multovl  1.3
Multiple overlaps of genomic regions
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Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCmultovl::MultiOverlap::Counter
oCmultovl::prob::Stat::Distr
oCmultovl::prob::EmpirDistr
oCmultovl::ErrorsSimple facility to keep track of errors and warnings
oCmultovl::prob::EmpirDistr::Exception
oCmultovl::io::Fileformat
oCmultovl::prob::FreeRegions
oCmultovl::BasePipeline::Input
oCless_than_comparable
|oCmultovl::AncestorRegionAncestorRegion 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
|\Cmultovl::RegionInstances of the Region class represent regions on a sequence. They have first and last coordinates, strand information and a name
| oCmultovl::AncestorRegionAncestorRegion 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
| \Cmultovl::MultiRegion
oCmultovl::io::LinereaderBase 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
|\Cmultovl::io::BedLinereaderLinereader 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)
| \Cmultovl::io::GffLinereaderLinereader for GFF-formatted lines. Only the columns containing coordinate information are parsed, the rest are ignored. No distinction between GFF2 and GFF3
oCmultovl::io::LinewriterBase class of stringifier objects
|oCmultovl::io::BedLinewriterLinewriter for BED-formatted lines. The BedLinewriter writes columns 1 to 6 of the BED format specification, (http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
|\Cmultovl::io::GffLinewriterLinewriter 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)
oClogic_error
|\Cmultovl::io::Linereader::ExceptionLinereader's own exception
oCmultovl::MultiRegLimit
|\Cmultovl::MultiOverlap
| \Cmultovl::prob::ShuffleOvlClass for calculating multiple overlaps repeatedly after reshuffling some of the tracks
oCnoncopyable
|oCmultovl::BasePipeline
||oCmultovl::PipelineAbstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class
|||\Cmultovl::ClassicPipeline
||\Cmultovl::prob::ProbPipeline
|| \Cmultovl::prob::ParProbPipeline
|oCmultovl::io::FileReader
|oCmultovl::io::TrackReader
||oCmultovl::io::BamReader
||\Cmultovl::io::TextReader
|\Cmultovl::prob::UniformGenConvenience class that wraps a uniform RND generator
oCmultovl::prob::Stat::NotfoundException
oCmultovl::prob::ProbPipeline::OvlenCounter
oCmultovl::PoliteProgram 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
|\Cmultovl::MultovlOptbaseBase class for option handling in the multovl family of tools
| oCmultovl::ClassicOptsOption handling for the file-based multovl tools
| \Cmultovl::prob::ProbOptsOption handling for the file-based multovl tools
|  \Cmultovl::prob::ParProbOptsOption handling for the file-based parallel overlap probability tool
oCmultovl::prob::RandomPlacer
oCmultovl::RegLimit
oCmultovl::prob::Stat
oCTempfile
\Cmultovl::Timer