multovl  1.3
Multiple overlaps of genomic regions
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Public Member Functions | List of all members
multovl::io::TrackReader Class Referenceabstract

#include "trackio.hh"

Inheritance diagram for multovl::io::TrackReader:
multovl::io::BamReader multovl::io::TextReader

Public Member Functions

 TrackReader ()
 default init
 
virtual std::string read_into (std::string &chrom, Region &reg)=0
 
const Errorserrors () const
 
virtual void add_error (const std::string &msg)
 

Detailed Description

Abstract base class for reading regions from a file. Subclasses contain implementations for reading text or binary files.

Member Function Documentation

const Errors& multovl::io::TrackReader::errors ( ) const
inline
Returns
const access to the internal error collecting object.
virtual std::string multovl::io::TrackReader::read_into ( std::string &  chrom,
Region reg 
)
pure virtual

Attempts to read from the wrapped input file into a region.

Parameters
chromstring to store the chromosome name for /reg/
regthe region this method tries to read into.
Returns
message containing information about how the parsing went. "" if all is OK, "EOF" if the internal stream was exhausted, or some error message.

Implemented in multovl::io::TextReader, and multovl::io::BamReader.


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