IHistogram Class Reference

Interface for kmers distribution management. More...

#include <IHistogram.hpp>

Inheritance diagram for IHistogram:

Public Member Functions
virtual	~IHistogram ()
virtual size_t	getLength ()=0
virtual size_t	getLength2 ()=0
virtual void	inc (u_int16_t index)=0
virtual void	inc2D (u_int16_t index1, u_int16_t index2)=0
virtual void	save (tools::storage::impl::Group &group)=0
virtual void	compute_threshold (int min_auto_threshold)=0
virtual u_int16_t	get_solid_cutoff ()=0
virtual u_int64_t	get_nbsolids_auto ()=0
virtual float	get_ratio_weak ()=0
virtual u_int16_t	get_first_peak ()=0
virtual u_int64_t &	get (u_int16_t idx)=0
virtual u_int64_t &	get2D (u_int16_t idx1, u_int16_t idx2)=0
Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()
virtual void	use ()=0
virtual void	forget ()=0

Detailed Description

Interface for kmers distribution management.

This interface allows to have an idea of the function y(x), where x is the occurrence number of a kmer and y is the number of kmers occurring x times.

It is often interesting to have a graphical display of this kind of distribution; for instance, it may give an estimation of the coverage of NGS data.

We can also find x0 at the first minimum of y(x) : for x<x0, we are likely to have sequencing errors. The first maximum at x1 (x1>x0) is also interesting because it provides an estimation of the reads coverage.

This interface is mainly used by the SortingCountAlgorithm.

Here is a command line for showing the histogram with gnuplot from the hdf5 file 'graph.h5'

• h5dump -y -d dsk/histogram graph.h5 | grep [0-9] | grep -v [A-Z].* | paste - - | gnuplot -p -e 'plot [][0:100] "-" with lines'

For the sum of the distribution, you can use:

• h5dump -y -d dsk/histogram graph.h5 | grep [0-9] | grep -v [A-Z].* | paste - - | gawk 'BEGIN{s=0; i=0} { s=s+$2; i=i+1; print i," ", s}' | gnuplot -p -e 'plot [0:10][0:] "-" with lines'

Constructor & Destructor Documentation

virtual ~IHistogram ( )

inlinevirtual

Destructor.

Member Function Documentation

virtual void compute_threshold ( int  min_auto_threshold )

pure virtual

Compute first minimum at x0 and firt maximum at x1 (x1>x0).

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual u_int64_t& get ( u_int16_t  idx )

pure virtual

Retrieve the value for x.

Parameters

[in]

idx

: x value.

Returns

y(x).

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual u_int64_t& get2D ( u_int16_t  idx1, u_int16_t  idx2  )

pure virtual

Retrieve the value for x and y of histo2D.

Parameters

[in]	idx1	: x value.
[in]	idx2	: y value.

Returns

cpt(x,y).

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual u_int16_t get_first_peak ( )

pure virtual

Get the x1 value at the first maximum after x0.

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual u_int64_t get_nbsolids_auto ( )

pure virtual

Get the number of kmers for x>x0, aka solid kmers for x0 threshold

Returns

number of kmers.

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual float get_ratio_weak ( )

pure virtual

Get the ratio of weak kmers in total volume

Returns

ratio

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual u_int16_t get_solid_cutoff ( )

pure virtual

Get the solid cutoff, ie the x0 at first minimum.

Returns

x0

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual size_t getLength ( )

pure virtual

Return the maximum allowed for X.

Returns

the max X value.

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual size_t getLength2 ( )

pure virtual

Return the maximum allowed for Y in case of 2D histogram.

Returns

the max Y value.

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual void inc ( u_int16_t  index )

pure virtual

Increase the number of kmers occurring X time

Parameters

[in]

index

: the X value.

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual void inc2D ( u_int16_t  index1, u_int16_t  index2  )

pure virtual

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.

Implemented in HistogramCache, HistogramNull, and Histogram.

virtual void save ( tools::storage::impl::Group &  group )

pure virtual

Save the distribution. It is saved into the bag provided at construction.

Implemented in HistogramCache, HistogramNull, and Histogram.

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The documentation for this class was generated from the following file:

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp