#include "multioverlap.hh"
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class | boost::serialization::access |
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Objects of the MultiOverlap class generate and store multiple overlaps of genomic regions. The class is derived from MultiRegLimit which is responsible for keeping track of where the ancestor regions begin or end. The MultiOverlap::find_* methods iterate along the limits and detect the overlaps.
unsigned int multovl::MultiOverlap::find_overlaps |
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unsigned int |
ovlen, |
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unsigned int |
minmult = 1 , |
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unsigned int |
maxmult = 0 , |
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bool |
intrack = true |
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) |
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Finds multiple overlaps. Whenever the multiplicity of the overlap changes, there will be a new MultiRegion in the returned vector. For instance, the region [50,150] and the region [100, 200] will give rise to the following three multiregions: [50-99] with multiplicity 1; [100-150] with multiplicity 2 (the actual overlap part); [151-200] again with multiplicity 1.
- Parameters
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multiregions | the overlaps found are appended to this vector |
ovlen | the minimum overlap length (>=1) required |
minmult | the minimum multiplicity required, >=1, if 0 –> solitaries also required |
maxmult | the maximum multiplicity required, >=2, or if 0 –> any multiplicity accepted if /minmult/ > /maxmult/ then they are swapped silently, except when /maxmult/ == 0 |
intrack | if /true/ (default), then overlaps within the same track are accepted |
- Returns
- the total count of the overlaps found
unsigned int multovl::MultiOverlap::find_unionoverlaps |
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unsigned int |
ovlen, |
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unsigned int |
minmult = 2 , |
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unsigned int |
maxmult = 0 |
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) |
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Finds 'unions' of overlaps. For instance, the region [50,150] and the region [100, 200] will give rise to the union region [50,200] with maximal multiplicity 2 (because in the middle the original regions overlap). The parameters and the return value have the same meaning as with /find_overlaps/. However, /minmult/ must be >=2 as it makes no sense to detect solitaries here. Also note that there is no /intrack/ parameter because I cannot understand what inter-track region unions could be good for.
void multovl::MultiOverlap::overlap_stats |
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Counter & |
counter | ) |
const |
Generates some overlap statistics using the overlaps found by the last find_overlaps or find_unionoverlaps operation.
- Parameters
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counter | a Counter object with track histogram data which will be updated. |
const multiregvec_t& multovl::MultiOverlap::overlaps |
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const |
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inline |
Returns the multiple overlaps found by the last find_overlaps or find_unionoverlaps operation.
- Returns
- a vector of MultiRegion objects.
The documentation for this class was generated from the following file: