This document describes the VCFLIB API as it is used by the vcflib modules and the python ffi. vcflib

       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.

   OpentheVCFfile
              VariantCallFile variantFile;

              if (optind < argc) {
                  string filename = argv[optind];
                  variantFile.open(filename);
              } else {
                  variantFile.open(std::cin);
              }

              if (!variantFile.is_open()) {
                  return 1;
              }

   Readrecords
       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;
              }

   Otherfields
       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.

   OutputaVCFrecord
       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.

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

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