marbl/rukki

Issues

• Support of polyploidy

  #29 opened 2 years ago by baozg
  0

• bioconda release

  #28 opened 3 years ago by snurk
  0

• Configuration

  #6 opened 3 years ago by snurk
  0

• Assign all nodes in localized tangles

  #27 opened 3 years ago by snurk
  0

• Improve gap size estimates

  #26 opened 3 years ago by snurk
  0

• Think of a more 'local' loop check

  #4 opened 3 years ago by snurk
  1

• Marker density threshold unused

  #21 opened 3 years ago by snurk
  0

• File with node assignments as input

  #25 opened 3 years ago by snurk
  0

• Gap closing can lead to issues in rare cases

  #24 opened 3 years ago by snurk
  0

• Tie issue-len to trusted-len

  #23 opened 3 years ago by snurk
  0

• Integration test cases

  #7 opened 3 years ago by snurk
  2

• Improve gap filling logic

  #22 opened 3 years ago by snurk
  0

• Generalized haplotype gap patching

  #20 opened 3 years ago by snurk
  0

• Add non-redundant SCC output

  #3 opened 3 years ago by snurk
  1

• Add jumping across localized tangles

  #9 opened 3 years ago by snurk
  0

• Add 'broken bubble' patching for trio

  #10 opened 3 years ago by snurk
  0

• Add small bubble jumping to trio

  #14 opened 3 years ago by snurk
  0

• Switch to gapped paths

  #16 opened 3 years ago by snurk
  0

• Add gap size estimation for all cases

  #19 opened 3 years ago by snurk
  0

• Support repeated link records

  #18 opened 3 years ago by snurk
  0

• Implement small component condensing for pri/alt exraction

  #17 opened 3 years ago by snurk
  1

• Add iterators for outgoing/incoming

  #15 opened 3 years ago by snurk
  0

• Het-mers instead for long node homology?

  #13 opened 3 years ago by snurk
  0

• Think about using het-mers

  #12 opened 3 years ago by snurk
  0

• Maybe borrow something from pangenomic graphs

  #11 opened 3 years ago by snurk
  0

• Add heterozygous node classification

  #2 opened 3 years ago by snurk
  0

• Implement superbubble and sb-chain search

  #1 opened 3 years ago by snurk
  0

• github CI integration

  #8 opened 3 years ago by snurk
  0

• Maybe add rule to choose between 'filling node' vs 'single link' using link coverage

  #5 opened 3 years ago by snurk
  0