edawson

Functions:

# encoding: ACTG

def nuc2int_nochecking(b):
    return (ord(b) >> 1) & 3, True
    
def nuc2int_if(b):
    if b == 'a' or b == 'c' or b == 'g' or b == 't' \

or b == 'A' or b == 'C' or b == 'G' or b == 'T':

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#Example 1:

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process AFcalc {

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

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

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

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#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

edawson

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

edawson

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

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

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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

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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))