# Module: RGFATools

- Includes:
- Artifacts, CopyNumber, InvertibleSegments, LinearPaths, Multiplication, PBubbles, SuperfluousLinks

- Included in:
- RGFA

- Defined in:
- lib/rgfatools.rb,

lib/rgfatools.rb

## Overview

Module defining additional methods for the RGFA class.

RGFATools is an extension to the RGFA library, which allow to perform further operations. Thereby additional conventions are required, with respect to the GFA specification, which are compatible with it.

The methods defined here allow, e.g., to randomly orient a segment which has the same connections on both sides, to compute copy numbers and multiply or delete segments according to them, to distribute the links of copies after multipling a segment, or to eliminate edges in the graph which are incompatible with an hamiltonian path.

Custom optional fields are defined, such as “cn” for the copy number of a segment, “or” for the original segment(s) of a duplicated or merged segment, “mp” for the starting position of original segments in a merged segment, “rp” for the position of possible inversions due to arbitrary orientation of some segments by the program.

Furthermore a convention for the naming of the segments is introduced, which gives a special meaning to the characters “_^()”.

## Defined Under Namespace

**Modules:** Artifacts, CopyNumber, InvertibleSegments, LinearPaths, Multiplication, PBubbles, SuperfluousLinks

## 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

### Methods included from SuperfluousLinks

#enforce_all_mandatory_links, #enforce_segment_mandatory_links, #remove_self_link, #remove_self_links

### Methods included from Multiplication

#multiply_extended, #multiply_with_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