Issues

• Investigate including duplicate sequences in the trees

  matsengrp/flu-usher#60 · Filter by author Haddox opened on Aug 24, 2026

• Rules that request the whole core budget starve one combination per run

  matsengrp/flu-usher#57 · Filter by author Haddox opened on Aug 21, 2026

• Follow-ups from the PR #50 review: gate hardening, duplicated parsing, config-as-input

  matsengrp/flu-usher#51 · Filter by author Haddox opened on Aug 9, 2026

• Insertions are mis-placed in any CDS fragment that does not start at curated position 1

  matsengrp/flu-usher#44 · Filter by author Haddox opened on Aug 6, 2026
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• Mark per-randomization intermediates temp() so they are deleted at end of run

  matsengrp/flu-usher#38 · Filter by author Haddox opened on May 15, 2026
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• Filter singleton-insertion sequences using phyz util alnqc

  matsengrp/flu-usher#26 · Filter by author matsen opened on Mar 23, 2026
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• Restructure pipeline to use per-rule conda environments

  matsengrp/flu-usher#21 · Filter by author Haddox opened on Feb 26, 2026
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