d63b7e753345e199748030d83e1d3aa497b350f9
braney
  Tue Aug 2 22:24:07 2016 -0700
fix problem in bigPsl with '-' as strand for target sequence #17829

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 8b6db66..e0383a9 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -6933,30 +6933,34 @@
 tStart = psl->tStart - 100;
 if (tStart < 0) tStart = 0;
 if (retTStart)
     *retTStart = tStart;
 
 tEnd  = psl->tEnd + 100;
 if (tEnd > psl->tSize) tEnd = psl->tSize;
 
 dnaSeq = hDnaFromSeq(database, seqName, tStart, tEnd, dnaLower);
 freez(&dnaSeq->name);
 dnaSeq->name = cloneString(psl->tName);
 if (retSeq)
     *retSeq = dnaSeq;
 
 tRcAdjustedStart = tStart;
+
+if (psl->strand[1] == '-')
+    pslRc(psl);
+
 if (psl->strand[0] == '-')
     {
     if (retIsRc)
 	*retIsRc = TRUE;
     reverseComplement(dnaSeq->dna, dnaSeq->size);
     pslRc(psl);
     tRcAdjustedStart = psl->tSize - tEnd;
     }
 return pslToFfAli(psl, qSeq, dnaSeq, tRcAdjustedStart);
 }
 
 int showPartialDnaAlignment(struct psl *wholePsl,
 			    struct dnaSeq *rnaSeq, FILE *body,
 			    int cdsS, int cdsE, boolean restrictToWindow)
 /* Show (part of) alignment for accession.  wholePsl is the whole alignment;