Simple C API htslib

c_api_htslib

downlaod and unzip htslib

/Users/sina/Downloads/htslib-1.10.2.tar.bz2

cd /Users/sina/Downloads/htslib-1.10.2

mkdir /installation_folder

./configure --prefix=/Users/sina/Downloads/htslib-1.10.2/installation_folder
make
make install


```

#include "sam.h"

void main()
	{

	samFile *fp_in = hts_open("small.bam","r");          //open bam file

	bam_hdr_t *bamHdr = sam_hdr_read(fp_in);            //read header
	bam1_t *aln = bam_init1();                         //initialize an alignment

	while(sam_read1(fp_in, bamHdr, aln) > 0){

    printf("\t%lld\n" aln->core.pos);

	}

	 bam_destroy1(aln);
	 sam_close(fp_in);

	}

```

cd /Users/sina/Downloads/test5

gcc  -I/Users/sina/Downloads/htslib-1.10.2/htslib -L/Users/sina/Downloads/htslib-1.10.2/ -lhts biostar151053.c

./a.out

note

note


here