molpopgen

/*
  A function to check that a file both exists and is in .gz format.
  
  It is done the easy way, using only C++ constructs instead of any lower-level calls
  
  Requires the boost iostreams library
  
  Programs compiled using this function need -lboost_iostreams
*/

molpopgen

/*
  Example of how to write binary stuff in C++
  
  Illustrates some of the various quirks/annoyances
*/

#include <iostream>
#include <fstream>
#include <string>
#include <vector>

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#!sh

#Must be executed with bash shell.
#If sh bwapetrick1.sh fails, then say bash bwapetrick1.sh

#bwa 0.7.5a-r405
#samtools 0.1.19

LEFTREADS=NY42_06_21_2010_54_1.fastq.gz
RIGHTREADS=NY42_06_21_2010_54_2.fastq.gz

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/*
  sizeof(iterator) and sizeof(pointer) are the same.
  They also act the same vis-a-vis dereferencing.

  But, they do not act the same with respect to traversal of a range
  
  Note that this example forces iterator and pointer invalidation to occur.
  
  Thus, the specifics of the output may vary with the optimization level 
  used to compile.  On OS X Mavericks, -O2 provides cleaner output

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//g++ -o readbgz readbgz.cc -lboost_iostreams -lz
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/filter/gzip.hpp>

#include <iostream>
#include <fstream>
#include <cstdlib>
#include <vector>

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//////////////////////////////////////////////////////////////////
//                                                              //
//           PLINK (c) 2005-2008 Shaun Purcell                  //
//                                                              //
// This file is distributed under the GNU General Public        //
// License, Version 2.  Please see the file COPYING for more    //
// details                                                      //
//                                                              //
//////////////////////////////////////////////////////////////////

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#include <boost/interprocess/sync/file_lock.hpp>
#include <boost/interprocess/sync/scoped_lock.hpp>

#include <fstream>

int main( int argc, char ** argv )
{
  std::ofstream o("monkey.txt",std::ios_base::app);

  boost::interprocess::file_lock ol("monkey.txt");

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library(Rcpp)
Sys.setenv("PKG_CXXFLAGS" = "-std=c++11")
sourceCpp("tuple.cc",verbose=TRUE)

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#!sh

##collect the simulation results.  This may have to be run as 'bash collate.sh' on some systems
echo "Simulation L time mem" > results.txt
paste <(find . -name "*.time" -type f ! -size 0 | sed 's/\.\///' | cut -d"." -f 1,2 | sed 's/\./ /') <(find . -name "*.time" -type f ! -size 0 | xargs cat) | sort -n -k 2,3 >> results.txt

molpopgen

Problem

You want to use Jupyter remotely. X11 forwarding is too slow for this.

Solution

SSH port forwarding!

The recipe