multovl  1.3
Multiple overlaps of genomic regions
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Classes
multovl::io Namespace Reference

Namespace for the MULTOVL input/output services. More...

Classes

class  BamReader
 
class  Fileformat
 
class  FileReader
 
class  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  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  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...
 
class  Linewriter
 Base class of stringifier objects. More...
 
class  BedLinewriter
 Linewriter for BED-formatted lines. The BedLinewriter writes columns 1 to 6 of the BED format specification, (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). More...
 
class  GffLinewriter
 Linewriter for GFF-formatted lines. The GffLinewriter class understands Versions 2 and 3 of the GFF format specification (http://www.sanger.ac.uk/resources/software/gff/spec.html). More...
 
class  TextReader
 
class  TrackReader
 

Detailed Description

Namespace for the MULTOVL input/output services.

All components live in the multovl::io namespace.