fixing misspelling and some bugs

btypes.h

@@ -8,7 +8,7 @@
 #define OFF_LEN_MASK 0xc000000000000000
 #define LS_SIZE 0x100000000000000
 #define OFF_SIZE 8
-#define CACHE_WRAPER_BIT 0x8000000000000000
+#define CACHE_WRAPPER_BIT 0x8000000000000000
 
 typedef uint64_t TIndexOffU;
 typedef int64_t TIndexOff;
@@ -18,7 +18,7 @@ typedef int64_t TIndexOff;
 #define OFF_LEN_MASK 0xc0000000
 #define LS_SIZE 0x10000000
 #define OFF_SIZE 4
-#define CACHE_WRAPER_BIT 0x80000000
+#define CACHE_WRAPPER_BIT 0x80000000
 
 typedef uint32_t TIndexOffU;
 typedef int TIndexOff;

ebwt_search_backtrack.h

@@ -1783,7 +1783,7 @@ class GreedyDFSRangeSource {
 	char                _trimc;
 	uint32_t            _seed;
 #ifndef NDEBUG
-	std::set<int64_t>   allTops_;
+	std::set<TIndexOff> allTops_;
 #endif
 };
 
@@ -2340,7 +2340,7 @@ class EbwtRangeSource : public RangeSource {
 				curRange_.ebwt    = ebwt_;
 				this->foundRange  = true;
 	#ifndef NDEBUG
-				int64_t top2 = (int64_t)br->top_;
+				TIndexOff top2 = (TIndexOff)br->top_;
 				top2++; // ensure it's not 0
 				if(ebwt_->fw()) top2 = -top2;
 				assert(allTops_.find(top2) == allTops_.end());
@@ -2627,7 +2627,7 @@ class EbwtRangeSource : public RangeSource {
 	// Object encapsulating metrics
 	AlignerMetrics*     metrics_;
 #ifndef NDEBUG
-	std::set<int64_t>   allTops_;
+	std::set<TIndexOff> allTops_;
 #endif
 };
 
@@ -3058,7 +3058,7 @@ class EbwtSeededRangeSourceDriver : public RangeSourceDriver<EbwtRangeSource> {
 			// top offset
 			assert_gt(range().bot, range().top);
 			assert(range().ebwt != NULL);
-			TIndexOffU top = (TIndexOffU)range().top;
+			TIndexOff top = (TIndexOff)range().top;
 			top++; // ensure it's not 0
 			if(!range().ebwt->fw()) top = -top;
 			assert(allTops_.find(top) == allTops_.end());

