Fixing warnings

color_dec.cpp

@@ -184,12 +184,10 @@ void decodeHit(
 
 	// Successive columns examine successive alignment positions
 	int omin = INT_MAX, t = 0;
-	int lastOmin = INT_MAX;
 	for(size_t c = readi; c < readf; c++) {
 		const int readc = (int)read[c];
 		assert_leq(readc, 4);
 		assert_geq(readc, 0);
-		lastOmin = omin;
 		omin = INT_MAX;
 		// t <- index of column in dynamic programming table
 		t = c - readi + 1;

ref_read.cpp

@@ -192,14 +192,11 @@ void reverseRefRecords(const vector<RefRecord>& src,
 			}
 			if(src[i].off) cur.push_back(RefRecord(src[i].off, 0, first));
 		}
-		bool mergedLast;
 		for(int i = 0; i < (int)cur.size(); i++) {
-			mergedLast = false;
 			assert(cur[i].off == 0 || cur[i].len == 0);
 			if(i < (int)cur.size()-1 && cur[i].off != 0 && !cur[i+1].first) {
 				dst.push_back(RefRecord(cur[i].off, cur[i+1].len, cur[i].first));
 				i++;
-				mergedLast = true;
 			} else {
 				dst.push_back(cur[i]);
 			}

sam.cpp

@@ -147,12 +147,12 @@ void SAMHitSink::appendAligned(ostream& ss,
 	int run = 0;
 	ss << "\tMD:Z:";
 	const FixedBitset<1024> *mms = &h.mms;
-	const String<Dna5>* pat = &h.patSeq;
+	ASSERT_ONLY(const String<Dna5>* pat = &h.patSeq);
 	const vector<char>* refcs = &h.refcs;
 	if(h.color && false) {
 		// Disabled: print MD:Z string w/r/t to colors, not letters
 		mms = &h.cmms;
-		pat = &h.colSeq;
+		ASSERT_ONLY(pat = &h.colSeq);
 		assert_eq(length(h.colSeq), len+1);
 		len = length(h.colSeq);
 		refcs = &h.crefcs;

search_23mm_phase3.c

@@ -24,7 +24,7 @@
 		}
 
 		// Try a half-and-half on the forward read
-		bool gaveUp = false;
+		//bool gaveUp = false;
 		bthh3.setQuery(patsrc->bufa());
 		// Processing the forward pattern with the forward index;
 		// s3 ("lo") half is on the right
@@ -34,9 +34,9 @@
 		              two ? s  : s3,
 		              s);
 		done = bthh3.backtrack();
-		if(bthh3.numBacktracks() == bthh3.maxBacktracks()) {
-			gaveUp = true;
-		}
+		//if(bthh3.numBacktracks() == bthh3.maxBacktracks()) {
+			//gaveUp = true;
+		//}
 		bthh3.resetNumBacktracks();
 		if(done) {
 			continue;
@@ -45,7 +45,7 @@
 
 	if(!norc) {
 		// Try a half-and-half on the reverse complement read
-		bool gaveUp = false;
+		//bool gaveUp = false;
 		params.setFw(false);
 		bthh3.setQuery(patsrc->bufa());
 		// Processing the forward pattern with the forward index;
@@ -56,9 +56,9 @@
 					  two ? s  : s5,
 					  s);
 		bool done = bthh3.backtrack();
-		if(bthh3.numBacktracks() == bthh3.maxBacktracks()) {
-			gaveUp = true;
-		}
+		//if(bthh3.numBacktracks() == bthh3.maxBacktracks()) {
+		//	gaveUp = true;
+		//}
 		bthh3.resetNumBacktracks();
 		if(done) {
 			continue;

search_seeded_phase3.c

@@ -61,7 +61,7 @@
 		// try the final case that might apply to the reverse
 		// complement pattern: 1 mismatch in each of the 3' and 5'
 		// halves of the seed.
-		bool gaveUp = false;
+		//bool gaveUp = false;
 		if(seedMms >= 2) {
 			btr23.setQuery(patsrc->bufa());
 			// Set up special seed bounds
@@ -79,9 +79,9 @@
 							  s);                      // 3revOff
 			}
 			done = btr23.backtrack();
-			if(btr23.numBacktracks() == btr23.maxBacktracks()) {
-				gaveUp = true;
-			}
+			//if(btr23.numBacktracks() == btr23.maxBacktracks()) {
+			//	gaveUp = true;
+			//}
 			if(done) {
 				DONEMASK_SET(patid);
 				btr23.resetNumBacktracks();

search_seeded_phase4.c

@@ -63,7 +63,7 @@
 		// try the final case that might apply to the forward
 		// pattern: 1 mismatch in each of the 3' and 5' halves of
 		// the seed.
-		bool gaveUp = false;
+		//bool gaveUp = false;
 		if(seedMms >= 2) {
 			btf24.setQuery(patsrc->bufa());
 			// Set up seed bounds
@@ -81,9 +81,9 @@
 							  s);                      // 3revOff
 			}
 			done = btf24.backtrack();
-			if(btf24.numBacktracks() == btf24.maxBacktracks()) {
-				gaveUp = true;
-			}
+			//if(btf24.numBacktracks() == btf24.maxBacktracks()) {
+			//	gaveUp = true;
+			//}
 			if(done) {
 				btf24.resetNumBacktracks();
 				continue;