multovl
1.3
Multiple overlaps of genomic regions
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Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class. More...
#include "pipeline.hh"
Protected Types | |
typedef std::map< std::string, MultiOverlap > | chrom_multovl_map |
There is one MultiOverlap object for each chromosome. | |
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typedef std::vector< Input > | input_seq_t |
Protected Member Functions | |
virtual unsigned int | detect_overlaps () |
const chrom_multovl_map & | cmovl () const |
chrom_multovl_map & | cmovl () |
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virtual unsigned int | read_input ()=0 |
virtual bool | write_output ()=0 |
bool | set_optpimpl (MultovlOptbase *optp) |
MultovlOptbase * | opt_pimpl () |
virtual MultovlOptbase * | opt_ptr ()=0 |
const input_seq_t & | inputs () const |
input_seq_t & | inputs () |
void | add_error (const std::string &prefix, const std::string &what) |
Adds an error message. | |
void | add_all_errors (const Errors &other) |
void | add_warning (const std::string &prefix, const std::string &what) |
Adds a warning message. | |
void | clear_errors () |
Clears the errors. | |
Additional Inherited Members | |
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BasePipeline () | |
Default init of a BasePipeline object. | |
bool | run () |
const Errors & | errors () const |
Abstract class that provides a framework for detecting multiple overlaps using the MultiOverlap class.
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inlineprotected |
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inlineprotected |
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protectedvirtual |
Detects the overlaps. The default implementation provided here uses 1 CPU core.
Implements multovl::BasePipeline.