| 1 | /*
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| 2 | * 2012.6.14 a faster version of vervet/src/mapper/CalculateMedianModeFromSAMtoolsDepthOutput.py
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| 3 | *
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| 4 | */
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| 5 |
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| 6 | #include <iostream>
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| 7 | #include <string>
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| 8 | #include <cmath> //sqrt
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| 9 | #include <assert.h>
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| 10 | #include <stdio.h>
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| 11 | #include <stdlib.h>
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| 12 | #include <ext/hash_map> //for hash_map
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| 13 | #include <boost/program_options.hpp> //for program options
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| 14 | #include <fstream>
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| 15 | #include <boost/tokenizer.hpp>
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| 16 |
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| 17 | #include "armadillo" //for mean/median calculation
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| 18 |
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| 19 | #include <boost/iostreams/filtering_streambuf.hpp>
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| 20 | #include <boost/iostreams/copy.hpp>
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| 21 | #include <boost/iostreams/filter/gzip.hpp>
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| 22 | #include <boost/random/mersenne_twister.hpp>
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| 23 | #include <boost/random/uniform_real.hpp>
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| 24 | #include <boost/random/variate_generator.hpp>
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| 25 | //#include <boost/generator_iterator.hpp>
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| 26 |
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| 27 | #include <boost/accumulators/accumulators.hpp>
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| 28 | #include <boost/accumulators/statistics/stats.hpp>
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| 29 | #include <boost/accumulators/statistics/mean.hpp>
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| 30 | #include <boost/accumulators/statistics/median.hpp>
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| 31 |
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| 32 | // This is a typedef for a random number generator.
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| 33 | // Try boost::mt19937 or boost::ecuyer1988 instead of boost::minstd_rand
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| 34 | typedef boost::mt19937 base_generator_type;
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| 35 |
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| 36 | using namespace arma;
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| 37 | using namespace std;
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| 38 | using namespace boost;
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| 39 | namespace ba = boost::accumulators;
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| 40 | namespace po = boost::program_options;
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| 41 |
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| 42 | class CalculateMedianMeanOfInputColumn{
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| 43 | string inputFname;
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| 44 | std::ifstream inputFile;
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| 45 | boost::iostreams::filtering_streambuf<boost::iostreams::input> input;
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| 46 | string outputFname;
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| 47 | std::ofstream outputFile;
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| 48 | int alignmentID;
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| 49 | float fractionToSample;
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| 50 | int noOfLinesInHeader;
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| 51 | int whichColumn;
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| 52 | int maxNumberOfSamplings;
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| 53 | arma::mat statList; //armadillo matrix storing all the sampled stats
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| 54 | __gnu_cxx::hash_map <int, int> stat2Occurrence;
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| 55 | int modeStat;
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| 56 | // Define an accumulator set for calculating the mean and the median
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| 57 | ba::accumulator_set<double, ba::stats<ba::tag::mean, ba::tag::median > > acc;
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| 58 |
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| 59 | public:
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| 60 | CalculateMedianMeanOfInputColumn(string _inputFname, string _outputFname, int _alignmentID,
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| 61 | float _fractionToSample, int _noOfLinesInHeader, int _whichColumn, int _maxNumberOfSamplings);
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| 62 | ~CalculateMedianMeanOfInputColumn();
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| 63 | void run();
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| 64 | };
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