multovl  1.3
Multiple overlaps of genomic regions
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linereader.hh File Reference

Text-based input. Classes for reading lines from ASCII genomic data files (BED, GFF). Parsing is simplified, only the coordinates and region names are processed. More...

#include <string>
#include <map>
#include <iostream>
#include <stdexcept>
#include "boost/regex.hpp"

Go to the source code of this file.

Classes

class  multovl::io::Linereader
 Base class of parser objects. Linereader objects process one line at a time, and change their internal state according to what they find in it. Parsing a complete data file involves reading it in line-by-line and submitting each line to a parser object for the appropriate format. Upon successful parsing the parser object stores the coordinate information plus additional data that can be read out and used to construct the appropriate region object. More...
 
class  multovl::io::Linereader::Exception
 Linereader's own exception. More...
 
class  multovl::io::BedLinereader
 Linereader for BED-formatted lines. The BedLinereader class parses columns 1 to 6 of the BED format specification, except Column 5 (score) which is skipped, and ignores the optional columns 7 to 12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). More...
 
class  multovl::io::GffLinereader
 Linereader for GFF-formatted lines. Only the columns containing coordinate information are parsed, the rest are ignored. No distinction between GFF2 and GFF3. More...
 

Namespaces

 multovl
 Namespace for the MULTOVL tools.
 
 multovl::io
 Namespace for the MULTOVL input/output services.
 

Detailed Description

Text-based input. Classes for reading lines from ASCII genomic data files (BED, GFF). Parsing is simplified, only the coordinates and region names are processed.

Author
Andras Aszodi
Date
2011-05-31.