diff --git a/annot.cpp b/annot.cpp
index 4db3282..648689f 100644
--- a/annot.cpp
+++ b/annot.cpp
@@ -17,7 +17,7 @@ void AnnotationMap::parse() {
 	ifstream in(fname_);
 	if(!in.good() && in.is_open()) {
 		cerr << "Could not open annotation file " << fname_ << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	while(in.peek() != EOF) {
 		U32Pair pos;
diff --git a/bitset.h b/bitset.h
index 70cd6f1..108c79e 100644
--- a/bitset.h
+++ b/bitset.h
@@ -34,7 +34,7 @@ bitsetRealloc(uint32_t& sz, uint32_t* words, const char *errmsg = NULL) {
 			// Output given error message
 			std::cerr << errmsg;
 		}
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if(oldsz > 0) {
 		// Move old values into new array
@@ -65,7 +65,7 @@ class SyncBitset {
 			if(_errmsg != NULL) {
 				std::cerr << _errmsg;
 			}
-			throw std::runtime_error("");
+			throw 1;
 		}
 		assert(_words != NULL);
 		memset(_words, 0, nwords * 4 /* words to bytes */);
@@ -174,7 +174,7 @@ class Bitset {
 			if(_errmsg != NULL) {
 				std::cerr << _errmsg;
 			}
-			throw std::runtime_error("");
+			throw 1;
 		}
 		assert(_words != NULL);
 		memset(_words, 0, nwords * 4);
diff --git a/blockwise_sa.h b/blockwise_sa.h
index 188d4f3..6891f24 100644
--- a/blockwise_sa.h
+++ b/blockwise_sa.h
@@ -233,7 +233,7 @@ class SillyBlockwiseDnaSA : public InorderBlockwiseSA<TStr> {
 					cerr << "Out of memory creating suffix array in "
 					     << "SillyBlockwiseDnaSA::SillyBlockwiseDnaSA()"
 					     << " at " << __FILE__ << ":" << __LINE__ << endl;
-					std::runtime_error("");
+					throw 1;
 				}
 			}
 			assert_eq(length(this->text())+1, length(_sa));
@@ -482,7 +482,7 @@ void KarkkainenBlockwiseSA<TStr>::buildSamples() {
 				cerr << "Could not allocate sample suffix container of " << (numSamples * 4) << " bytes." << endl
 				     << "Please try using a smaller number of blocks by specifying a larger --bmax or" << endl
 				     << "a smaller --bmaxdivn" << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 		}
 	}
@@ -531,7 +531,7 @@ void KarkkainenBlockwiseSA<TStr>::buildSamples() {
 				cerr << "Could not allocate sizes, representatives (" << ((numBuckets*8)>>10) << " KB) for blocks." << endl
 				     << "Please try using a smaller number of blocks by specifying a larger --bmax or a" << endl
 				     << "smaller --bmaxdivn." << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 		}
 		// Iterate through every suffix in the text, determine which
@@ -844,7 +844,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBlock() {
 				cerr << "Could not allocate a master suffix-array block of " << ((len+1) * 4) << " bytes" << endl
 				     << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
 				     << "a larger --bmaxdivn" << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 		}
 	} else {
@@ -860,7 +860,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBlock() {
 				cerr << "Could not allocate a suffix-array block of " << ((this->bucketSz()+1) * 4) << " bytes" << endl;
 				cerr << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
 				     << "a larger --bmaxdivn" << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 		}
 		// Select upper and lower bounds from _sampleSuffs[] and
@@ -899,7 +899,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBlock() {
 				cerr << "Could not allocate a z-array of " << (_dcV * 4) << " bytes" << endl;
 				cerr << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
 				     << "a larger --bmaxdivn" << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 		}
 
@@ -942,7 +942,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBlock() {
 						cerr << "Could not append element to block of " << ((length(bucket)) * 4) << " bytes" << endl;
 						cerr << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
 						     << "a larger --bmaxdivn" << endl;
-						std::runtime_error("");
+						throw 1;
 					}
 				}
 				// Not necessarily true; we allow overflowing buckets
diff --git a/bowtie_inspect.cpp b/bowtie_inspect.cpp
index 21a5796..746e9d6 100644
--- a/bowtie_inspect.cpp
+++ b/bowtie_inspect.cpp
@@ -16,13 +16,17 @@ static int verbose     = 0;  // be talkative
 static int names_only  = 0;  // just print the sequence names in the index
 static int across      = 60; // number of characters across in FASTA output
 
-static const char *short_options = "vh?na:";
+static const char *short_options = "vhna:";
 
-static const int ARG_VERSION = 256;
+enum {
+	ARG_VERSION = 256,
+	ARG_USAGE
+};
 
 static struct option long_options[] = {
 	{(char*)"verbose", no_argument,       0, 'v'},
 	{(char*)"version", no_argument,       0, ARG_VERSION},
+	{(char*)"usage",   no_argument,       0, ARG_USAGE},
 	{(char*)"names",   no_argument,       0, 'n'},
 	{(char*)"help",    no_argument,       0, 'h'},
 	{(char*)"across",  required_argument, 0, 'a'},
@@ -41,6 +45,7 @@ static void printUsage(ostream& out) {
 	<< "  -n/--names         Print reference sequence names only" << endl
 	<< "  -v/--verbose       Verbose output (for debugging)" << endl
 	<< "  -h/--help          print detailed description of tool and its options" << endl
+	<< "  --help             print this usage message" << endl
 	;
 }
 
