scottfrazer

"My First WDL" Template

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

chenshuo

#pragma once

#include <stdint.h>
#include <stdlib.h>
#include <string.h>

#include <type_traits>

typedef uint32_t khint_t;
typedef khint_t khiter_t;

dfjenkins3

IGV Batch Screenshots

IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.

Table of Contents

1. Requirements
2. Workflow
3. Create BED File

arq5x

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

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

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;

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)

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=[]

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

davfre

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)