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Handle no-persistent-ID-for-given-distance case

edgecase

Status: Open.

#52 In aofarrel/tree_nine;

· aofarrel opened on Mar 6, 2026

Certain persistent cluster IDs throw errors

bugSomething isn't workingSomething isn't working

edgecase

Status: Open.

#50 In aofarrel/tree_nine;

· aofarrel opened on Mar 4, 2026

If sample-level metadata marks sample as invalid, flag clusters containing ONLY invalid samples

enhancementNew feature or requestNew feature or request

stakeholder_request

Status: Open.

#45 In aofarrel/tree_nine;

· aofarrel opened on Feb 27, 2026

5-clusters should not have a line for child clusters in MR description

Status: Open.

#44 In aofarrel/tree_nine;

· aofarrel opened on Feb 23, 2026

Unclustered samples nearest relatives file should exclude base tree

invalidThis doesn't seem rightThis doesn't seem right

Status: Open.

#41 In aofarrel/tree_nine;

· aofarrel opened on Dec 29, 2025

Make subcluster iteration faster

Status: Open.

#33 In aofarrel/tree_nine;

· aofarrel opened on Nov 17, 2025

Add ability to include SRA samples in cluster without cluster_entire_tree

enhancementNew feature or requestNew feature or request

stakeholder_request

Status: Open.

#29 In aofarrel/tree_nine;

· aofarrel opened on Oct 31, 2025

Investigate if initial distance matrix creation could be faster

enhancementNew feature or requestNew feature or request

Status: Open.

#28 In aofarrel/tree_nine;

· aofarrel opened on Oct 31, 2025

Explictly complain when a clustered sample is removed

enhancementNew feature or requestNew feature or request

Status: Open.

#27 In aofarrel/tree_nine;

· aofarrel opened on Oct 31, 2025

Create comprehensive test datasets for clustering

Status: Open.

#26 In aofarrel/tree_nine;

· aofarrel opened on Oct 31, 2025

Cluster information JSON needs even more fields

enhancementNew feature or requestNew feature or request

Status: Open.

#25 In aofarrel/tree_nine;

· aofarrel opened on Oct 31, 2025

n_samples_in_clusters is inaccurate

bugSomething isn't workingSomething isn't working

Status: Open.

#18 In aofarrel/tree_nine;

· aofarrel opened on Jun 18, 2025