Imported Upstream version 2.2.1

1 files changed, 28 insertions, 54 deletions

diff --git a/bt2_io.cpp b/bt2_io.cpp
index d8332aa..62b37c9 100644
--- a/bt2_io.cpp
+++ b/bt2_io.cpp
@@ -57,25 +57,6 @@ void Ebwt::readIntoMemory(
 			cerr << "  About to open input files: ";
 			logTime(cerr);
 		}
-#ifdef BOWTIE_MM
-		// Initialize our primary and secondary input-stream fields
-		if(_in1 != -1) close(_in1);
-		if(_verbose || startVerbose) {
-			cerr << "Opening \"" << _in1Str.c_str() << "\"" << endl;
-		}
-		if((_in1 = open(_in1Str.c_str(), O_RDONLY)) < 0) {
-			cerr << "Could not open index file " << _in1Str.c_str() << endl;
-		}
-		if(loadSASamp) {
-			if(_in2 != -1) close(_in2);
-			if(_verbose || startVerbose) {
-				cerr << "Opening \"" << _in2Str.c_str() << "\"" << endl;
-			}
-			if((_in2 = open(_in2Str.c_str(), O_RDONLY)) < 0) {
-				cerr << "Could not open index file " << _in2Str.c_str() << endl;
-			}
-		}
-#else
 		// Initialize our primary and secondary input-stream fields
 		if(_in1 != NULL) fclose(_in1);
 		if(_verbose || startVerbose) cerr << "Opening \"" << _in1Str.c_str() << "\"" << endl;
@@ -89,7 +70,6 @@ void Ebwt::readIntoMemory(
 				cerr << "Could not open index file " << _in2Str.c_str() << endl;
 			}
 		}
-#endif
 		if(_verbose || startVerbose) {
 			cerr << "  Finished opening input files: ";
 			logTime(cerr);
@@ -98,7 +78,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 		if(_useMm /*&& !justHeader*/) {
 			const char *names[] = {_in1Str.c_str(), _in2Str.c_str()};
-			int fds[] = { _in1, _in2 };
+			int fds[] = { fileno(_in1), fileno(_in2) };
 			for(int i = 0; i < (loadSASamp ? 2 : 1); i++) {
 				if(_verbose || startVerbose) {
 					cerr << "  Memory-mapping input file " << (i+1) << ": ";
@@ -267,7 +247,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 		_plen.init((TIndexOffU*)(mmFile[0] + bytesRead), _nPat, false);
 		bytesRead += _nPat*OFF_SIZE;
-		MM_SEEK(_in1, _nPat*OFF_SIZE, SEEK_CUR);
+		fseeko(_in1, _nPat*OFF_SIZE, SEEK_CUR);
 #endif
 	} else {
 		try {
@@ -281,8 +261,8 @@ void Ebwt::readIntoMemory(
 					plen()[i] = readU<TIndexOffU>(_in1, switchEndian);
 				}
 			} else {
-				MM_READ_RET r = MM_READ(_in1, (void*)(plen()), _nPat*OFF_SIZE);
-				if(r != (MM_READ_RET)(_nPat*OFF_SIZE)) {
+				size_t r = MM_READ(_in1, (void*)(plen()), _nPat*OFF_SIZE);
+				if(r != (size_t)(_nPat*OFF_SIZE)) {
 					cerr << "Error reading _plen[] array: " << r << ", " << _nPat*OFF_SIZE << endl;
 					throw 1;
 				}
@@ -315,7 +295,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 			_rstarts.init((TIndexOffU*)(mmFile[0] + bytesRead), _nFrag*3, false);
 			bytesRead += this->_nFrag*OFF_SIZE*3;
-			MM_SEEK(_in1, this->_nFrag*OFF_SIZE*3, SEEK_CUR);
+			fseeko(_in1, this->_nFrag*OFF_SIZE*3, SEEK_CUR);
 #endif
 		} else {
 			_rstarts.init(new TIndexOffU[_nFrag*3], _nFrag*3, true);
@@ -328,8 +308,8 @@ void Ebwt::readIntoMemory(
 					this->rstarts()[i+2] = readU<TIndexOffU>(_in1, switchEndian);
 				}
 			} else {
-				MM_READ_RET r = MM_READ(_in1, (void *)rstarts(), this->_nFrag*OFF_SIZE*3);
-				if(r != (MM_READ_RET)(this->_nFrag*OFF_SIZE*3)) {
+				size_t r = MM_READ(_in1, (void *)rstarts(), this->_nFrag*OFF_SIZE*3);
+				if(r != (size_t)(this->_nFrag*OFF_SIZE*3)) {
 					cerr << "Error reading _rstarts[] array: " << r << ", " << (this->_nFrag*OFF_SIZE*3) << endl;
 					throw 1;
 				}
@@ -339,7 +319,7 @@ void Ebwt::readIntoMemory(
 		// Skip em
 		assert(rstarts() == NULL);
 		bytesRead += this->_nFrag*OFF_SIZE*3;
-		MM_SEEK(_in1, this->_nFrag*OFF_SIZE*3, SEEK_CUR);
+		fseeko(_in1, this->_nFrag*OFF_SIZE*3, SEEK_CUR);
 	}
 	
