multovl
1.3
Multiple overlaps of genomic regions
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#include "classicpipeline.hh"
Public Member Functions | |
ClassicPipeline (int argc, char *argv[]) | |
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BasePipeline () | |
Default init of a BasePipeline object. | |
bool | run () |
const Errors & | errors () const |
Protected Member Functions | |
virtual unsigned int | read_input () |
virtual bool | write_output () |
virtual ClassicOpts * | opt_ptr () |
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virtual unsigned int | detect_overlaps () |
const chrom_multovl_map & | cmovl () const |
chrom_multovl_map & | cmovl () |
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bool | set_optpimpl (MultovlOptbase *optp) |
MultovlOptbase * | opt_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 | |
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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 |
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.
multovl::ClassicPipeline::ClassicPipeline | ( | int | argc, |
char * | argv[] | ||
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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.
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inlineprotectedvirtual |
Implements multovl::BasePipeline.
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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.
Implements multovl::BasePipeline.
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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.