elowy01

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

holyjak

#!/bin/sh
##
## BEWARE: Check with your impl. of top what exactly it returns, it migth differ from mine
##
# Usage: ./monitor-usage.sh <PID of the process>
# Output: top.dat with lines such as `1539689171 305m 2.0`, i.e. unix time - memory with m suffix - CPU load in %
# To plot the output, see https://gist.github.com/holyjak/1b58dedae3207b4a56c9abcde5f3fdb5
export PID=$1
rm top.dat
while true; do top -p $PID -bn 1 -em | egrep '^ *[0-9]+' | awk -v now=$(date +%s.%N) '{print now,$6,$9}' >> top.dat; done

ericnormand

#!/bin/sh
#_(

   #_DEPS is same format as deps.edn. Multiline is okay.
   DEPS='
   {:deps {clj-time {:mvn/version "0.14.2"}}}
   '

   #_You can put other options here
   OPTS='

pjstadig

The Pledge

One thing that always made me a little sad about transducers was how map lost its ability to iterate multiple collections in parallel. This is actually my favorite feature of map. For example:

(map + (range 5) (range 5 10))
=> (5 7 9 11 13)

One somewhat practical use of this is if you want to compare two sequences, pairwise, using a comparator. Though I wish that every? took multiple collections, this is an adequate substitute:

ravenkls

import matplotlib.pyplot as plt
from PyQt5 import QtCore
import numpy as np
import time
import math


class VisualiseFrequency(QtCore.QThread):

    def __init__(self, song, canvas, player):

Efimero

(defproject test-3d "0.1.0-SNAPSHOT"
  :description "FIXME: write description"
  :url "http://example.com/FIXME"
  :license {:name "EPL-2.0 OR GPL-2.0-or-later WITH Classpath-exception-2.0"
            :url "https://www.eclipse.org/legal/epl-2.0/"}
  :dependencies [[org.clojure/clojure "1.10.0"]
                 [org.lwjgl/lwjgl "3.2.2"]
                 [org.lwjgl/lwjgl "3.2.2" :classifier "natives-linux"]
                 [org.lwjgl/lwjgl-opengl "3.2.2"]
                 [org.lwjgl/lwjgl-opengl "3.2.2" :classifier "natives-linux"]

andy-thomason

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

rusrushal13

Conferences

• Hydraconf

Summer School

• Summer school on practice and theory of Distributed Computing

Books

• Distributed Systems 3rd Edition by Maarten van Steen and Andrew S. Tanenbaum
• Data Intensive Applications by Martin Kleppmann

m-radzikowski

#!/usr/bin/env bash

set -Eeuo pipefail
trap cleanup SIGINT SIGTERM ERR EXIT

script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P)

usage() {
  cat <<EOF
Usage: $(basename "${BASH_SOURCE[0]}") [-h] [-v] [-f] -p param_value arg1 [arg2...]

borkdude

Here's a list of things I collected a conversation on partial. Personally I think using partial almost never has a benefit, while there are some downsides to using it. There are exceptional cases where partial has a benefit, e.g. if you want to "wrap" a multi-arity function or a function with an unknown amount of arguments.

Some reasons not to use partial:

• Some people find it harder to find out what's happening*
• https://ask.clojure.org/index.php/8373/when-should-prefer-comp-and-partial-to-anonymous-functions?show=8374#a8374
• https://www.tiagoespinha.net/2016/12/clojure-beware-of-the-partial/
• https://twitter.com/borkdude/status/796018276044247041
• Better stack traces from SCI (if your code runs through SCI)
• Better performance in some cases (inlining / intrinsics)