How to print alternative allele from VCF with htslib c++

Question

I would like to print the alternative allele from a vcf file which i load in with htslib. The description of some functions: https://github.com/samtools/htslib/blob/develop/htslib/vcf.h

I have used bcf1_t objects by creating a header and reading the information.

htsFile *test_vcf = NULL;

  // creates header
  bcf_hdr_t *test_header = NULL;
  
  // initialize and allocate bcf1_t object
  bcf1_t *test_record = bcf_init();

  test_vcf = vcf_open("Testfile.vcf", "r");

  // returning a bcf_hdr_t struct 
  test_header = bcf_hdr_read(test_vcf);
  
  while(bcf_read(test_vcf, test_header, test_record) == 0){
    std::cout << "chr" << bcf_hdr_id2name(test_header, test_record->rid) << ":" <<test_record->pos+1 << std::endl;
  }
  bcf_hdr_destroy(test_header);
  bcf_destroy(test_record); 
  bcf_close(test_vcf);

But im not able to extract the reference or alternative allele information using this structure bcf1_t.

As far as i can read its perhaps possible with the structure and function:

bcf_dec_t
bcf_unpack()

But i am not able to get it to work since all the other functions seems limited to the bcf1_t struct.

Can anyone help with extracting the REF and ALT sequence? Thanks for your time

Answer 1

see the code in https://github.com/samtools/htslib/blob/develop/vcf.c#L3104

 bcf_unpack((bcf1_t*)v, BCF_UN_ALL);// if you need genotypes too, might use another constant to avoid decoding all the structure
 (...)
 kputc('\t', s); // ALT
 if (v->n_allele > 1) {
        for (i = 1; i < v->n_allele; ++i) {
            if (i > 1) kputc(',', s);
            kputs(v->d.allele[i], s);
        }
    }