 	_ebwt.reset();
@@ -347,7 +327,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 		_ebwt.init((uint8_t*)(mmFile[0] + bytesRead), eh->_ebwtTotLen, false);
 		bytesRead += eh->_ebwtTotLen;
-		MM_SEEK(_in1, eh->_ebwtTotLen, SEEK_CUR);
+		fseek(_in1, eh->_ebwtTotLen, SEEK_CUR);
 #endif
 	} else {
 		// Allocate ebwt (big allocation)
@@ -381,7 +361,7 @@ void Ebwt::readIntoMemory(
 			char *pebwt = (char*)this->ebwt();
 
 			while (bytesLeft>0){
-				MM_READ_RET r = MM_READ(_in1, (void *)pebwt, bytesLeft);
+				size_t r = MM_READ(_in1, (void *)pebwt, bytesLeft);
 				if(MM_IS_IO_ERR(_in1,r,bytesLeft)) {
 					cerr << "Error reading _ebwt[] array: " << r << ", "
 						 << bytesLeft << gLastIOErrMsg << endl;
@@ -404,7 +384,7 @@ void Ebwt::readIntoMemory(
 #endif
 		} else {
 			// Seek past the data and wait until master is finished
-			MM_SEEK(_in1, eh->_ebwtTotLen, SEEK_CUR);
+			fseeko(_in1, eh->_ebwtTotLen, SEEK_CUR);
 #ifdef BOWTIE_SHARED_MEM
 			if(useShmem_) WAIT_SHARED(ebwt(), eh->_ebwtTotLen);
 #endif
@@ -424,7 +404,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 			_fchr.init((TIndexOffU*)(mmFile[0] + bytesRead), 5, false);
 			bytesRead += 5*OFF_SIZE;
-			MM_SEEK(_in1, 5*OFF_SIZE, SEEK_CUR);
+			fseek(_in1, 5*OFF_SIZE, SEEK_CUR);
 #endif
 		} else {
 			_fchr.init(new TIndexOffU[5], 5, true);
@@ -450,7 +430,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 				_ftab.init((TIndexOffU*)(mmFile[0] + bytesRead), eh->_ftabLen, false);
 				bytesRead += eh->_ftabLen*OFF_SIZE;
-				MM_SEEK(_in1, eh->_ftabLen*OFF_SIZE, SEEK_CUR);
+				fseeko(_in1, eh->_ftabLen*OFF_SIZE, SEEK_CUR);
 #endif
 			} else {
 				_ftab.init(new TIndexOffU[eh->_ftabLen], eh->_ftabLen, true);
@@ -458,8 +438,8 @@ void Ebwt::readIntoMemory(
 					for(TIndexOffU i = 0; i < eh->_ftabLen; i++)
 						this->ftab()[i] = readU<TIndexOffU>(_in1, switchEndian);
 				} else {
-					MM_READ_RET r = MM_READ(_in1, (void *)ftab(), eh->_ftabLen*OFF_SIZE);
-					if(r != (MM_READ_RET)(eh->_ftabLen*OFF_SIZE)) {
+					size_t r = MM_READ(_in1, (void *)ftab(), eh->_ftabLen*OFF_SIZE);
+					if(r != (size_t)(eh->_ftabLen*OFF_SIZE)) {
 						cerr << "Error reading _ftab[] array: " << r << ", " << (eh->_ftabLen*OFF_SIZE) << endl;
 						throw 1;
 					}
@@ -480,7 +460,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 				_eftab.init((TIndexOffU*)(mmFile[0] + bytesRead), eh->_eftabLen, false);
 				bytesRead += eh->_eftabLen*OFF_SIZE;
-				MM_SEEK(_in1, eh->_eftabLen*OFF_SIZE, SEEK_CUR);
+				fseeko(_in1, eh->_eftabLen*OFF_SIZE, SEEK_CUR);
 #endif
 			} else {
 				_eftab.init(new TIndexOffU[eh->_eftabLen], eh->_eftabLen, true);
@@ -488,8 +468,8 @@ void Ebwt::readIntoMemory(
 					for(TIndexOffU i = 0; i < eh->_eftabLen; i++)
 						this->eftab()[i] = readU<TIndexOffU>(_in1, switchEndian);
 				} else {
-					MM_READ_RET r = MM_READ(_in1, (void *)this->eftab(), eh->_eftabLen*OFF_SIZE);
-					if(r != (MM_READ_RET)(eh->_eftabLen*OFF_SIZE)) {
+					size_t r = MM_READ(_in1, (void *)this->eftab(), eh->_eftabLen*OFF_SIZE);
+					if(r != (size_t)(eh->_eftabLen*OFF_SIZE)) {
 						cerr << "Error reading _eftab[] array: " << r << ", " << (eh->_eftabLen*OFF_SIZE) << endl;
 						throw 1;
 					}
@@ -507,10 +487,10 @@ void Ebwt::readIntoMemory(
 			assert(eftab() == NULL);
 			// Skip ftab
 			bytesRead += eh->_ftabLen*OFF_SIZE;
-			MM_SEEK(_in1, eh->_ftabLen*OFF_SIZE, SEEK_CUR);
+			fseeko(_in1, eh->_ftabLen*OFF_SIZE, SEEK_CUR);
 			// Skip eftab
 			bytesRead += eh->_eftabLen*OFF_SIZE;
-			MM_SEEK(_in1, eh->_eftabLen*OFF_SIZE, SEEK_CUR);
+			fseeko(_in1, eh->_eftabLen*OFF_SIZE, SEEK_CUR);
 		}
 	} catch(bad_alloc& e) {
 		cerr << "Out of memory allocating fchr[], ftab[] or eftab[] arrays for the Bowtie index." << endl
@@ -523,7 +503,7 @@ void Ebwt::readIntoMemory(
 	if(loadNames) {
 		while(true) {
 			char c = '\0';
-			if(MM_READ(_in1, (void *)(&c), (size_t)1) != (MM_READ_RET)1) break;
+			if(MM_READ(_in1, (void *)(&c), (size_t)1) != (size_t)1) break;
 			bytesRead++;
 			if(c == '\0') break;
 			else if(c == '\n') {
@@ -582,8 +562,8 @@ void Ebwt::readIntoMemory(
 					}
 					for(TIndexOffU i = 0; i < offsLen; i += blockMaxSzU) {
 						TIndexOffU block = min<TIndexOffU>(blockMaxSzU, offsLen - i);
-						MM_READ_RET r = MM_READ(_in2, (void *)buf, block << (OFF_SIZE/4 + 1));
-						if(r != (MM_READ_RET)(block << (OFF_SIZE/4 + 1))) {
+						size_t r = MM_READ(_in2, (void *)buf, block << (OFF_SIZE/4 + 1));
+						if(r != (size_t)(block << (OFF_SIZE/4 + 1))) {
 							cerr << "Error reading block of _offs[] array: " << r << ", " << (block << (OFF_SIZE/4 + 1)) << endl;
 							throw 1;
 						}
@@ -603,9 +583,7 @@ void Ebwt::readIntoMemory(
 #ifdef BOWTIE_MM
 						_offs.init((TIndexOffU*)(mmFile[1] + bytesRead), offsLen, false);
 						bytesRead += offsSz;
-						// Argument to lseek can be 64 bits if compiled with
-						// _FILE_OFFSET_BITS
-						MM_SEEK(_in2, offsSz, SEEK_CUR);
+						fseeko(_in2, offsSz, SEEK_CUR);
 #endif
 					} else {
 						// Workaround for small-index mode where MM_READ may
@@ -615,7 +593,7 @@ void Ebwt::readIntoMemory(
 						char *offs = (char *)this->offs();
 
