d261f558e0a577ee269fe55215505668cdcb6f2a
markd
  Wed Jul 7 07:09:11 2021 -0700
Address several cases of possible uninitialized variables detected by -O3.  None of these appear to be actually bugs due to the flow of the code

diff --git src/jkOwnLib/supStitch.c src/jkOwnLib/supStitch.c
index c8525cf..430f0cb 100644
--- src/jkOwnLib/supStitch.c
+++ src/jkOwnLib/supStitch.c
@@ -306,31 +306,31 @@
 static void ssGraphFree(struct ssGraph **pGraph)
 /* Free graph. */
 {
 struct ssGraph *graph;
 if ((graph = *pGraph) != NULL)
     {
     freeMem(graph->nodes);
     freeMem(graph->edges);
     freez(pGraph);
     }
 }
 
 boolean tripleCanFollow(struct ffAli *a, struct ffAli *b, aaSeq *qSeq, struct trans3 *t3List)
 /* Figure out if a can follow b in any one of three reading frames of haystack. */
 {
-int ahStart, ahEnd, bhStart, bhEnd;
+int ahStart = 0, ahEnd = 0, bhStart = 0, bhEnd = 0;
 trans3Offsets(t3List, a->hStart, a->hEnd, &ahStart, &ahEnd);
 trans3Offsets(t3List, b->hStart, b->hEnd, &bhStart, &bhEnd);
 return  (a->nStart < b->nStart && a->nEnd < b->nEnd && ahStart < bhStart && ahEnd < bhEnd);
 }
 
 
 static struct ssGraph *ssGraphMake(struct ffAli *ffList, bioSeq *qSeq,
 	enum ffStringency stringency, boolean isProt, struct trans3 *t3List)
 /* Make a graph corresponding to ffList */
 {
 int nodeCount = ffAliCount(ffList);
 int maxEdgeCount = (nodeCount+1)*(nodeCount)/2;
 int edgeCount = 0;
 struct ssEdge *edges, *e;
 struct ssNode *nodes;
@@ -374,31 +374,31 @@
 	    {
 	    canFollow = (ff->nStart < mid->nStart && ff->nEnd < mid->nEnd 
 			&& ff->hStart < mid->hStart && ff->hEnd < mid->hEnd);
 	    }
 	if (canFollow)
 	    {
 	    struct ssNode *ffNode = &nodes[i];
 	    int score;
 	    int hGap;
 	    int nGap;
 	    int crossover;
 
 	    nGap = mid->nStart - ff->nEnd;
 	    if (t3List)
 	        {
-		int fhStart, fhEnd;
+		int fhStart = 0, fhEnd = 0;
 		trans3Offsets(t3List, ff->hStart, ff->hEnd, &fhStart, &fhEnd);
 		hGap = mhStart - fhEnd;
 		}
 	    else
 		{
 		hGap = mid->hStart - ff->hEnd;
 		}
 	    e = &edges[edgeCount++];
 	    assert(edgeCount <= maxEdgeCount);
 	    e->nodeIn = ffNode;
 	    e->overlap = overlap = -nGap;
 	    if (overlap > 0)
 		{
 		int midSize = mid->hEnd - mid->hStart;
 		int ffSize = ff->hEnd - ff->hStart;