Regression from v0.13.2 to v0.13.3 allowed marginal entries from controls to be accepted into the 'all reads' FASTA if below the given threshold but above half of it (heuristic used in prepare-reads to ensure that -a setting didn't prevent auto-increase to the -f setting, and vice versa).
In switching from fasta-nr to sample-tally to make the "all reads" FASTA, ws missing the -t / --total value in the pipeline (set to -a).
TODO: Can probably drop the heuristic if move all the control-driven abundance thresholding into sample-tally only...
Regression from v0.13.2 to v0.13.3 allowed marginal entries from controls to be accepted into the 'all reads' FASTA if below the given threshold but above half of it (heuristic used in prepare-reads to ensure that
-asetting didn't prevent auto-increase to the-fsetting, and vice versa).In switching from
fasta-nrtosample-tallyto make the "all reads" FASTA, ws missing the-t/--totalvalue in the pipeline (set to-a).TODO: Can probably drop the heuristic if move all the control-driven abundance thresholding into sample-tally only...