Basic implementation of the IHistogram interface.
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#include <Histogram.hpp>
Basic implementation of the IHistogram interface.
This implementation is the one actually used by SortingCountAlgorithm.
Constructor.
- Parameters
-
[in] | length | : maximum value for the X axis |
[in] | bag | : bag where the values can be saved. |
void compute_threshold |
( |
int |
min_auto_threshold | ) |
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virtual |
Compute first minimum at x0 and firt maximum at x1 (x1>x0).
Implements IHistogram.
u_int64_t& get |
( |
u_int16_t |
idx | ) |
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inlinevirtual |
Retrieve the value for x.
- Parameters
-
- Returns
- y(x).
Implements IHistogram.
u_int64_t& get2D |
( |
u_int16_t |
idx1, |
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u_int16_t |
idx2 |
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) |
| |
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inlinevirtual |
Retrieve the value for x and y of histo2D.
- Parameters
-
[in] | idx1 | : x value. |
[in] | idx2 | : y value. |
- Returns
- cpt(x,y).
Implements IHistogram.
u_int16_t get_first_peak |
( |
| ) |
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inlinevirtual |
Get the x1 value at the first maximum after x0.
Implements IHistogram.
u_int64_t get_nbsolids_auto |
( |
| ) |
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inlinevirtual |
Get the number of kmers for x>x0, aka solid kmers for x0 threshold
- Returns
- number of kmers.
Implements IHistogram.
Get the ratio of weak kmers in total volume
- Returns
- ratio
Implements IHistogram.
u_int16_t get_solid_cutoff |
( |
| ) |
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inlinevirtual |
Get the solid cutoff, ie the x0 at first minimum.
- Returns
- x0
Implements IHistogram.
Return the maximum allowed for X.
- Returns
- the max X value.
Implements IHistogram.
Return the maximum allowed for Y in case of 2D histogram.
- Returns
- the max Y value.
Implements IHistogram.
void inc |
( |
u_int16_t |
index | ) |
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inlinevirtual |
Increase the number of kmers occurring X time
- Parameters
-
Implements IHistogram.
void inc2D |
( |
u_int16_t |
index1, |
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u_int16_t |
index2 |
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) |
| |
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inlinevirtual |
Increase the number of kmers occurring X time in genome and Y times in read
- Parameters
-
[in] | index1 | : the X value. |
[in] | index2 | : the Y value. |
Implements IHistogram.
Save the distribution. It is saved into the bag provided at construction.
Implements IHistogram.
The documentation for this class was generated from the following files:
- /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp
- /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp