multovl  1.3
Multiple overlaps of genomic regions
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File List
Here is a list of all documented files with brief descriptions:
o*ancregion.hhAncestor regions representing the regions giving rise to overlaps
o*bamio.hhClasses to read BAM-formatted binary files and maybe later to write them, too
o*basepipeline.hh
o*classicopts.hh
o*classicpipeline.hh
o*empirdistr.hh
o*errors.hh
o*fileformat.hhModule to handle file format recognition
o*fileio.hhClasses to read input files and to write output
o*freeregions.hh
o*linereader.hhText-based input. Classes for reading lines from ASCII genomic data files (BED, GFF). Parsing is simplified, only the coordinates and region names are processed
o*linewriter.hhText-based output. Classes for writing MultiRegions to text line strings
o*multioverlap.hhMultiple genomic region overlaps
o*multiregion.hhRegion representing multiple overlaps for file-based "multovl"
o*multireglimit.hhCollection of multiple region limits
o*multovlopts.hh
o*parprobopts.hh
o*parprobpipeline.hh
o*pipeline.hh
o*polite.hhWrapper around the overengineered boost::program_options
o*probopts.hh
o*probpipeline.hh
o*randomgen.hh
o*randomplacer.hh
o*region.hhGenomic regions with coordinates and a name
o*reglimit.hhHelper class to keep track of the limits (first, last position) of regions to be overlapped
o*shuffleovl.hh
o*stat.hh
o*tempfile.hh
o*textio.hhClasses to read ASCII text input streams (or files) and (later) to write text output
o*timer.hh
\*trackio.hhBase classes to read/write input/output tracks (collections of regions)