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pileup_driver.cc
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pileup_driver.cc
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/**
* @file pileup_driver.cc
* @author Melissa Ip
*
* This file accepts 3 input pileup files. The pileup data is read and parsed
* into sequencing read data that the TrioModel can process. Default parameter
* values are used. Assume that all pileup files have the same number of sites
* and thus can be aligned.
*
* To compile on Herschel without using cmake and include GSL:
* c++ -std=c++11 -L/usr/local/lib -lgsl -lgslcblas -lm -I/usr/local/include -o pileup_driver pileup_utility.cc pileup_driver.cc
*
* To run this file, provide the following command line inputs:
* ./pileup_driver <output>.txt <child>.pileup <mother>.pileup <father>.pileup
*
* See top of pileup_utility.h for additional information.
*/
#include "pileup_utility.h"
int main(int argc, const char *argv[]) {
if (argc < 5) {
Die("USAGE: pileup_driver <output>.txt <child>.pileup <mother>.pileup "
"<father>.pileup");
}
const string file_name = argv[1];
const string child_pileup = argv[2];
const string mother_pileup = argv[3];
const string father_pileup = argv[4];
ProcessPileup(file_name, child_pileup, mother_pileup, father_pileup);
return 0;
}