dc6d6e4b842178bd00a20da9a03ddf6deeee9e94
hiram
  Thu May 7 10:55:45 2020 -0700
and fixup pointer arithmetic due to correct needLargeMem argument and hence much larger array sizes for difficult alignments no redmine

diff --git src/lib/pairHmm.c src/lib/pairHmm.c
index 587a914..c864228 100644
--- src/lib/pairHmm.c
+++ src/lib/pairHmm.c
@@ -84,31 +84,31 @@
 	char *name, char emitLetter)
 /* Give a name to a state and return a pointer to it. */
 {
 struct phmmState *state;
 assert(stateIx < am->stateCount);
 state = &am->states[stateIx];
 state->name = name;
 state->emitLetter = emitLetter;
 return state;
 }
 
 static void phmmFindMatrixIx(struct phmmMatrix *am, struct phmmMommy *cell, 
 	int *retStateIx, int *retQix, int *retTix)
 /* Given a cell in matrix return state, query, and target index. */
 {
-int cellIx = cell - am->allCells;
+size_t cellIx = cell - am->allCells;
 *retStateIx = cellIx/am->stateSize;
 cellIx %= am->stateSize;
 *retTix = cellIx / am->qDim;
 *retQix = cellIx % am->qDim;
 }
 
 static struct phmmMommy *phmmFindMommy(struct phmmMatrix *am, 
 	struct phmmMommy *baby)
 /* Find baby's mommy and return it. */
 {
 int momStateIx, qOff, tOff;
 int babyStateIx, qIx, tIx;
 UBYTE mommy;
 
 if ((mommy = baby->mommy) == phmmNullMommy)