molpopgen

//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>

molpopgen

/*
  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

molpopgen

#!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

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>

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
*/