Issues

• Find a way to better apply geometric restrictions to tschainalign

  enhancement
  algbio/tsalign#207 · Filter by author sebschmi opened on Sep 14, 2026

• Allow inexact k-mer matches for tschainalign

  enhancement
  algbio/tsalign#203 · Filter by author sebschmi opened on Aug 13, 2026
  

• Costs of repeats are not computed correctly

  bug
  algbio/tsalign#166 · Filter by author sebschmi opened on May 7, 2026

• Initialising chaining cost function takes too long

  bug
  algbio/tsalign#142 · Filter by author sebschmi opened on Dec 19, 2025
  1

  

• Try using linear heap for non-chaining A*s

  algbio/tsalign#139 · Filter by author sebschmi opened on Dec 19, 2025

• Strengthen initial chaining lower bound by requiring it to start and end with non-matches

  algbio/tsalign#124 · Filter by author sebschmi opened on Dec 16, 2025

• Allow to restrict anti-primary gap in chainalign

  algbio/tsalign#112 · Filter by author sebschmi opened on Dec 5, 2025

• Allow to restrict 12-jump in chainalign

  algbio/tsalign#111 · Filter by author sebschmi opened on Dec 5, 2025

• Allow to continue alignment in case of memory limit exhaustion

  algbio/tsalign#104 · Filter by author sebschmi opened on Nov 11, 2025

• In a mode where we prune based on suffix array matches, create template switch entrance and exit nodes all at once

  algbio/tsalign#97 · Filter by author sebschmi opened on Sep 11, 2025

• use suffix array for every prefix when deciding the lower bound of a ts

  algbio/tsalign#96 · Filter by author sebschmi opened on Sep 11, 2025
  2

• one cost matrix per flank index

  algbio/tsalign#95 · Filter by author sebschmi opened on Sep 11, 2025

• Inner TS flank costs

  algbio/tsalign#94 · Filter by author sebschmi opened on Sep 11, 2025

• Forbid palindromic TSes

  algbio/tsalign#69 · Filter by author sebschmi opened on May 15, 2025

• Hashmap operations take most of the time

  algbio/tsalign#68 · Filter by author sebschmi opened on May 14, 2025
  1

• Possibly allow to reuse preprocessed data between calls to libtsalign

  algbio/tsalign#66 · Filter by author sebschmi opened on May 13, 2025
  1

• Flexible flank length

  algbio/tsalign#46 · Filter by author sebschmi opened on Apr 25, 2025

• Flank costs based on TS length

  algbio/tsalign#45 · Filter by author sebschmi opened on Apr 25, 2025

• Score forward TS based on closeness to backward TS

  algbio/tsalign#44 · Filter by author sebschmi opened on Apr 25, 2025

• Investigate possible integration with rust-bio

  algbio/tsalign#13 · Filter by author jeeeesper opened on Apr 7, 2025

• Compute cost for each TS case in show

  algbio/tsalign#6 · Filter by author sebschmi opened on Mar 13, 2025

• Fast mode that is not accurate

  algbio/tsalign#5 · Filter by author sebschmi opened on Jan 22, 2025

• Use non-generative A* for TSA lower bound computation

  algbio/tsalign#2 · Filter by author sebschmi opened on Dec 19, 2024