libStatGen Software 1
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Main.cpp
1#include <iostream>
2#include <time.h>
3#include "GenomeSequence.h"
4#include "InputFile.h"
5
6void readDbsnp(mmapArrayBool_t& dbSNP, const char* fileName, GenomeSequence& ref);
7
8int main(int argc, char ** argv)
9{
10 // time_t startTime;
11 // time_t endTime;
12 // startTime = time(NULL);
13 GenomeSequence* refPtr = new GenomeSequence("testFiles/chr1_partial.fa");
14 // endTime = time(NULL);
15
16 // std::cerr << "Time to read reference: " << endTime - startTime << std::endl;
17 if(refPtr == NULL)
18 {
19 std::cerr << "Failed to read the reference\n";
20 return(-1);
21 }
22 std::cerr << "\nStandard VCF DBSNP test\n";
23 mmapArrayBool_t dbsnpArray1;
24 const char* dbsnpFileName = "testFiles/dbsnp.vcf";
25
26 // startTime = time(NULL);
27 refPtr->loadDBSNP(dbsnpArray1, dbsnpFileName);
28 // endTime = time(NULL);
29 // std::cerr << "Time to read dbsnp through reference: " << endTime - startTime << std::endl;
30
31
32 genomeIndex_t mapPos =
33 refPtr->getGenomePosition("1", 10233);
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;
40
41
42 std::cerr << "\nGZIP VCF DBSNP test\n";
43
44 mmapArrayBool_t dbsnpArray2;
45 dbsnpFileName = "testFiles/dbsnp.vcf.gz";
46
47 // startTime = time(NULL);
48 refPtr->loadDBSNP(dbsnpArray2, dbsnpFileName);
49 // endTime = time(NULL);
50 // std::cerr << "Time to read dbsnp through reference: " << endTime - startTime << std::endl;
51
52
53 mapPos = refPtr->getGenomePosition("1", 10233);
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;
60 return(0);
61}
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