multovl
1.3
Multiple overlaps of genomic regions
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#include "parprobpipeline.hh"
Public Member Functions | |
ParProbPipeline (int argc, char *argv[]) | |
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ProbPipeline (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 | detect_overlaps () |
virtual ParProbOpts * | opt_ptr () |
virtual Stat & | stat () |
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ProbPipeline () | |
virtual unsigned int | read_input () |
unsigned int | calc_actual_overlaps () |
virtual bool | write_output () |
const chrom_shufovl_map & | csovl () const |
chrom_shufovl_map & | csovl () |
const Stat & | stat () const |
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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, ShuffleOvl > | chrom_shufovl_map |
There is one ShuffleOvl object for each chromosome. | |
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typedef std::vector< Input > | input_seq_t |
The ParProbPipeline implements the parallel version of the MULTOVL probability pipeline. The inputs are files (text or binary), the overlap calculations are serial/single core, the repetitions after reshuffling (some) tracks to estimate the probability of overlaps by chance are done in parallel.
multovl::prob::ParProbPipeline::ParProbPipeline | ( | 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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protectedvirtual |
Detects overlaps. First the overlaps without shuffling are calculated. Then the shufflable tracks are permuted and the number of overlaps counted again and again which will provide an estimate of the null distribution (ie. the extent of overlaps by chance). The reshufflings are done in parallel.
Reimplemented from multovl::prob::ProbPipeline.
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inlineprotectedvirtual |
Reimplemented from multovl::prob::ProbPipeline.
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inlineprotectedvirtual |
Reimplemented from multovl::prob::ProbPipeline.