4aa77873cb618e254b2f90d091d7bdef844947c2
max
  Wed Jul 8 04:28:42 2026 -0700
Let assembly hubs assign genetic codes per sequence for amino acid display

Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1
NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to
show amino acids for each sequence.  New hGeneticCodeForChrom(db, chrom) in
hdb.c resolves the code (per-db cached), falling back to the previous behavior:
chrM/chrMT use the vertebrate mitochondrial code, everything else the standard
code.

Wired into the two browser display paths, which both go through cds.c's
baseColorLookupCodon: the base position track three-frame translation and
codon-colored annotation tracks such as gene predictions (also PSL/BAM).  Also
used for the hgc SNP amino acid details, and genePredTranslate gains a db
parameter (genePredToProt gains an optional -db flag) so command-line
translation can honor the same setting.  Documented in assemblyHubHelp.html.
refs #16550

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 5c0bfcd230a..e453aff4613 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -19289,34 +19289,31 @@
 int snpCodonPos = geneIsRc ? (2 - ((exonEnd - snpEnd) + exonFrame) % 3) :
 			     (((snpStart - exonStart) + exonFrame) % 3);
 refCodon[0] = getSnpTxBase(gene, exonIx, snpStart, -snpCodonPos);
 refCodon[1] = getSnpTxBase(gene, exonIx, snpStart, 1 - snpCodonPos);
 refCodon[2] = getSnpTxBase(gene, exonIx, snpStart, 2 - snpCodonPos);
 refCodon[3] = '\0';
 if (geneIsRc)
     {
     reverseComplement(refCodon, strlen(refCodon));
     snpCodonPos = 2 - snpCodonPos;
     }
 if (pSnpCodonPos != NULL)
     *pSnpCodonPos = snpCodonPos;
 if (pRefAA != NULL)
     {
-    if (isMito(seqName))
-        *pRefAA = lookupMitoCodon(refCodon);
-    else
-        *pRefAA = lookupCodon(refCodon);
+    *pRefAA = lookupCodonInCode(hGeneticCodeForChrom(database, seqName), refCodon);
     if (*pRefAA == '\0') *pRefAA = '*';
     }
 }
 
 static char *highlightCodonBase(char *codon, int offset)
 /* If codon is a triplet and offset is 0 to 2, highlight the base at the offset.
  * Otherwise just return the given codon sequence unmodified.
  * Don't free the return value! */
 {
 static struct dyString *dy = NULL;
 if (dy == NULL)
     dy = dyStringNew(0);
 dyStringClear(dy);
 if (strlen(codon) != 3)
     dyStringAppend(dy, codon);
@@ -19369,35 +19366,31 @@
 		   geneTrack, geneName, snpMisoLinkFromFunc("frameshift"));
 	else if (diff > 0)
 	    printf(firstTwoColumnsPctS "%s (insertion of %d codon%s)\n",
 		   geneTrack, geneName, snpMisoLinkFromFunc("inframe_insertion"),
 		   (int)(diff/3), (diff > 3) ?  "s" : "");
 	else
 	    printf(firstTwoColumnsPctS "%s (deletion of %d codon%s)\n",
 		   geneTrack, geneName, snpMisoLinkFromFunc("inframe_deletion"),
 		   (int)(-diff/3), (diff < -3) ?  "s" : "");
 	}
     else if (alSize == 1 && refIsSingleBase)
         {
         char snpCodon[4];
         safecpy(snpCodon, sizeof(snpCodon), refCodon);
         snpCodon[snpCodonPos] = alBase;
-        char snpAA = '\0';
-        if (isMito(seqName))
-            snpAA = lookupMitoCodon(snpCodon);
-        else
-            snpAA = lookupCodon(snpCodon);
+        char snpAA = lookupCodonInCode(hGeneticCodeForChrom(database, seqName), snpCodon);
         if (snpAA == '\0') snpAA = '*';
         char refCodonHtml[16], snpCodonHtml[16];
         safecpy(refCodonHtml, sizeof(refCodonHtml), highlightCodonBase(refCodon, snpCodonPos));
         safecpy(snpCodonHtml, sizeof(snpCodonHtml), highlightCodonBase(snpCodon, snpCodonPos));
         if (refAA != snpAA)
             {
             if (refAA == '*')
                 printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n",
                        geneTrack, geneName, snpMisoLinkFromFunc("stop-loss"),
                        refAA, refCodonHtml, snpAA, snpCodonHtml);
             else if (snpAA == '*')
                 printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n",
                        geneTrack, geneName, snpMisoLinkFromFunc("nonsense"),
                        refAA, refCodonHtml, snpAA, snpCodonHtml);
             else