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phi <- 0
while(TRUE){
  plot(sin(phi + 1:20), col=c("black","black","red"), cex=3, pch=c("☢","☠","♥"))
  Sys.sleep(0.1)
  phi = phi +0.3
}

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library("qtl")      # Load the library
data(multitrait)    # Load the data
multitrait          # Show the library

pull.pheno(multitrait, pheno.col = 1)        # Shows the phenotype values of phenotype 1
hist(pull.pheno(multitrait, pheno.col = 1))  # Create a histogram

# Plot a map versus the other ones
plot.map(multitrait, est.map(multitrait))

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*~
*.rdf
*.n3

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module rotationmatrices;

import std.stdio;
import cordicalgorithm;

struct mat(T = float){
  T[][] data;
  
  pure mat!T opBinary(string op)(mat!T rhs){
    static if (op == "*" || op == "+" || op == "-"){

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module cordicalgorithm;

import std.traits, std.conv;

immutable PI      = 3.14159265359;
immutable trigono = gen_trigonometric!double();

pure int degreeloop(int deg){
  while(deg < 0 || deg >= 360){
    (deg < 0) ? deg += 360 : deg -= 360;

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Reset to the commit before the wrong one

 git reset YYY --hard
 git push origin master --force

Update to the current 'blessed repos'

 git pull molgenis master

Get any commits we did AFTER the wrong one

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import std.stdio;

interface CrossDef{
  abstract int init();
  abstract int emit();
}

class RIL : CrossDef{
  int init(){ return 1; }
  int emit(){ return 2; }

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/**
  A minimal example to use the random number generator of R (calling into Rlib.so from D)
  dmd test_rlib.d ; ./test_rlib
  It is a copy of the C code I wrote for BioLib
  (c) Pjotr Prins, 2012
  Win32 support was added by Danny Arends
  See the latest version at: https://github.com/pjotrp/qtlHD/blob/master/src/D/test/rlib/test_rlib.d
*/

module test.rlib.test_rlib;

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#Stop maui
ps -ef | grep maui
kill <pid>

#Start maui
/usr/local/maui/sbin/maui

#Terminate PBS quick n dirty
qterm -t quick

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R and R/qtl tutorial

Loading example data

R/qtl provides many example data sets in several species and crosses. After loading the package by using either a library() or require() call, these can be loaded into the work space by using the data() function. To load the hyper data set containing measurements on hypertension in mice give the following commands in the R interpreter:

 library(qtl) #Load the R/qtl library