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.

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