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.\" Automatically generated by Pandoc 2.19.2
.\"
.\" Define V font for inline verbatim, using C font in formats
.\" that render this, and otherwise B font.
.ie "\f[CB]x\f[]"x" \{\
. ftr V B
. ftr VI BI
. ftr VB B
. ftr VBI BI
.\}
.el \{\
. ftr V CR
. ftr VI CI
. ftr VB CB
. ftr VBI CBI
.\}
.TH "-\f[I]- coding: utf-8 -\f[R]-" "" "" "" ""
.hy
.SH VCFLib API
.PP
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).
.PP
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.
.SS Open the VCF file
.IP
.nf
\f[C]
VariantCallFile variantFile;
if (optind < argc) {
string filename = argv[optind];
variantFile.open(filename);
} else {
variantFile.open(std::cin);
}
if (!variantFile.is_open()) {
return 1;
}
\f[R]
.fi
.SS Read records
.PP
The following will parse the records and you can print out the first two
fields with
.IP
.nf
\f[C]
Variant var(variantFile);
while (variantFile.getNextVariant(var)) {
cout << var.sequenceName << \[dq] \[dq] << var.position << endl;
}
\f[R]
.fi
.SS Other fields
.PP
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
.IP
.nf
\f[C]
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
\f[R]
.fi
.PP
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.
.SS Output a VCF record
.PP
The default string outputter of the Variant class outputs a VCF record
using the field that are defined:
.IP
.nf
\f[C]
Variant var(variantFile);
while (variantFile.getNextVariant(var)) {
cout << var << endl;
}
\f[R]
.fi
.PP
will output VCF.
.SS Mirroring in the Python FFI
.PP
The Python FFI follows this API though some accessors may be renamed.
See pythonffi.cpp and pyvcflib.md.
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