Shians

# parallel iteration pattern for processing chunks of data in parallel
fetch_and_process <- function(get_data_chunk, process_func, reduce_func) {
    n_workers <- future::nbrOfWorkers()
    results <- list()
    
    i <- 1
    out_of_data <- FALSE
    
    while(TRUE) {
        for (. in 1:n_workers) {

Shians

split_n_chunks <- function(x, n) {
    stopifnot(is(x, "data.frame"))
    f <- ceiling(seq_len(nrow(x)) / (nrow(x) / n))
    split(x, f)
}

Shians

#!/usr/bin/env bash

# called by
# sh extract_bam_tag.sh input.bam BC
# to print read_id and BC tag value

# two arguments, a bam file and the tag to extract
BAM=$1
TAG=$2

Shians

library(GenomicAlignments)

alignments <- GAlignments(
    seqnames = Rle(factor(rep("chrX", 3))),
    pos = c(37701723L, 37753335L, 37753335L),
    cigar = c(
        "24H6M1I13M2D5M1D12M1I16M3I6M2D20M1D18M1I34M2I116M2D9M1D9M1I30M1D9M1D44M6I3M2I4M2D19M9D7M1I5M1D18M1I17M2D1M1D16M1D32M1D3M1D18M1I3M1D49M2D34M2D8M1D7M2D1M1D5M1I2M5D4M1D2M1I3M2D10M1I21M1D20M2D1M1D2M1D18M2I3M2D74M1D9M1D5M2D34M1D12M2D20M1I2M1I35M1D10M2D16M1I55M3D82M1D6M1I65M2I8M1I30M1D7M2I15M1D15M1D20M1I2M1I14M1D29M3D12M2D3M1D5M1D20M1D21M2D56M1D7M4D2M1I60M2I9M1D49M2I5M2I28M13206H",
        "6994H26M2I6M1I1M1I50M1D15M2I4M4D35M1D9M1D5M2D37M1I54M1D59M3I27M1I3M1D5M1I8M1I4M2I10M1I47M1D25M1I84M1D8M7D8M1D69M1I23M3D6M1D1M1D11M2D8M1I17M1D43M1I17M1D60M1I1M3D17M1D17M2D1M1D4M1I12M1D28M1D13M1D7M2I44M5D30M1D2M2D1M1D20M1D23M1I7M1D22M1D3M2D73M1I4M5D23M3D4M2D23M1D13M1D9M3D12M1I9M1D11M1D1M3I31M2I56M1D5M6461H",
        "308H103M1D16M2D47M1D1M1D18M1D36M1I26M3I51M1D2M1I8M1D9M1D17M3I53M1D15M1D7M3I22M1D60M3I10M2D20M7D8M1D65M2I16M1D12M1D6M1D11M3D4M1D4M1I8M1I31M3I7M2I5M1I10

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) {

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

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

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

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

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