Ernesto Lowy elowy01

## Parse_VCF_BCFs_with_htslib_C++.md

      
              3 files
            
          
              0 forks
            
          
              0 comments
            
          
              1 star
            
          
                elowy01
                / Parse_VCF_BCFs_with_htslib_C++.md
            
            
              Created
              November 16, 2020 10:28
                — forked from gatoravi/Parse_VCF_BCFs_with_htslib_C++.md
            
              
                Parse VCF/BCFs with htslib (C++)
              
          
    #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

  
## test.sh
# 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!

----------
	# 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!

	----------