nathanhaigh

#!/bin/bash
# Usage: interleave_fastq.sh f.fastq r.fastq > interleaved.fastq
# 
# Interleaves the reads of two FASTQ files specified on the
# command line and outputs a single FASTQ file of STDOUT.
# 
# Can interleave 100 million paired reads (200 million total
# reads; a 2 x 22Gbyte files), in memory (/dev/shm), in 6m54s (414s)
# 
# Latest code: https://gist.github.com/4544979

sjolsen

#include <sys/mman.h>
#include <fcntl.h>
#include <unistd.h>
#include <cuda_runtime.h>

#include <cerrno>
#include <cstring>
#include <memory>
#include <stdexcept>

explodecomputer

library(ggbio)
library(grid)
library(gridExtra)
library(plyr)
library(GenomicRanges)
library(qgraph)

multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL)
{
  require(grid)

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (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)

nicktoumpelis

git clean -xfd
git submodule foreach --recursive git clean -xfd
git reset --hard
git submodule foreach --recursive git reset --hard
git submodule update --init --recursive

Winterflower

# -*- coding: utf-8 -*-
def kmer(sequence,k):
  length=len(sequence)
 #if the kmer size if greater than the lenght of the sequene
  if k>=length:
    print "You specified a kmer size, which if greater or equal to the length of the sequence"
    return 
  stepsize=k-1
  i=0
  kmers=[]

djhocking

one <- seq(1:10)
two <- rnorm(10)
three <- runif(10, 1, 2)
four <- -10:-1

df <- data.frame(one, two, three)
df2 <- data.frame(one, two, three, four)

str(df)

lh3

/*
  For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means
  hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of
  hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x.
*/

// Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot.
uint64_t hash_64(uint64_t key, uint64_t mask)
{
	key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;

PoisonAlien

#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

arq5x

chmod a+x vcfsort.sh
vcfsort.sh trio.trim.vep.vcf.gz