Eric T. Dawson edawson

Let's Destroy C

I have a pet project I work on, every now and then. CNoEvil.

The concept is simple enough.

What if, for a moment, we forgot all the rules we know. That we ignore every good idea, and accept all the terrible ones. That nothing is off limits. Can we turn C into a new language? Can we do what Lisp and Forth let the over-eager programmer do, but in C?

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

"My First WDL" Template

task name {
  String in
  command {
    echo '${in}'
  }
  output {
 String out = read_string(stdout())

	/**
	Pierre Lindenbaum, 2019

	gcc -o a.out -O3 -Wall -Isamtools/include discordant.c -Lsamtools/lib -lhts

	*/
	#include <stdio.h>
	#include <stdlib.h>
	#include <errno.h>
	#include <string.h>

	#Example 1:

	#!/usr/bin/env nextflow

	params.str = 'Hello world!'

	process AFcalc {

	"""
	echo '${params.str}'

	REF="/path/to/human_g1k_v37.fasta"
	java_exe="java"
	gatk_jar="/path/to/GenomeAnalysisTK.jar"
	params.test_flag="F"
	params.prefix="20180515.NEXTFLOW"
	params.callers=["samtools","freebayes","hapcaller"]
	params.description="${params.prefix} : Pierre test Nextflow "

	- Skelley et al 2013:
	- paper: http://genome.cshlp.org/content/23/9/1496.long
	- ena: http://www.ebi.ac.uk/ena/data/view/SRP018005 (includes RNA-seq)
	- 22 diverse Scer strains

	- Bergstrom et al 2014
	- paper: https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu037
	- SGRP2
	- 19 Scer
	- 22 Spar

	library(vcfR)

	# Import VCF
	my.vcf <- read.vcfR('my.vcf.gz')
	# Combine CHROM thru FILTER cols + INFO cols
	my.vcf.df <- cbind(as.data.frame(getFIX(my.vcf)), INFO2df(my.vcf))

	#!/usr/bin/env python
	# -- coding: utf-8 --

	"""
	Outputs some information on CUDA-enabled devices on your computer,
	including current memory usage.

	It's a port of https://gist.github.com/f0k/0d6431e3faa60bffc788f8b4daa029b1
	from C to Python with ctypes, so it can run without compiling anything. Note
	that this is a direct translation with no attempt to make the code Pythonic.

	# Make sure you grab the latest version
	curl -OL https://github.com/google/protobuf/releases/download/v3.2.0/protoc-3.2.0-linux-x86_64.zip

	# Unzip
	unzip protoc-3.2.0-linux-x86_64.zip -d protoc3

	# Move protoc to /usr/local/bin/
	sudo mv protoc3/bin/* /usr/local/bin/

	# Move protoc3/include to /usr/local/include/