1.4.1

[1.4.1] - 20251007

Bug fix

• Fixed missing args3 in pangenome map module

Parameters

• Tweaked default minimum allele support to allow leniency for aDNA (matches EAGER)

Others

• Small fixes to docs
• Added threads flag to samtools index
• Minor annotation changes
• Removed old --max-fragment-length argument in ancient DNA mapping script blocks - these will always be "single ended" at the mapping stage.

Wiki

• Wiki boilerplate pushed