	// JVM sizing options
	-server -Xms40g -Xmx40g -XX:MaxDirectMemorySize=4096m -XX:PermSize=256m -XX:MaxPermSize=256m
	// Young generation options
	-XX:NewSize=6g -XX:MaxNewSize=6g -XX:+UseParNewGC -XX:MaxTenuringThreshold=2 -XX:SurvivorRatio=8 -XX:+UnlockDiagnosticVMOptions -XX:ParGCCardsPerStrideChunk=32768
	// Old generation options
	-XX:+UseConcMarkSweepGC -XX:CMSParallelRemarkEnabled -XX:+ParallelRefProcEnabled -XX:+CMSClassUnloadingEnabled -XX:CMSInitiatingOccupancyFraction=80 -XX:+UseCMSInitiatingOccupancyOnly
	// Other options
	-XX:+AlwaysPreTouch -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintTenuringDistribution -XX:+PrintGCApplicationStoppedTime -XX:-OmitStackTraceInFastThrow

	<html>
	<head>
	<script type="text/javascript">
	//<![CDATA[

	/* from R code https://github.com/genome-vendor/r-bioc-biostrings/blob/master/src/match_PWM.c */

	function compute_pwm_score(pwm, S,offset)
	{
	var score=0.0;

	import java.awt.Insets
	import groovy.xml.StreamingMarkupBuilder
	import groovy.transform.*

	class Biostar77288 {
	private int ALN_WIDTH = 1000

	private Map<String,Seq> sequences = [:].withDefault { new Seq( name:it ) }

	private int maxLength = 0