multovl
1.3
Multiple overlaps of genomic regions
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#include "probpipeline.hh"
Classes | |
class | OvlenCounter |
Public Member Functions | |
ProbPipeline (int argc, char *argv[]) | |
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BasePipeline () | |
Default init of a BasePipeline object. | |
bool | run () |
const Errors & | errors () const |
Protected Types | |
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 |
Protected Member Functions | |
ProbPipeline () | |
virtual unsigned int | read_input () |
virtual unsigned int | detect_overlaps () |
unsigned int | calc_actual_overlaps () |
virtual bool | write_output () |
virtual ProbOpts * | opt_ptr () |
const chrom_shufovl_map & | csovl () const |
chrom_shufovl_map & | csovl () |
const Stat & | stat () const |
virtual Stat & | stat () |
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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. | |
The ProbPipeline implements the MULTOVL probability pipeline. The inputs are files (text or binary), the overlap calculations are serial/single core, which are repeated after reshuffling (some) tracks to estimate the probability of overlaps by chance.
multovl::prob::ProbPipeline::ProbPipeline | ( | 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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protected |
Default ctor that does not set the option processing object used by ParProbPipeline ctor only
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protected |
Calculates the actual overlaps using the original input tracks without reshuffling.
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inlineprotected |
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inlineprotected |
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protectedvirtual |
Detects overlaps. First the overlaps without shuffling are calculated, see calc_actual_overlaps(). 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).
Implements multovl::BasePipeline.
Reimplemented in multovl::prob::ParProbPipeline.
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inlineprotectedvirtual |
Implements multovl::BasePipeline.
Reimplemented in multovl::prob::ParProbPipeline.
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protectedvirtual |
Reads the input tracks. In addition to the "shufflable" tracks specified as positional arguments, a track containing free regions must also be read. All regions must fall within these free regions. Optionally, a set of "fixed" tracks may be defined which won't be shuffled; they are also read here.
Implements multovl::BasePipeline.
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inlineprotected |
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inlineprotectedvirtual |
Reimplemented in multovl::prob::ParProbPipeline.
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protectedvirtual |
Writes the results to standard output. Only the statistics are printed.
Implements multovl::BasePipeline.