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#include<iostream>
#include "../src/trim_primer_quality.h"
#include "htslib/sam.h"
int main(){
int success = 0;
std::string bam = "../data/test.sorted.bam";
std::string region_;
samFile *in = hts_open(bam.c_str(), "r");
hts_idx_t *idx = sam_index_load(in, bam.c_str());
bam_hdr_t *header = sam_hdr_read(in);
region_.assign(header->target_name[0]);
std::string temp(header->text);
hts_itr_t *iter = NULL;
iter = sam_itr_querys(idx, header, region_.c_str());
bam1_t *aln = bam_init1();
cigar_ t;
int lengths[6] = {150,99,99, 24,146,144}, ctr = 0;
int start_pos_rev[6] = {19, 114, 209, 325, 199, 231};
while(sam_itr_next(in, iter, aln) >= 0) {
t = quality_trim(aln, 20, 4);
std::cout << bam_get_qname(aln) << std::endl;
std::cout << "POS: " << t.start_pos << " Length: " << bam_cigar2rlen(t.nlength, t.cigar) << std::endl;
if(t.start_pos != start_pos_rev[ctr]){
success = -1;
}
if(bam_cigar2rlen(t.nlength, t.cigar) != lengths[ctr]){
success = -1;
}
free_cigar(t);
ctr++;
}
bam_destroy1(aln);
bam_itr_destroy(iter);
sam_hdr_destroy(header);
hts_idx_destroy(idx);
hts_close(in);
return success;
}
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