Simplify numOverlapsPerRead(). Issue marbl#619.

sgblanch · Sep 11, 2017 · 651b37b · 651b37b
1 parent c8f3151
commit 651b37b
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Showing 3 changed files with 21 additions and 39 deletions.
diff --git a/src/stores/ovStore.C b/src/stores/ovStore.C
@@ -487,51 +487,38 @@ ovStore::numOverlapsInRange(void) {
 
 
 
-//  Fills olapsPerRead with the number of overlaps per read.
-//  olapsPerRead must be at least 'lastRead+1' in size, not just lastRead-firstRead+1.
-//  olapsPerRead is not initialized; must be cleared before calling.
+//  Returns array with the number of overlaps per read.  If numReads is more than zero,
+//  only those reads will be loaded.
 //
-void
-ovStore::numOverlapsPerRead(uint32 *olapsPerRead,
-                            uint32  firstRead,
-                            uint32  lastRead) {
-
-  off_t  originalPosition = AS_UTL_ftell(_offtFile);
-
-  AS_UTL_fseek(_offtFile, (off_t)firstRead * sizeof(ovStoreOfft), SEEK_SET);
-
-  uint64        len     = lastRead - firstRead + 1;
-
-  ovStoreOfft  *offsets = new ovStoreOfft [len];
-
-  uint64 act = AS_UTL_safeRead(_offtFile, offsets, "ovStore::numOverlapsPerRead", sizeof(ovStoreOfft), len);
-
-  if (len != act)
-    fprintf(stderr, "ovStore::numOverlapsPerRead()-- short read on offsets!  Expected len=" F_U64 " read act=" F_U64 "\n", len, act), exit(1);
+uint32 *
+ovStore::numOverlapsPerRead(uint32 numReads) {
 
-  for (uint64 i=0; i<len; i++)
-    olapsPerRead[firstRead+i] = offsets[i]._numOlaps;
+  if ((numReads == 0) && (_gkp != NULL))
+    numReads = _gkp->gkStore_getNumReads();
 
-  delete [] offsets;
+  assert(numReads > 0);
 
-  AS_UTL_fseek(_offtFile, originalPosition, SEEK_SET);
-}
+  numReads++;  //  Because read 0 doesn't exist.
 
+  uint32       *olapsPerRead = new uint32      [numReads];
+  ovStoreOfft  *offsets      = new ovStoreOfft [numReads];
 
+  off_t  originalPosition = AS_UTL_ftell(_offtFile);
 
-uint32 *
-ovStore::numOverlapsPerRead(uint32 numReads) {
+  AS_UTL_fseek(_offtFile, 0, SEEK_SET);
 
-  if ((numReads == 0) && (_gkp != NULL))
-    numReads = _gkp->gkStore_getNumReads();
+  uint64 act = AS_UTL_safeRead(_offtFile, offsets, "ovStore::numOverlapsPerRead", sizeof(ovStoreOfft), numReads);
 
-  assert(numReads > 0);
+  if (numReads != act)
+    fprintf(stderr, "ovStore::numOverlapsPerRead()-- short read on offsets!  Expected len=" F_U64 " read act=" F_U64 "\n",
+            numReads, act), exit(1);
 
-  uint32 *olapsPerRead = new uint32 [numReads+1];
+  for (uint64 i=0; i<numReads; i++)
+    olapsPerRead[i] = offsets[i]._numOlaps;
 
-  memset(olapsPerRead, 0, (numReads+1) * sizeof(uint32));
+  delete [] offsets;
 
-  numOverlapsPerRead(olapsPerRead, 1, numReads);
+  AS_UTL_fseek(_offtFile, originalPosition, SEEK_SET);
 
   return(olapsPerRead);
 }

diff --git a/src/stores/ovStore.H b/src/stores/ovStore.H
@@ -317,9 +317,6 @@ public:
 
   uint64       numOverlapsInRange(void);
 
-  void         numOverlapsPerRead(uint32 *olapsPerRead,
-                                  uint32  firstRead,
-                                  uint32  lastRead);
   uint32      *numOverlapsPerRead(uint32  numReads=0);
 
   //  Add new evalues for reads between bgnID and endID.  No checking of IDs is done, but the number

diff --git a/src/stores/ovStoreDump.C b/src/stores/ovStoreDump.C
@@ -276,9 +276,7 @@ dumpStore(ovStore                *ovlStore,
   //  bgnID, so we need to rewrite everything.
 
   if ((asCounts) && (dumpType == 0)) {
-    counts = new uint32 [endID - bgnID + 1];
-
-    ovlStore->numOverlapsPerRead(counts, bgnID, endID);
+    counts = ovlStore->numOverlapsPerRead(endID);
     ovlStore->setRange(1, 0);
 
     for (uint32 ii=bgnID; ii<=endID; ii++)