multovl  1.3
Multiple overlaps of genomic regions
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Namespaces | Classes | Typedefs
multovl Namespace Reference

Namespace for the MULTOVL tools. More...

Namespaces

 io
 Namespace for the MULTOVL input/output services.
 
 prob
 Namespace for the multiple overlap probability tools.
 

Classes

class  AncestorRegion
 AncestorRegion objects represent the regions that give rise to overlaps. They are essentially Region-s, with the additional track ID attribute (an uint) that indicates which track they belong to. Track IDs are assigned by client programs and may indirectly refer to files or database objects. More...
 
class  BasePipeline
 
class  Errors
 Simple facility to keep track of errors and warnings. More...
 
class  ClassicOpts
 Option handling for the file-based multovl tools. More...
 
class  ClassicPipeline
 
class  MultiOverlap
 
class  MultiRegion
 
class  MultiRegLimit
 
class  MultovlOptbase
 Base class for option handling in the multovl family of tools. More...
 
class  Pipeline
 Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class. More...
 
class  Polite
 Program Options LITE base class. The Polite class provides a wrapper over boost::program_options to make life a bit easier. Functionality includes parsing the default –help and –version options, and access to positional parameters. Apps using this are supposed to subclass Polite and add their own extra options. More...
 
class  Region
 Instances of the Region class represent regions on a sequence. They have first and last coordinates, strand information and a name. More...
 
class  RegLimit
 
class  Timer
 

Typedefs

typedef std::multiset
< AncestorRegion
ancregset_t
 

Detailed Description

Namespace for the MULTOVL tools.

All components of the MULTOVL suite live in the genreg namespace.

Typedef Documentation

typedef std::multiset<AncestorRegion> multovl::ancregset_t

Collection of ancestors for a descendant region. Under certain conditions the same region may occur multiple times in the input, therefore a multiset is used to hold the ancestors of an overlap.