gamgee::ReferenceMap Class Reference

Utility class to create a reference object for all reference operations in Foghorn. More...

#include <reference_map.h>

Inheritance diagram for gamgee::ReferenceMap:

Public Member Functions
	ReferenceMap (const std::string &filename)
	opens a fasta/fastq reference file and creates a ReferenceMap from it More...
std::string	get_sequence (const Interval &interval, const bool reverse_strand=false) const
	locates the DNA sequence for a given Interval More...

Detailed Description

Utility class to create a reference object for all reference operations in Foghorn.

It hash table stores chr -> sequence as strings internally.

Constructor & Destructor Documentation

gamgee::ReferenceMap::ReferenceMap

(

const std::string &

filename

)

opens a fasta/fastq reference file and creates a ReferenceMap from it

Parameters

filename

reference genome fasta or fastq file

Member Function Documentation

string gamgee::ReferenceMap::get_sequence	(	const Interval &	interval,
		const bool	reverse_strand = false
	)		const

locates the DNA sequence for a given Interval

Returns

DNA sequence for the requested Intervals

Parameters

interval	location in the genome
reverse_strand	which strand, releative to the reference genome, to produce the sequence for

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

• gamgee/reference_map.h
• gamgee/reference_map.cpp