 						while(bytesLeft > 0) {
-							MM_READ_RET r = MM_READ(_in2, (void*)offs, bytesLeft);
+							size_t r = MM_READ(_in2, (void*)offs, bytesLeft);
 							if(MM_IS_IO_ERR(_in2,r,bytesLeft)) {
 								cerr << "Error reading block of _offs[] array: "
 								     << r << ", " << bytesLeft << gLastIOErrMsg << endl;
@@ -631,7 +609,7 @@ void Ebwt::readIntoMemory(
 #endif
 			} else {
 				// Not the shmem leader
-				MM_SEEK(_in2, offsLenSampled*OFF_SIZE, SEEK_CUR);
+				fseeko(_in2, offsLenSampled*OFF_SIZE, SEEK_CUR);
 #ifdef BOWTIE_SHARED_MEM				
 				if(useShmem_) WAIT_SHARED(offs(), offsLenSampled*OFF_SIZE);
 #endif
@@ -650,12 +628,8 @@ done: // Exit hatch for both justHeader and !justHeader
 	
 	// Be kind
 	if(deleteEh) delete eh;
-#ifdef BOWTIE_MM
-	MM_SEEK(_in1, 0, SEEK_SET);
-	MM_SEEK(_in2, 0, SEEK_SET);
-#else
-	rewind(_in1); rewind(_in2);
-#endif
+	rewind(_in1);
+	rewind(_in2);
 }
 
 /**