vg::VcfBuffer Class Reference

#include <vcf_buffer.hpp>

Public Member Functions
vcflib::Variant *	get ()
void	handle_buffer ()
void	fill_buffer ()
bool	has_tabix () const
bool	set_region (const string &contig, int64_t start=-1, int64_t end=-1)
	VcfBuffer (vcflib::VariantCallFile *file=nullptr)

Protected Attributes
bool	has_buffer = false
bool	safe_to_get = true
vcflib::Variant	buffer
vcflib::VariantCallFile *const	file

Private Member Functions
	VcfBuffer (const VcfBuffer &other)=delete
VcfBuffer &	operator= (const VcfBuffer &other)=delete

Detailed Description

Provides a one-variant look-ahead buffer on a vcflib::VariantFile. Lets construction functions peek and see if they want the next variant, or lets them ignore it for the next construction function for a different contig to handle. Ought not to be copied.

Constructor & Destructor Documentation

VcfBuffer() [1/2]

vg::VcfBuffer::VcfBuffer

(

vcflib::VariantCallFile *

file = nullptr

)

Make a new VcfBuffer buffering the file at the given pointer (which must outlive the buffer, but which may be null).

VcfBuffer() [2/2]

vg::VcfBuffer::VcfBuffer ( const VcfBuffer &  other )

privatedelete

Member Function Documentation

fill_buffer()

void vg::VcfBuffer::fill_buffer

(

)

Can be called when the buffer is filled or empty. If there is no variant in the buffer, tries to load a variant into the buffer, if one can be obtained from the file.

get()

vcflib::Variant * vg::VcfBuffer::get

(

)

Return a pointer to the buffered variant, or null if no variant is buffered. Pointer is invalidated when the buffer is handled.

Although the variant is not const, it may not be moved out of or modified in ways that confuse vcflib.

handle_buffer()

void vg::VcfBuffer::handle_buffer

(

)

To be called when the buffer is filled. Marks the buffered variant as handled, discarding it, and allowing another to be read.

has_tabix()

bool vg::VcfBuffer::has_tabix

(

)

const

This returns true if we have a tabix index, and false otherwise. If this is false, set_region may be called, but will do nothing and return false.

operator=()

VcfBuffer& vg::VcfBuffer::operator= ( const VcfBuffer &  other )

privatedelete

set_region()

bool vg::VcfBuffer::set_region	(	const string &	contig,
		int64_t	start = -1,
		int64_t	end = -1
	)

This tries to set the region on the underlying vcflib VariantCallFile to the given contig and region, if specified. Coordinates coming in should be 0-based, and will be converted to 1-based internally.

Returns true if the region was successfully set, and false otherwise (for example, if there is not tabix index, or if the given region is not part of this VCF. Note that if there is a tabix index, and set_region returns false, the position in the VCF file is undefined until the next successful set_region call.

If either of start and end are specified, then both of start and end must be specified.

Discards any variants previously in the buffer.

Member Data Documentation

buffer

vcflib::Variant vg::VcfBuffer::buffer

protected

file

vcflib::VariantCallFile* const vg::VcfBuffer::file

protected

has_buffer

bool vg::VcfBuffer::has_buffer = false

protected

safe_to_get

bool vg::VcfBuffer::safe_to_get = true

protected

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The documentation for this class was generated from the following files:

• src/vcf_buffer.hpp
• src/vcf_buffer.cpp