5234cfcb4a8b7c971f749002bfa4c26ff6f05804
hiram
  Tue May 5 11:33:58 2020 -0700
fixup needLargeMem argument type to get this to work with SARS MERS alignment no redmine

diff --git src/lib/pairHmm.c src/lib/pairHmm.c
index 67eda43..587a914 100644
--- src/lib/pairHmm.c
+++ src/lib/pairHmm.c
@@ -14,49 +14,49 @@
 void phmmUnpackMommy(UBYTE mommy, int *retStateIx, int *retQoff, 
 	int *retToff)
 /* Unpack state, query, and target offset. */
 {
 *retStateIx = (mommy&31);
 *retQoff = -((mommy&32)>>5);
 *retToff = -((mommy&64)>>6);
 }
 
 struct phmmMatrix *phmmMatrixNew(int stateCount,
     char *query, int querySize, char *target, int targetSize)
 /* Allocate all memory required for an phmmMatrix. Set up dimensions. */
 {
 int i;
 struct phmmMommy *allCells;
-int allCellSize;
+size_t allCellSize;
 int rowSize;
 int *allScores;
 struct phmmMatrix *am;
 
 AllocVar(am);
 am->query = query;
 am->target = target;
 am->querySize = querySize;
 am->targetSize = targetSize;
 am->qDim = rowSize = am->querySize + 1;
 am->tDim = am->targetSize + 1;
 am->stateCount = stateCount;
 am->stateSize = rowSize * am->tDim;
 am->stateByteSize = am->stateSize * sizeof(struct phmmMommy);
 am->states = needMem(stateCount * sizeof(struct phmmState));
 
 /* Initialize matrix of cells for each state. */
-allCellSize = stateCount * am->stateByteSize;
+allCellSize = (size_t)stateCount * (size_t)am->stateByteSize;
 am->allCells = allCells = needLargeMem(allCellSize); 
 memset(allCells, 0, allCellSize);
 for (i=0; i<stateCount; ++i)
     {
     am->states[i].cells = allCells;
     allCells += am->stateSize;
     am->states[i].stateIx = i;
     }
 
 /* Initialize two rows of scores for each state. */
 allScores = am->allScores = needMem(rowSize * 2 * stateCount * sizeof(int) );
 for (i=0; i<stateCount; ++i)
     {
     am->states[i].scores = allScores;
     allScores += rowSize;