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CorrelationMatrixCreator.hpp
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CorrelationMatrixCreator.hpp
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#ifndef CORRELATIONMATRIXCREATOR_HPP
#define CORRELATIONMATRIXCREATOR_HPP
#include <string>
#include <list>
#include <future>
#include <seqan/bam_io.h> // BamFileIn
#include <seqan/bed_io.h> // BedFileIn
#include <ReadMatrixCreator.hpp>
#include <matrices.hpp>
/*!
* \brief The CorrelationMatrixCreator class allows
* to create correlation matrices.
* A correlation matrix contains the number of target
* mapped at different positions around a set of
* reference positions.
* This class will read the reference positions from
* a BED file and the targets from a BAM file. For each
* reference, the region center is computed and then a
* region covering the interval [from,to] is build
* around the middle and divided into equally sized
* bins. Finally, each bin is assigned the number of
* target present in the BAM file that are mapped at
* that position.
* The final matrix contains one row per reference,
* with the number of targets counted at each possible
* position (bin). relative to this reference.
*/
class CorrelationMatrixCreator: public ReadMatrixCreator
{
public:
CorrelationMatrixCreator() = delete ;
/*!
* \brief Constructs an object to build a
* correlation matrix.
* \param bed_file_path the path to the file containing
* the references.
* \param bam_file_path the path to the file containing
* the targets.
* \param bai_file_path the path to index file of the bam
* file containing the targets.
* \param from the upstream most relative position
* to consider around the references. It may
* be changed to make sure that the central bin
* is centered on +/- 0.
* \param to the dowmstream most relative position
* to consider around the references. It may
* be changed to make sure that the central bin
* is centered on +/- 0.
* \param bin_size the bin size in base pair.
* \param method how the targets should be counted.
* READ all the positions inside the reads are
* counted.
* READ_ATAC only the +4bp position of +strand reads
* and the -5bp of -strand reads are counted. It
* correspond to the insertion position in ATAC-seq
* data.
* FRAGMENT all the positions within fragments (the
* genome segment between a pair of reads, reads
* included) are counted.
* FRAGMENT_CENTER only the central position of the
* fragements (the genome segment between a pair of
* reads, reads included) are counted.
*/
CorrelationMatrixCreator(const std::string& bed_file_path,
const std::string& bam_file_path,
const std::string& bai_file_path,
int from,
int to,
int bin_size,
CorrelationMatrixCreator::methods method) ;
/*!
* Destructor.
*/
virtual ~CorrelationMatrixCreator() ;
/*!
* \brief Computes the matrix and returns it.
* \return the count matrix.
*/
virtual matrix2d_i create_matrix() override ;
protected:
/*!
* \brief Seek in the BAM file right before the last
* record upstream the given region. The margin
* parameters allows to modify the region start
* value.
* To read a record within the region, a read
* operation is required to get ride of the
* record right
* \param region the region in front of which the
* pointer is desired.
* \param margin
* which streams in the stream vectors to use.
* \return whether the reading pointer could be moved
* to the desired position.
*/
bool jump_upstream(const GenomeRegion& region,
int margin) ;
/*!
* \brief A generic routine that reads the following records
* until finding the first one located downstream the region
* of interest (the definition of the first target downstream
* the region of interest depends if READ/READ_ATAC/FRAGMENT
* or FRAGMENT_CENTER is set as method).
* All record overlapping the region of interest are stored
* in the target lists.
* The reading pointer is supposed to be located
* upstream the region of interest. If this is note the case,
* the method will read records until reaching the end of
* the file.
* \param region the region of interest.
*/
void to_downstream_target(const GenomeRegion& region) ;
/*!
* \brief The routine that reads the following records
* until finding the first one located downstream the region
* of interest if READ or READ_ATAC is set as method.
* All record overlapping the region of interest are stored
* in the target lists.
* The reading pointer is supposed to be located
* upstream the region of interest. If this is note the case,
* the method will read records until reaching the end of
* the file.
* \param region the region of interest.
*/
void to_downstream_read(const GenomeRegion& region) ;
/*!
* \brief The routine that reads the following records
* until finding the first one located downstream the region
* of interest if FRAGMENT or FRAGMENT_CENTER is set as
* method.
* All record overlapping the region of interest are stored
* in the target lists.
* The reading pointer is supposed to be located
* upstream the region of interest. If this is note the case,
* the method will read records until reaching the end of
* the file.
* \param region the region of interest.
*/
void to_downstream_fragment(const GenomeRegion& region) ;
/*!
* \brief Clear the content of the target lists.
*/
void clear_target_lists() ;
/*!
* \brief Update the given row of the count matrix with
* the content of the target lists.
* \param matrix_row_index the index of the row, in the
* count matrix.
*/
void update_count_matrix(size_t row_index) ;
/*!
* \brief A buffers containing the
* target mapped on the forward strand.
* Target without strand (fragments)
* are also stored in this list.
*/
std::list<GenomeRegion> target_list_fw ;
/*!
* \brief A buffers containing the
* target mapped on the reverse strand.
*/
std::list<GenomeRegion> target_list_rv ;
} ;
#endif // CORRELATIONMATRIXCREATOR_HPP

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