d93f47cd567bb70aba94de233054e8b4fae00f7d
braney
  Fri May 29 15:33:58 2020 -0700
remove frameshifts from psls in hgVai

diff --git src/hg/lib/annoGratorGpVar.c src/hg/lib/annoGratorGpVar.c
index 5baccbf..ab8f230 100644
--- src/hg/lib/annoGratorGpVar.c
+++ src/hg/lib/annoGratorGpVar.c
@@ -565,30 +565,31 @@
         }
     }
 }
 
 static struct annoRow *aggvGenRowsGp(struct annoGratorGpVar *self, struct variant *variant,
                                      struct genePred *pred, struct annoRow *inRow,
                                      struct lm *callerLm)
 // put out annoRows for all the gpFx that arise from variant and pred
 {
 struct annoStreamer *sSelf = &(self->grator.streamer);
 struct genbankCds cds;
 genePredToCds(pred, &cds);
 struct dnaSeq *txSeq = genePredToGenomicSequence(pred, sSelf->assembly, self->lm);
 int chromSize = 0;  // unused
 struct psl *psl = genePredToPsl(pred, chromSize, txSeq->size);
+pslRemoveFrameShifts(psl);
 vpExpandIndelGaps(psl, self->gSeqWin, txSeq);
 struct dnaSeq *protSeq = NULL;
 if (cds.end > cds.start)
     {
     //#*** what if cds.startComplete is not true??
     protSeq = translateTx(txSeq, &cds);
     lookupProtAcc(self, protSeq);
     }
 struct annoRow *rowList = aggvPredict(self, variant, psl, &cds, txSeq, protSeq, inRow, callerLm);
 pslFree(&psl);
 dnaSeqFree(&protSeq);
 return rowList;
 }
 
 static struct annoRow *aggvGenRowsPsl(struct annoGratorGpVar *self, struct variant *variant,