multovl
1.3
Multiple overlaps of genomic regions
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![]() ![]() | Namespace for the MULTOVL tools |
![]() ![]() ![]() | Namespace for the MULTOVL input/output services |
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![]() ![]() ![]() ![]() | 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 |
![]() ![]() ![]() ![]() ![]() | Linereader's own exception |
![]() ![]() ![]() ![]() | 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) |
![]() ![]() ![]() ![]() | Linereader for GFF-formatted lines. Only the columns containing coordinate information are parsed, the rest are ignored. No distinction between GFF2 and GFF3 |
![]() ![]() ![]() ![]() | Base class of stringifier objects |
![]() ![]() ![]() ![]() | 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) |
![]() ![]() ![]() ![]() | 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) |
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![]() ![]() ![]() | Namespace for the multiple overlap probability tools |
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![]() ![]() ![]() ![]() | Option handling for the file-based parallel overlap probability tool |
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![]() ![]() ![]() ![]() | Option handling for the file-based multovl tools |
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![]() ![]() ![]() ![]() | Convenience class that wraps a uniform RND generator |
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![]() ![]() ![]() ![]() | Class for calculating multiple overlaps repeatedly after reshuffling some of the tracks |
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![]() ![]() ![]() | 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 |
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![]() ![]() ![]() | Simple facility to keep track of errors and warnings |
![]() ![]() ![]() | Option handling for the file-based multovl tools |
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![]() ![]() ![]() | Base class for option handling in the multovl family of tools |
![]() ![]() ![]() | Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class |
![]() ![]() ![]() | 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 |
![]() ![]() ![]() | Instances of the Region class represent regions on a sequence. They have first and last coordinates, strand information and a name |
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