Shians

OS X Screencast to animated GIF

This gist shows how to create a GIF screencast using only free OS X tools: QuickTime, ffmpeg, and gifsicle.

Instructions

To capture the video (filesize: 19MB), using the free "QuickTime Player" application:

Shians

star_align <- function(
  read_files_in,
  genome_dir,
  out_file_type = "BAM",
  sort_output = FALSE,
  out_file_prefix = "",
  nthreads = 2
) {
  # use lexical scoping to grab cmd from outer scope
  # saves having to pass in cmd at each step

Shians

bool is_gzipped(std::string filename) {
    std::ifstream in_file;
    char byte1, byte2;

    in_file.open(filename, ios::binary|ios::ate);
    if (in_file.is_open()) {
        in_file.seekg(0, ios::beg);
        std::string bytes;
        in_file.read(&byte1, 1);
        in_file.read(&byte2, 1);

Shians

my_palette <- c(
    "red3",
    "royalblue4",
    "green4",
    "darkmagenta",
    "gold",
    "darkslategrey",
    "darkorange3",
    "palevioletred1",
    "khaki4",

Shians

# search google for query
google <- function(query) {
    browseURL(glue::glue("https://www.google.com/search?q={URLencode(query)}"))
}

Shians

lorem <- function(ipsum) {
    dolor <- sit(amet, consectetur)
    dolor <- adipiscing(dolor, elit, sed, do)
    
    # aliqua Ut enim ad minim veniam, quis nostrud exercitation
    eiusmod <- tempor(incididunt, ut)
    labore <- et(dolor, magna)

    # ullamco laboris nisi ut aliquip ex ea commodo consequat duis aute 
    reprehenderit <- numeric()

Shians

theme_set(
    theme_classic() + 
        theme(
            panel.grid.major = element_line(colour = "gray"),
            plot.title = element_text(
                face = "plain",
                size = rel(20/12),
                hjust = 1/2,
                margin = margin(t = 10, b = 20)
            )

Shians

echo 'export PS1="\W \[\e[1;31m\]❯\[\e[1;33m\]❯\[\e[1;32m\]❯\[\e[0m\] "' >> ~/.bash_profile
. ~/.bash_profile

Shians

This gist is a summary of roxygen2 tags, see roxygen2 docs for source of information.

Header Section

The initial three sections are automatically placed into title, description and details fields of the documentation. The details field is optional.

#' Title goes here
#'
#' Description goes here

Shians

#!/usr/bin/env Rscript
library(fs)
library(rhdf5)
library(parallel)
library(purrr)
library(stringr)
library(dplyr)
library(tidyr)

index_fast5 <- function(fastq_file, fast5_dir) {