elowy01

#Gist of the gist This is a simple example showing how htslib can be used to parse VCF/BCF files in C++. Compiling options are shown in compile_and_run.sh, this assumes that you have compiled htslib into a static library - libhts.a, post a comment if you'd like help doing that.

The program takes a VCF file and spits out chromosome, position and number_of_alleles for each record in the VCF.

This test in the Samtools repo - [https://github.com/samtools/htslib/blob/1.2.1/test/test-vcf-api.c] also has some useful examples, note you might have to switch to the master branch version of that file to keep up with the currently rapidly evolving htslib API.

#Acknowledgements

PoisonAlien

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <htslib/sam.h>

int main(int argc, char *argv[]){
	
	samFile *fp_in = hts_open(argv[1],"r"); //open bam file
	bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header
	bam1_t *aln = bam_init1(); //initialize an alignment

arq5x

# compile
$ g++ zlib-example.cpp -lz -o zlib-example

# run
$ ./zlib-example
Uncompressed size is: 36
Uncompressed string is: Hello Hello Hello Hello Hello Hello!

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