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test.cc
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test.cc
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#include <iostream>
#include <vector>
#include <BamReader.h>
#include <BamAux.h>
#include <BamAlignment.h>
/*
* For more attributes and function of one aligned read, please visit
* http://pezmaster31.github.io/bamtools/struct_bam_tools_1_1_bam_alignment.html
* for more detail
*/
int main(int argc, char* argv[])
{
BamTools::BamReader bw;
BamTools::BamAlignment r;
//open BAM file for reading
if(!bw.Open(argv[1])){
std::cout << "Failed to open file" << std::endl;
exit(1);
}
//set the intersted region
//ex: chr22:16050199-16050300
//chromosomes were encoded from 0 to 23, which 0 represent chr1
BamTools::BamRegion reg(21,16050199, 21, 16050300);
//set region for reader
bw.SetRegion(reg);
//collect all the alignment in interested region
while(bw.GetNextAlignment(r)){
//Name: read name std::string
std::cout << r.Name << std::endl;
//Position: position of first aligned based
std::cout << r.Position << std::endl;
//RefID: Get chromosome ID int32_t
std::cout << r.RefID << std::endl;
//CigarData: CIGAR operations for this alignment.
std::vector<BamTools::CigarOp> cigar_d;
cigar_d = r.CigarData;
//iterate this cigar data
/*
* CIGAR in SAM/BAM Description
* M 0 alignment match (can be a sequence match or mismatch)
* I 1 insertion to the reference
* D 2 deletion from the reference
* N 3 skipped region from the reference
* S 4 soft clipping (clipped sequences present in SEQ)
* H 5 hard clipping (clipped sequences NOT present in SEQ)
* P 6 padding (silent deletion from padded reference)
* = 7 sequence match
* X 8 sequence mismatch
*/
for(int i = 0; i < cigar_d.size(); i++){
std::cout << "Type: " << cigar_d[i].Type << " ";
std::cout << "Length: " << cigar_d[i].Length << std::endl;
}
/*
* For more attributes and function of one aligned read, please visit
* http://pezmaster31.github.io/bamtools/struct_bam_tools_1_1_bam_alignment.html
* for more detail
*/
}
return 0;
}