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#!/usr/bin/env python3 | |
import sys | |
import os | |
import json | |
import subprocess | |
from itertools import tee, filterfalse | |
import markdown_link_extractor |
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#!/usr/bin/env bash | |
set -euo pipefail | |
# set -x | |
rm likes | |
curl -sS -n -G -H 'Content-Type: application/json' https://intranet.gimr.garvan.org.au/rest/api/content/ --data-urlencode limit=500 --data-urlencode type=page --data-urlencode type=page > tmpdata | |
for i in $(seq 500); do |
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##fileformat=VCFv4.2 | |
##FILTER=<ID=PASS,Description="All filters passed"> | |
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | |
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | |
##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz | |
##contig=<ID=1,length=249250621,md5=1b22b98cdeb4a9304cb5d48026a85128> | |
##contig=<ID=2,length=243199373,md5=a0d9851da00400dec1098a9255ac712e> |
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File is ~100 million lines, with ~30 categories in the first column. So sort type 1 should execute ~30 subprocesses. | |
Takes ~ 180 seconds, so subprocess overhead should be very minimal. | |
Type 1, multiple sub-sorts: | |
$ time env time -v -o sort1.time awk -v cmd="sort -k2,2n" '$1 != prev {close(cmd); prev=$1} {print | cmd}' vcf.bed > vcf.sort1.bed | |
real 2m57.867s | |
user 0m46.381s | |
sys 4m14.309s |
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function autolike () { | |
[].forEach.call( | |
document.getElementById("likes-and-labels-container") | |
.getElementsByClassName("like-button-text"), | |
function (e) { | |
console.error(e); | |
if (e.innerText === "Like") { | |
e.parentNode.click(); | |
// [].forEach.call( | |
// document.getElementsByClassName("like-button"), |
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#!/usr/bin/env bash | |
set -euo pipefail | |
CACHE_FILE="$HOME"/.cache/qstat.map | |
# a 1 minute timed cache | |
# does not actually handle failures properly. todo | |
if ! test -e $CACHE_FILE || (( $(find "$CACHE_FILE" -mmin +1 | wc -l) > 0)); then | |
CACHE_FILE_TMP="$CACHE_FILE.$$.$RANDOM" | |
trap 'rm '"$CACHE_FILE_TMP" EXIT |
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import random | |
import collections | |
def num_cards(): | |
cures = [0] * 48 + [1] * 4 | |
random.shuffle(cures) | |
def split(x, n): | |
return [x[i:len(x):n] for i in range(n)] | |
cures = [c + [2] for c in split(cures, 5)] | |
[random.shuffle(c) for c in cures] |
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#!/bin/bash | |
set -xeuo pipefail | |
IFS=$'\n\t' | |
# git clone https://github.com/cloudflare/zlib & | |
[ -d "zlib-1.2.8" ] || curl -L https://github.com/cloudflare/zlib/archive/v1.2.8.tar.gz | tar zx & | |
# git clone https://github.com/ebiggers/libdeflate.git & | |
[ -d "libdeflate-1.0" ] || curl -L https://github.com/ebiggers/libdeflate/archive/v1.0.tar.gz | tar zx & | |
# git clone https://github.com/samtools/htslib.git & | |
[ -d "htslib-1.8" ] || curl -L https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2 | tar jx & |
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task bwa_mem_tool { | |
Int threads | |
Int min_seed_length | |
Int min_std_max_min | |
command { | |
echo ${threads} ${min_seed_length} ${sep=',' min_std_max_min+} > output.sam | |
} | |
output { | |
File sam = "output.sam" |
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#define TIMEIT(F, N, REPS) \ | |
{\ | |
clock_t start = clock();\ | |
for (int i = 0; i < N; ++i)\ | |
{\ | |
}\ | |
clock_t diff_loop = clock() - start;\ | |
double results[REPS];\ | |
for (int i = 0; i < REPS; ++i)\ | |
{\ |
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