Scroll to navigation

-- coding: utf-8 --() -- coding: utf-8 --()

VCFLib API

This document describes the VCFLIB API as it is used by the vcflib modules and the python ffi. vcflib follows the VCF standard (http://samtools.github.io/hts-specs/VCFv4.1.pdf).

VCFLIB contains a lot of functionality, but the basis of going through a VCF file and fetching record (by record) information is straightforward and visible in all modules. A recent example can be found in vcfwave.

Open the VCF file

VariantCallFile variantFile;
if (optind < argc) {


    string filename = argv[optind];


    variantFile.open(filename);
} else {


    variantFile.open(std::cin);
}
if (!variantFile.is_open()) {


    return 1;
}

Read records

The following will parse the records and you can print out the first two fields with

Variant var(variantFile);
while (variantFile.getNextVariant(var)) {


  cout << var.sequenceName << " " << var.position << endl;
}

Other fields

In the file Variant.h (https://github.com/vcflib/vcflib/blob/master/src/Variant.h) the Variant class is defined with fields/accessors, such as



    string sequenceName;


    long position;


    long zeroBasedPosition(void) const;


    string id;


    string ref;


    vector<string> alt;      // a list of all the alternate alleles present at this locus


    vector<string> alleles;  // a list all alleles (ref + alt) at this locus

See above read records example to parse a file. Some things to know are that info fields are split into fields with values in `info' and flags that are true in `infoFlags'. The order of info fields is not kept in the C++ map data structure so we have to keep track of order in an infoKeys vector.

Output a VCF record

The default string outputter of the Variant class outputs a VCF record using the field that are defined:

Variant var(variantFile);
while (variantFile.getNextVariant(var)) {


  cout << var << endl;
}

will output VCF.

Mirroring in the Python FFI

The Python FFI follows this API though some accessors may be renamed. See pythonffi.cpp and pyvcflib.md.