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Costs of repeats are not computed correctly

bugSomething isn't workingSomething isn't working

Status: Open.

#166 In algbio/tsalign;

· sebschmi opened on May 7, 2026

Initialising chaining cost function takes too long

bugSomething isn't workingSomething isn't working

Status: Open.

#142 In algbio/tsalign;

· sebschmi opened on Dec 19, 2025

Try using linear heap for non-chaining A*s

Status: Open.

#139 In algbio/tsalign;

· sebschmi opened on Dec 19, 2025

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

Status: Open.

#124 In algbio/tsalign;

· sebschmi opened on Dec 16, 2025

Allow to restrict anti-primary gap in chainalign

Status: Open.

#112 In algbio/tsalign;

· sebschmi opened on Dec 5, 2025

Allow to restrict 12-jump in chainalign

Status: Open.

#111 In algbio/tsalign;

· sebschmi opened on Dec 5, 2025

Allow to continue alignment in case of memory limit exhaustion

Status: Open.

#104 In algbio/tsalign;

· 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

Status: Open.

#97 In algbio/tsalign;

· sebschmi opened on Sep 11, 2025

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

Status: Open.

#96 In algbio/tsalign;

· sebschmi opened on Sep 11, 2025

one cost matrix per flank index

Status: Open.

#95 In algbio/tsalign;

· sebschmi opened on Sep 11, 2025

Inner TS flank costs

Status: Open.

#94 In algbio/tsalign;

· sebschmi opened on Sep 11, 2025

Forbid palindromic TSes

Status: Open.

#69 In algbio/tsalign;

· sebschmi opened on May 15, 2025