multovl  1.3
Multiple overlaps of genomic regions
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Public Member Functions | Protected Member Functions | List of all members
multovl::ClassicPipeline Class Reference

#include "classicpipeline.hh"

Inheritance diagram for multovl::ClassicPipeline:
multovl::Pipeline multovl::BasePipeline

Public Member Functions

 ClassicPipeline (int argc, char *argv[])
 
- Public Member Functions inherited from multovl::BasePipeline
 BasePipeline ()
 Default init of a BasePipeline object.
 
bool run ()
 
const Errorserrors () const
 

Protected Member Functions

virtual unsigned int read_input ()
 
virtual bool write_output ()
 
virtual ClassicOptsopt_ptr ()
 
- Protected Member Functions inherited from multovl::Pipeline
virtual unsigned int detect_overlaps ()
 
const chrom_multovl_mapcmovl () const
 
chrom_multovl_mapcmovl ()
 
- Protected Member Functions inherited from multovl::BasePipeline
bool set_optpimpl (MultovlOptbase *optp)
 
MultovlOptbaseopt_pimpl ()
 
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

- Protected Types inherited from multovl::Pipeline
typedef std::map< std::string,
MultiOverlap
chrom_multovl_map
 There is one MultiOverlap object for each chromosome.
 
- Protected Types inherited from multovl::BasePipeline
typedef std::vector< Inputinput_seq_t
 

Detailed Description

The ClassicPipeline implements the "classic" MULTOVL pipeline. The inputs are files (text or binary), the overlap calculations are serial/single core, the output goes to a GFF2-formatted text file to standard output.

Constructor & Destructor Documentation

multovl::ClassicPipeline::ClassicPipeline ( int  argc,
char *  argv[] 
)

Inits the pipeline with the command-line arguments. These will be parsed inside and the program exits with an error message if parsing goes wrong.

Member Function Documentation

virtual ClassicOpts* multovl::ClassicPipeline::opt_ptr ( )
inlineprotectedvirtual
Returns
access to the option-handling object

Implements multovl::BasePipeline.

virtual unsigned int multovl::ClassicPipeline::read_input ( )
protectedvirtual

Reads the input tracks from files if no –load option was specified. The file names are parsed from the command line when the constructor runs. If the –load <archfile> option was specified, then the complete status of the program including all input details is read from a binary archive <archfile>. In this case the input track file name arguments are ignored.

Returns
the number of tracks successfully read, 0 on error.

Implements multovl::BasePipeline.

virtual bool multovl::ClassicPipeline::write_output ( )
protectedvirtual

Writes the results to standard output. Format will be decided based on the options. If the –save <archfile> option was specified, then the complete status of the program except the results will be serialized to a binary archive <archfile> as well.

Implements multovl::BasePipeline.


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