range_cache.h

@@ -63,7 +63,7 @@ class RangeCacheMemPool {
 	TIndexOffU alloc(TIndexOffU numElts) {
 		assert_gt(numElts, 0);
 		assert_leq(occ_, lim_);
-		if(occ_ + numElts > lim_ || numElts >= CACHE_WRAPER_BIT) {
+		if(occ_ + numElts > lim_ || numElts >= CACHE_WRAPPER_BIT) {
 			return RANGE_CACHE_BAD_ALLOC;
 		}
 		assert_gt(lim_, 0);
@@ -96,7 +96,7 @@ class RangeCacheMemPool {
 		assert_lt(off, lim_);
 		assert(allocs_.find(off) != allocs_.end());
 		TIndexOffU *ret = buf_ + off;
-		assert_neq(CACHE_WRAPER_BIT, ret[0]);
+		assert_neq(CACHE_WRAPPER_BIT, ret[0]);
 		assert_neq(OFF_MASK, ret[0]);
 		return ret;
 	}
@@ -153,12 +153,12 @@ class RangeCacheEntry {
 		top_ = top;
 		ebwt_ = ebwt;
 		TIndexOffU *ents = pool.get(ent);
-		assert_neq(CACHE_WRAPER_BIT, ents[0]);
+		assert_neq(CACHE_WRAPPER_BIT, ents[0]);
 		// Is hi bit set?
-		if((ents[0] & CACHE_WRAPER_BIT) != 0) {
+		if((ents[0] & CACHE_WRAPPER_BIT) != 0) {
 			// If so, the target is a wrapper and the non-hi bits
 			// contain the # jumps
-			jumps_ = (ents[0] & ~CACHE_WRAPER_BIT);
+			jumps_ = (ents[0] & ~CACHE_WRAPPER_BIT);
 			assert_gt(jumps_, 0);
 			assert_leq(jumps_, ebwt_->_eh._len);
 			// Get the target entry
@@ -197,7 +197,7 @@ class RangeCacheEntry {
 		jumps_ = jumps;
 		TIndexOffU *ents = pool.get(ent);
 		// Must not be a wrapper
-		assert_eq(0, ents[0] & CACHE_WRAPER_BIT);
+		assert_eq(0, ents[0] & CACHE_WRAPPER_BIT);
 		// Get the length from the target entry
 		len_ = ents[0];
 		assert_gt(len_, 0);
@@ -397,8 +397,8 @@ class RangeCache {
 			TIndexOffU jumps = 0;
 			assert_leq(top, ebwt_->_eh._len);
 			TIndexOffU *ents = pool_.get(idx);
-			if((ents[0] & CACHE_WRAPER_BIT) != 0) {
-				jumps = ents[0] & ~CACHE_WRAPER_BIT;
+			if((ents[0] & CACHE_WRAPPER_BIT) != 0) {
+				jumps = ents[0] & ~CACHE_WRAPPER_BIT;
 				assert_leq(jumps, ebwt_->_eh._len);
 				idx = ents[1];
 				ents = pool_.get(idx);
@@ -453,11 +453,11 @@ class RangeCache {
 					// entry already, so use that
 					TIndexOffU idx = itr->second;
 					TIndexOffU *ents = pool_.get(idx);
-					if((ents[0] & CACHE_WRAPER_BIT) != 0) {
+					if((ents[0] & CACHE_WRAPPER_BIT) != 0) {
 						// The cache entry we found was a wrapper; make
 						// a new wrapper that points to that wrapper's
 						// target, with the appropriate number of jumps
-						jumps += (ents[0] & ~CACHE_WRAPER_BIT);
+						jumps += (ents[0] & ~CACHE_WRAPPER_BIT);
 						idx = ents[1];
 					}
 					// Allocate a new wrapper
@@ -467,7 +467,7 @@ class RangeCache {
 						// now populate it and install it in map_
 						TIndexOffU *newent = pool_.get(newentIdx); // get ptr to it
 						assert_eq(0, newent[0]);
-						newent[0] = CACHE_WRAPER_BIT | jumps; // set jumps
+						newent[0] = CACHE_WRAPPER_BIT | jumps; // set jumps
 						newent[1] = idx;                // set target
 						assert(map_.find(top) == map_.end());
 						map_[top] = newentIdx;
@@ -498,7 +498,7 @@ class RangeCache {
 			assert_eq(0, newent[0]);
 			// Store cache-range length in first word
 			newent[0] = spread;
-			assert_lt(newent[0], CACHE_WRAPER_BIT);
+			assert_lt(newent[0], CACHE_WRAPPER_BIT);
 			assert_eq(spread, newent[0]);
 			TIndexOffU entTop = top;
 			TIndexOffU jumps = 0;
@@ -519,7 +519,7 @@ class RangeCache {
 				if(wrapentIdx != RANGE_CACHE_BAD_ALLOC) {
 					TIndexOffU *wrapent = pool_.get(wrapentIdx);
 					assert_eq(0, wrapent[0]);
-					wrapent[0] = CACHE_WRAPER_BIT | jumps;
+					wrapent[0] = CACHE_WRAPPER_BIT | jumps;
 					wrapent[1] = newentIdx;
 					assert(map_.find(top) == map_.end());
 					map_[top] = wrapentIdx;

range_source.h

@@ -1729,7 +1729,7 @@ class RangeSourceDriver {
 			// top offset
 			assert_gt(range().bot, range().top);
 			assert(range().ebwt != NULL);
-			int64_t top = (int64_t)range().top;
+			TIndexOff top = (TIndexOff)range().top;
 			top++; // ensure it's not 0
 			if(!range().ebwt->fw()) top = -top;
 			assert(allTops_.find(top) == allTops_.end());
@@ -1787,7 +1787,7 @@ class RangeSourceDriver {
 protected:
 
 #ifndef NDEBUG
-	std::set<int64_t> allTops_;
+	std::set<TIndexOff> allTops_;
 #endif
 };
 
@@ -1910,7 +1910,7 @@ class SingleRangeSourceDriver : public RangeSourceDriver<TRangeSource> {
 			// top offset
 			assert_gt(range().bot, range().top);
 			assert(range().ebwt != NULL);
-			int64_t top = (int64_t)range().top;
+			TIndexOff top = (TIndexOff)range().top;
 			top++; // ensure it's not 0
 			if(!range().ebwt->fw()) top = -top;
 			assert(allTops_.find(top) == allTops_.end());
@@ -1965,7 +1965,7 @@ class SingleRangeSourceDriver : public RangeSourceDriver<TRangeSource> {
 	TRangeSource*                   rs_; // delete this in destructor
 	bool ebwtFw_;
 	PathManager pm_;
-	ASSERT_ONLY(std::set<int64_t> allTops_);
+	ASSERT_ONLY(std::set<TIndexOff> allTops_);
 };
 
 /**
@@ -2378,7 +2378,7 @@ class CostAwareRangeSourceDriver : public RangeSourceDriver<TRangeSource> {
 		// top offset
 		assert_gt(r->bot, r->top);
 		assert(r->ebwt != NULL);
-		int64_t top = (int64_t)r->top;
+		TIndexOff top = (TIndexOff)r->top;
 		top++; // ensure it's not 0
 		if(!r->ebwt->fw()) top = -top;
 		if(r->fw) {
@@ -2549,7 +2549,7 @@ class CostAwareRangeSourceDriver : public RangeSourceDriver<TRangeSource> {
 	bool verbose_;
 	bool quiet_;
 	bool mixesReads_;
-	ASSERT_ONLY(std::set<int64_t> allTopsRc_);
+	ASSERT_ONLY(std::set<TIndexOff> allTopsRc_);
 };
 
 #endif /* RANGE_SOURCE_H_ */