alienzj

#include <random>
#include <algorithm>
#include <iostream>
#include <cmath>

// header file for the hc API
#include <hcc/hc.hpp>

#define N  (1024 * 500)

alienzj

banded kraken - example usage

Prepare the database:

mkdir ecoli_many_sigs
cd ecoli_many_sigs
curl -O -L https://github.com/dib-lab/sourmash/raw/master/data/eschericia-sigs.tar.gz
tar xzf eschericia-sigs.tar.gz
cd ../

alienzj

# Script to silently install MATLAB components, run as root if installing to /opt
# Requires: `license.lic`, `packages` list and `file-install-key` files

# Download license.lic and create file-install-key file from [MATLAB license centre](https://uk.mathworks.com/licensecenter/licenses)
# Download and extract latest [MATLAB installer](https://uk.mathworks.com/downloads/)
# Download packages `archive` files by running installer graphically first
# Make a package list, uncommenting lines from installer_input, `tail -87 installer_input.txt > packages`
# Check destination directories are correct below

# Destination, MATLAB installer and config files directory

alienzj

QTabBar,
QTabBar::tab
{
    font-family: "Noto Sans";
    font-size: 11px;
    height: 16px;
    padding: 2px;
    border: 0px;
    border-bottom: 3px solid palette(dark);
    background-color: palette(dark);

alienzj

#!/bin/sh
# compute reads length distribution from a fastq file
awk 'NR%4 == 2 {lengths[length($0)]++} END {for (l in lengths) {print l, lengths[l]}}'  file.fastq

alienzj

Extracting paired FASTQ read data from a BAM mapping file

Sometimes FASTQ data is aligned to a reference and stored as a BAM file, instead of the normal FASTQ read files. This is okay, because it is possible to recreate raw FASTQ files based on the BAM file. The following outlines this process. The useful software samtools and bedtools are both required.

From each bam, we need to extract:

1. reads that mapped properly as pairs
2. reads that didn’t map properly as pairs (both didn’t map, or one didn’t map)

For #1, the following command will work. This was taken from this webpage.

alienzj

// Sample custom iterator.
// By perfectly.insane (http://www.dreamincode.net/forums/index.php?showuser=76558)
// From: http://www.dreamincode.net/forums/index.php?showtopic=58468

#include <iostream>
#include <vector>
#include <algorithm>
#include <iterator>
#include <cassert>

alienzj

#!/usr/bin/env bash
# memusg -- Measure memory usage of processes
# Usage: memusg COMMAND [ARGS]...
#
# Author: Jaeho Shin <netj@sparcs.org>
# Created: 2010-08-16
############################################################################
# Copyright 2010 Jaeho Shin.                                               #
#                                                                          #
# Licensed under the Apache License, Version 2.0 (the "License");          #

alienzj

#pragma once

#include <boost/noncopyable.hpp>

#include <boost/beast/websocket.hpp>

#include <boost/beast/websocket/ssl.hpp>

struct websocket_stream : boost::noncopyable

alienzj

Useful Spacemacs commands

• SPC q q - quit
• SPC w / - split window vertically
• SPC w - - split window horizontally
• SPC 1 - switch to window 1
• SPC 2 - switch to window 2
• SPC w c - delete current window
• SPC TAB - switch to previous buffer
• SPC b b - switch buffers