Colm Ryan caryan

I hereby claim:

I am caryan on github.
I am caryan (https://keybase.io/caryan) on keybase.
I have a public key whose fingerprint is 437A E338 3B0B DB58 2F86 1E08 DE63 FA60 3D8F 1124

To claim this, I am signing this object:

	import hashlib
	import html
	import json
	import sys
	from typing import Optional

	from pylint.reporters import JSONReporter
	from pylint.lint import Run

	# map pylint categories to CodeClimate severity

	using Glob
	using DataFrames

	const PICARD = "/home/cryan/Downloads/picard-tools-2.1.0/picard.jar"
	const GATK = "/home/cryan/Downloads/GATK/GenomeAnalysisTK.jar"

	function prepare_reference(ref)
	#index the reference for bwa
	run(`bwa index $ref.fasta`)
	#sort the reference TODO: does it need to be sorted? .fai file seems minimal