gatk-3.8/public/c++/VectorPairHMM/pairhmm-1-base.cc

46 lines
1004 B
C++

//#define DEBUG 1
//#define DEBUG0_1 1
//#define DEBUG3 1
#include "headers.h"
#include "utils.h"
#include "LoadTimeInitializer.h"
using namespace std;
int main(int argc, char** argv)
{
#define BATCH_SIZE 10000
if(argc < 2)
{
cerr << "Needs path to input file as argument\n";
exit(0);
}
bool use_old_read_testcase = false;
if(argc >= 3 && string(argv[2]) == "1")
use_old_read_testcase = true;
unsigned chunk_size = 10000;
bool do_check = true;
uint64_t mask = ~(0ull);
for(int i=3;i<argc;++i)
{
if(strncmp(argv[i], "-chunk_size", 15) == 0)
{
++i;
chunk_size = strtol(argv[i],0,10);
}
else
if(strncmp(argv[i], "-mask", 15) == 0)
{
++i;
mask = strtoll(argv[i],0,16);
}
else
if(strncmp(argv[i], "-no-check", 15) == 0)
do_check = false;
}
if(mask != (~0ull))
initialize_function_pointers(mask);
do_compute(argv[1], use_old_read_testcase, chunk_size, do_check);
return 0;
}