multovl
1.3
Multiple overlaps of genomic regions
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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 |
Namespace for the MULTOVL tools.
All components of the MULTOVL suite live in the genreg
namespace.
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.