bpow

#!/bin/sh

<<comment

REQUIREMENTS:
- kubectl (of course)
- krew "neat" plugin to remove some extra cruft
- yq to decode secrets to stringData

The resource types are:

bpow

### Keybase proof

I hereby claim:

  * I am bpow on github.
  * I am bpow (https://keybase.io/bpow) on keybase.
  * I have a public key ASB_4EE6sX3jIuLAkQFDo_M-24lqAxWXNhJjGy_FNzBJugo

To claim this, I am signing this object:

bpow

#!/usr/bin/python

from pyld import jsonld
import json

j = json.loads('''
{
  "@context": "http://schema.org/",
  "@type": "Person",
  "name": "Jane Doe",

bpow

{
  "cg:id": "VarInterp001",
  "cg:type": "VariantInterpretation",
  "variant": {
    "cg:id": "CanAll035",
    "cg:type": "CanonicalAllele",
    "preferredCtxAllele": "CtxAll039",
    "identifier": "http://reg.genome.network/allele/CA090919"
  },
  "condition": {

bpow

##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

bpow

An illustration of how stochastic X-chromosome inactivation leads to functional mosaicism.

bpow

#!/usr/bin/python

import errno
import stat
import sys
import llfuse
import time
import dxpy
import os
import json

bpow

.SECONDARY:

LUMPY:=./lumpy-sv
YAHADB:=./refs/hg19.X11_01_65525S
YAHA:=./yaha
BWA:=./bwa-0.6.2/bin/bwa
BWADB:=./refs/hg19.fa
READ_LENGTH=100

%.um.fq : %.bam

bpow

#!/bin/bash                                                                                                                                                                 
JAVA_OPTS="-Dgroovy.grape.report.downloads=true" //usr/bin/env groovy "$0" $@; exit $?


@GrabResolver(name="maven-sandbox-picard", root="https://github.com/bpow/maven-sandbox/raw/master/picard")
@Grab(group="net.sf.picard", module="picard", version="1.86-SNAPSHOT")
import net.sf.samtools.*
import net.sf.picard.sam.*

def mergeAndRemap(chromosome, mapfile, infiles, outfile) {