GARD codon jobs fail: genetic --code not passed to HyPhy

[stevenweaver]

Summary

GARD analyses on codon alignments fail deterministically because app/gard/gard.sh never passes --code to the HyPhy GARD invocation. HyPhy's codon model setup (models.codon.MG_REV.ModelDescription) requires a genetic code argument; without it the function is called with one argument instead of two and HyPhy aborts at load time:

Error: User-defined function 'models.codon.MG_REV.ModelDescription' needs 2 parameters, but 1 were supplied.

Nucleotide/protein GARD jobs are unaffected (that path does not require a genetic code). Every other codon-capable method in this repo already passes --code on its invocation; gard.sh is the only one that does not.

Root cause

In app/gard/gard.sh, the genetic code is resolved into GENETIC_CODE (and correctly defaults to Universal), and is even echoed to the log — but it is omitted from every GARD command line. The invocation passes --type … --alignment … --tree … --model … --mode … --rv … --rate-classes … --max-breakpoints … with no --code.

Fix

Always pass --code, keeping the existing Universal default:

GENETIC_CODE="${genetic_code:-Universal}"     # already present
# add --code to every $GARD invocation line:
$GARD --type $DATATYPE --code $GENETIC_CODE --alignment $FN --tree $TREE_FN --model $MODEL ...

Reproduction

Submit any in-frame codon alignment (DNA, equal-length sequences, length divisible by 3, no premature stop codons) to GARD with datatype = codon. The job fails within seconds with the arity error above. Adding --code Universal to the HyPhy invocation resolves it; the identical alignment run as --type nucleotide succeeds. Confirmed node-independent and fully deterministic.

Scope

• Confirmed & reproduced: GARD.
• Not affected: fade (FADE is a protein/amino-acid method) and hivtrace (distance-based) legitimately take no genetic code.
• Worth a quick audit (not confirmed here): any other codon-based analysis to ensure --code is always supplied with a sane default.