reedacartwright

#!/bin/sh
# Copyright (c) 2014-2015 Reed A. Cartwright <cartwright@asu.edu>
# Copyright (c) 2014-2015 Alberto Villa <avilla@FreeBSD.org>
# Copyright (c) 2015 Mike Clarke <jmc-freebsd2@milibyte.co.uk>
#
# This script determines the revision number used to build FreeBSD packages
# and syncs a local ports directory to match it.
#
# USAGE: sync-ports [name or abs_path]
#

reedacartwright

# Taken from https://github.com/reedacartwright/shell-config
#
# The following commands will produce a prompt that includes the error code of the
# last command run if it is not zero. E.g.
#      [user@host dir $?=123]$ 
# If the user is not root, the prompt is green, except the error information which is red.
# If the user is root, the prompt is read, except the error information which is green.
# If the last commend exited with a 0, then the prompt looks normal.  E.g.
#      [user@host dir]$ 
#

reedacartwright

// "License": Public Domain
// I, Mathias Panzenböck, place this file hereby into the public domain. Use it at your own risk for whatever you like.
// In case there are jurisdictions that don't support putting things in the public domain you can also consider it to
// be "dual licensed" under the BSD, MIT and Apache licenses, if you want to. This code is trivial anyway. Consider it
// an example on how to get the endian conversion functions on different platforms.

#ifndef PORTABLE_ENDIAN_H__
#define PORTABLE_ENDIAN_H__

#if (defined(_WIN16) || defined(_WIN32) || defined(_WIN64)) && !defined(__WINDOWS__)

reedacartwright

#include <cstring>
#include <cstdint>
#include <cstdio>

uint8_t pack_a(const char *cs) {
	uint32_t u;
	memcpy(&u,cs,4);
	u &= 0x06060606;
	u = (u | (u << 6) | (u << 12) | (u << 18)) >> 19;
	return u;

reedacartwright

/*******************************************************************************
Copyright (C) 2009-2017 Reed A. Cartwright, PhD <reed@cartwrig.ht>
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,

reedacartwright

#!/usr/bin/Rscript
# Authors: David Winter
#          Joanna Malukiewicz
#          Reed A. Cartwright

library(HiddenMarkov)
library(data.table) #makes reading a data table faster than using R data frame functions 
library(jsonlite)

cat("Started at ", as.character(Sys.time()), "\n")

reedacartwright

# This script calculates the average entropy and effective number of 
# possible mutants for the human mutation spectrum.

# Preparing to run this script
# > wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/common_all_20170710.vcf.gz
# > wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/common_all_20170710.vcf.gz.tbi
# > bcftools query -f '%REF\t%ALT\n' common_all_20170710.vcf.gz | zstd > altref.txt.zst

library(data.table)
library(stringr)

reedacartwright

// Compile with -std=c++14

#include <array>
#include <memory>
#include <iostream>
#include <algorithm>

struct A {
    virtual void operator()() = 0;
    std::array<int,10> data;

reedacartwright

#!/usr/bin/Rscript --vanilla

suppressPackageStartupMessages(library(stringr))
suppressPackageStartupMessages(library(Biostrings))

G = BString("-")

main = function(infile, dnafile, outfile) {
    ARGS = commandArgs(trailingOnly=TRUE)
    if(missing(infile)) {

reedacartwright

# uncomment and reinstall rbedrock to get the latest code.
# devtools::install_github("reedacartwright/rbedrock", INSTALL_opts="--no-multiarch")

library(tidyverse)
library(rbedrock)

# Local copy of the Advanced Automation Realm
# replace with your own world id
dbpath <- "XBdsXqo+AAA="