algbio/practical-omnitigs

Issues

• Make project citable

  #45 opened 4 years ago by sebschmi
  1

• Implement command to output the length of safe walks in edges

  #95 opened 4 years ago by sebschmi
  2

• Implement command to convert the bcalm2 output into an efficient binary representation and make this usable in all other commands (except verify)

  #96 opened 4 years ago by sebschmi
  1

• Compute the hydrostructure non-incrementally

  #83 opened 4 years ago by sebschmi
  0

• Benchmark if LinkedList or VecDeque is faster in graph traversals

  #40 opened 4 years ago by sebschmi
  0

• Comment all the things

  #61 opened 4 years ago by sebschmi
  0

• Compute restricted reachabilities

  #84 opened 4 years ago by sebschmi
  0

• Make out_neighbors_to and in_neighbors_from return edge ids instead of struct Neighbor

  #89 opened 4 years ago by sebschmi
  0

• Let NavigableGraph return Iterators instead of IntoIterators

  #88 opened 4 years ago by sebschmi
  0

• Use mirror instead of partner throughout the code

  #70 opened 4 years ago by sebschmi
  0

• Turn on target-cpu=native for release builds

  #82 opened 4 years ago by sebschmi
  0

• Integrate QUAST into the pipeline

  #94 opened 4 years ago by sebschmi
  0

• Integrate ContigValidator into the pipeline

  #93 opened 4 years ago by sebschmi
  0

• Rename yaml files to yml

  #64 opened 4 years ago by sebschmi
  0

• Add command to circularise genome

  #92 opened 4 years ago by sebschmi
  0

• Add command to check if a genome has no holes

  #91 opened 4 years ago by sebschmi
  0

• Compute macronode centers for strongly connected graphs

  #77 opened 4 years ago by sebschmi
  0

• Check if input genome characters are valid

  #86 opened 4 years ago by sebschmi
  0

• Create omnitigs crate

  #85 opened 4 years ago by sebschmi
  0

• Decompose graph into SCCs

  #76 opened 4 years ago by sebschmi
  0

• Compute the DAG of SCCs and check if it is a path

  #81 opened 4 years ago by sebschmi
  0

• Print more detailed statistics about WCCs and SCCs

  #80 opened 4 years ago by sebschmi
  0

• Make decompose WCC method return a node mapping instead of a vector of graphs

  #78 opened 4 years ago by sebschmi
  0

• Add snakemake test case to CI

  #74 opened 4 years ago by sebschmi
  0

• Why can there be an uneven amount of compactable unitigs?

  #60 opened 4 years ago by sebschmi
  0

• Speed up script make_bcalm_output_deterministic.sh

  #59 opened 4 years ago by sebschmi
  0

• Replace `binode_mapping_function` parameter with trait `BidirectedNodeData`

  #19 opened 4 years ago by sebschmi
  0

• Add functions for edge-centric de Bruijn graph

  #68 opened 4 years ago by sebschmi
  0

• Add test cases with multigraphs to everything

  #66 opened 4 years ago by sebschmi
  0

• Read the output of bcalm into an edge-centric de-Bruijn graph

  #57 opened 4 years ago by sebschmi
  0

• Remove conda from environment.yaml

  #63 opened 4 years ago by sebschmi
  0

• Compactable unitig check is broken

  #58 opened 4 years ago by sebschmi
  0

• Add experiments script

  #17 opened 4 years ago by sebschmi
  0

• Refacor compact genome into interface and implementation

  #54 opened 4 years ago by sebschmi
  0

• Expose the internal module structure of crates

  #37 opened 4 years ago by sebschmi
  0

• Document the CLI

  #51 opened 4 years ago by sebschmi
  0

• Set up coveralls

  #46 opened 4 years ago by sebschmi
  1

• Verify that graph is either SCC or decomposes into maximal SCCs that are also maximal WCCs

  #23 opened 4 years ago by sebschmi
  0

• Add logging

  #21 opened 4 years ago by sebschmi
  0

• Fix links and docs

  #38 opened 4 years ago by sebschmi
  0

• Make node and edge indices type safe

  #22 opened 4 years ago by sebschmi
  1

• Refactor trait generic types into associated types.

  #42 opened 4 years ago by sebschmi
  0

• Add type aliases for genome-graph trait

  #20 opened 4 years ago by sebschmi
  0

• Decompose bigraph crate into bigraph and general graph crate

  #34 opened 4 years ago by sebschmi
  0

• Use petgraph traits whereever possible

  #29 opened 4 years ago by sebschmi
  1

• Add serde support for all datastructures

  #25 opened 4 years ago by sebschmi
  0

• Use `bio` crate to represent genomes

  #18 opened 4 years ago by sebschmi
  0

• Squat crate names, including some meta-crate

  #12 opened 4 years ago by sebschmi
  1

• Switch to 2-clause BSD

  #11 opened 4 years ago by sebschmi
  0

• Document crates a tiny bit and publish them on crates.io to reserve the names and get badges

  #10 opened 4 years ago by sebschmi
  1