Fix additional warnings

Makefile

@@ -15,8 +15,7 @@ EXTRA_CFLAGS =
 EXTRA_CXXFLAGS =
 CFLAGS += $(EXTRA_CFLAGS)
 CXXFLAGS += $(EXTRA_CXXFLAGS)
-WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder \
-		-Wno-unused-private-field
+WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder
 
 RELEASE_DEPENDENCIES = $(if $(RELEASE_BUILD),static-libs)
 

aligner_0mm.h

@@ -26,7 +26,6 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 public:
 	UnpairedExactAlignerV1Factory(
 			Ebwt& ebwtFw,
-			Ebwt* ebwtBw,
 			bool doFw,
 			bool doRc,
 			HitSink& sink,
@@ -45,7 +44,6 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
-			ebwtBw_(ebwtBw),
 			doFw_(doFw), doRc_(doRc),
 			sink_(sink),
 			sinkPtFactory_(sinkPtFactory),
@@ -117,7 +115,6 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 
 private:
 	Ebwt& ebwtFw_;
-	Ebwt* ebwtBw_;
 	bool doFw_;
 	bool doRc_;
 	HitSink& sink_;
@@ -146,7 +143,6 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 public:
 	PairedExactAlignerV1Factory(
 			Ebwt& ebwtFw,
-			Ebwt* ebwtBw,
 			bool doFw,
 			bool doRc,
 			bool v1,
@@ -345,7 +341,6 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 
 private:
 	Ebwt& ebwtFw_;
-	Ebwt* ebwtBw_;
 	bool doFw_;
 	bool doRc_;
 	bool v1_;

ebwt_search.cpp

@@ -1243,7 +1243,6 @@ static void exactSearchWorkerStateful(void *vp) {
 	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 	UnpairedExactAlignerV1Factory alSEfact(
 			ebwt,
-			NULL,
 			!nofw,
 			!norc,
 			_sink,
@@ -1263,7 +1262,6 @@ static void exactSearchWorkerStateful(void *vp) {
 			seed);
 	PairedExactAlignerV1Factory alPEfact(
 			ebwt,
-			NULL,
 			!nofw,
 			!norc,
 			useV1,
@@ -3209,7 +3207,7 @@ static void driver(const char * type,
 					outBatchSz, partitionSz);
 		} else if(outType == OUTPUT_SAM) {
 			SAMHitSink *sam = new SAMHitSink(
-				*fout, 1,
+				*fout,
 				fullRef, samNoQnameTrunc,
 				dumpAlBase,
 				dumpUnalBase,

sam.h

@@ -40,7 +40,6 @@ class SAMHitSink : public HitSink {
 	 */
 	SAMHitSink(
 		OutFileBuf& out,
-		int offBase,
 		bool fullRef,
 		bool noQnameTrunc,
 		const std::string& dumpAl,
@@ -63,7 +62,6 @@ class SAMHitSink : public HitSink {
 			nthreads,
 			perThreadBufSize,
 			reorder),
-		offBase_(offBase),
 		fullRef_(fullRef),
 		noQnameTrunc_(noQnameTrunc) { }
 
@@ -117,9 +115,6 @@ class SAMHitSink : public HitSink {
 	}
 
 private:
-	int  offBase_;        /// Add this to reference offsets before outputting.
-	                      /// (An easy way to make things 1-based instead of
-	                      /// 0-based)
 	bool fullRef_;        /// print full reference name, not just up to whitespace
 	bool noQnameTrunc_;   /// true -> don't truncate QNAME at first whitespace
 };

shmem.h

@@ -102,7 +102,7 @@ bool allocSharedMem(std::string fname,
 			cerr << "shmctl returned " << ret << " for IPC_STAT and errno is " << errno << endl;
 			throw 1;
 		}
-		if(ds.shm_segsz != shmemLen) {
+		if(ds.shm_segsz != (int)shmemLen) {
 			cerr << "Warning: shared-memory chunk's segment size (" << ds.shm_segsz
 				 << ") doesn't match expected size (" << shmemLen << ")" << endl
 				 << "Deleting old shared memory block and trying again." << endl;