3 #include "GenomeSequence.h"
8 int main(
int argc,
char ** argv)
19 std::cerr <<
"Failed to read the reference\n";
22 std::cerr <<
"\nStandard VCF DBSNP test\n";
24 const char* dbsnpFileName =
"testFiles/dbsnp.vcf";
27 refPtr->
loadDBSNP(dbsnpArray1, dbsnpFileName);
32 genomeIndex_t mapPos =
34 std::cerr <<
"dbsnp " << mapPos <<
": "
35 << dbsnpArray1[mapPos] << std::endl;
36 std::cerr <<
"dbsnp " << mapPos+1 <<
": "
37 << dbsnpArray1[mapPos+1] << std::endl;
38 std::cerr <<
"dbsnp " << mapPos+2 <<
": "
39 << dbsnpArray1[mapPos+2] << std::endl;
42 std::cerr <<
"\nGZIP VCF DBSNP test\n";
45 dbsnpFileName =
"testFiles/dbsnp.vcf.gz";
48 refPtr->
loadDBSNP(dbsnpArray2, dbsnpFileName);
54 std::cerr <<
"dbsnp " << mapPos <<
": "
55 << dbsnpArray2[mapPos] << std::endl;
56 std::cerr <<
"dbsnp " << mapPos+1 <<
": "
57 << dbsnpArray2[mapPos+1] << std::endl;
58 std::cerr <<
"dbsnp " << mapPos+2 <<
": "
59 << dbsnpArray2[mapPos+2] << std::endl;
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
bool loadDBSNP(mmapArrayBool_t &dbSNP, const char *inputFileName) const
user friendly dbSNP loader.
genomeIndex_t getGenomePosition(const char *chromosomeName, unsigned int chromosomeIndex) const
given a chromosome name and position, return the genome position