Module: RGFATools

Includes:
Artifacts, CopyNumber, InvertibleSegments, LinearPaths, Multiplication, PBubbles, SuperfluousLinks
Included in:
RGFA
Defined in:
lib/rgfatools.rb

Overview

Module defining additional methods for the RGFA class. In the main file is only the method redefinition infrastructure (private methods). The public methods are in the included modules.

Defined Under Namespace

Modules: Artifacts, CopyNumber, InvertibleSegments, LinearPaths, Multiplication, PBubbles, SuperfluousLinks Classes: Error

Constant Summary

Constants included from Multiplication

Multiplication::LINKS_DISTRIBUTION_POLICY

Method Summary

Methods included from PBubbles

#remove_p_bubble, #remove_p_bubbles

Methods included from LinearPaths

#merge_linear_path

Methods included from SuperfluousLinks

#enforce_all_mandatory_links, #enforce_segment_mandatory_links, #remove_self_link, #remove_self_links

Methods included from Multiplication

#multiply_with_rgfatools, #multiply_without_rgfatools

Methods included from InvertibleSegments

#randomly_orient_invertible, #randomly_orient_invertibles

Methods included from CopyNumber

#apply_copy_number, #apply_copy_numbers, #compute_copy_numbers, #delete_low_coverage_segments, #set_count_unit_length, #set_default_count_tag

Methods included from Artifacts

#remove_dead_ends, #remove_small_components