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

VCFLib API
       This document describes the VCFLIB API as it is used by the vcflib mod-
       ules  and the python ffi.  vcflib follows the VCF standard (http://sam-
       tools.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 straightfor-
       ward 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/mas-
       ter/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.

							 -- coding: utf-8 --()

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