@@ -108,13 +113,13 @@ static int parseInt(int lower, const char *errmsg) {
 		if (l < lower) {
 			cerr << errmsg << endl;
 			printUsage(cerr);
-			throw std::runtime_error("");
+			throw 1;
 		}
 		return (int32_t)l;
 	}
 	cerr << errmsg << endl;
 	printUsage(cerr);
-	throw std::runtime_error("");
+	throw 1;
 	return -1;
 }
 
@@ -122,19 +127,23 @@ static int parseInt(int lower, const char *errmsg) {
  * Read command-line arguments
  */
 static void parseOptions(int argc, char **argv) {
-    int option_index = 0;
+	int option_index = 0;
 	int next_option;
 	do {
 		next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
 		switch (next_option) {
-	   		case 'h':
-	   		case '?': {
-	   			printLongUsage(cout);
-	   			throw std::runtime_error("");
-	   			break;
-	   		}
-	   		case 'v': verbose = true; break;
-	   		case ARG_VERSION: showVersion = true; break;
+			case ARG_USAGE: {
+				printUsage(cout);
+				throw 0;
+				break;
+			}
+			case 'h': {
+				printLongUsage(cout);
+				throw 0;
+				break;
+			}
+			case 'v': verbose = true; break;
+			case ARG_VERSION: showVersion = true; break;
 			case 'n': names_only = true; break;
 			case 'a': across = parseInt(-1, "-a/--across arg must be at least 1"); break;
 			case -1: break; /* Done with options. */
@@ -142,9 +151,8 @@ static void parseOptions(int argc, char **argv) {
 				if (long_options[option_index].flag != 0)
 					break;
 			default:
-				cerr << "Unknown option: " << (char)next_option << endl;
 				printUsage(cerr);
-				throw std::runtime_error("");
+				throw 1;
 		}
 	} while(next_option != -1);
 }
@@ -322,6 +330,16 @@ int main(int argc, char **argv) {
 		driver(ebwtFile, query);
 		return 0;
 	} catch(std::exception& e) {
+		cerr << "Command: ";
+		for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+		cerr << endl;
 		return 1;
+	} catch(int e) {
+		if(e != 0) {
+			cerr << "Command: ";
+			for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+			cerr << endl;
+		}
+		return e;
 	}
 }
diff --git a/ebwt.cpp b/ebwt.cpp
index de2306e..4d1fa46 100644
--- a/ebwt.cpp
+++ b/ebwt.cpp
@@ -59,7 +59,7 @@ string adjustEbwtBase(const string& cmdline,
 	}
 	if(!in.is_open()) {
 		cerr << "Could not locate a Bowtie index corresponding to basename \"" << ebwtFileBase << "\"" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	return str;
 }
diff --git a/ebwt.h b/ebwt.h
index aba36d2..bcfab79 100644
--- a/ebwt.h
+++ b/ebwt.h
@@ -414,14 +414,14 @@ class Ebwt {
 			cerr << "Could not open index file for writing: \"" << _in1Str << "\"" << endl
 			     << "Please make sure the directory exists and that permissions allow writing by" << endl
 			     << "Bowtie." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		ofstream fout2(_in2Str.c_str(), ios::binary);
 		if(!fout2.good()) {
 			cerr << "Could not open index file for writing: \"" << _in2Str << "\"" << endl
 			     << "Please make sure the directory exists and that permissions allow writing by" << endl
 			     << "Bowtie." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		// Build
 		initFromVector(is,
@@ -458,7 +458,7 @@ class Ebwt {
 		}
 		if(err) {
 			cerr << "Please check if there is a problem with the disk or if disk is full." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		// Reopen as input streams
 		VMSG_NL("Re-opening _in1 and _in2 as input streams");
@@ -542,7 +542,7 @@ class Ebwt {
 				cerr << "If this computer has more than 4 GB of memory, try using a 64-bit executable;" << endl
 				     << "this executable is 32-bit." << endl;
 			}
-			throw std::runtime_error("");
+			throw 1;
 		}
 		// Succesfully obtained joined reference string
 		assert_geq(length(s), jlen);
@@ -579,7 +579,7 @@ class Ebwt {
 					cerr << "If this computer has more than 4 GB of memory, try using a 64-bit executable;" << endl
 						 << "this executable is 32-bit." << endl;
 				}
-				throw std::runtime_error("");
+				throw 1;
 			}
 			if((iter % 6) == 5 && dcv < 4096 && dcv != 0) {
 				dcv <<= 1; // double difference-cover period
@@ -629,7 +629,7 @@ class Ebwt {
 				out1.flush(); out2.flush();
 				if(out1.fail() || out2.fail()) {
 					cerr << "An error occurred writing the index to disk.  Please check if the disk is full." << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				break;
 			} catch(bad_alloc& e) {
@@ -638,7 +638,7 @@ class Ebwt {
 				} else {
 					cerr << "Out of memory while constructing suffix array.  Please try using a smaller" << endl
 						 << "number of blocks by specifying a smaller --bmax or a larger --bmaxdivn" << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 			}
 			first = false;
@@ -653,7 +653,7 @@ class Ebwt {
 		out1.flush(); out2.flush();
 		if(out1.fail() || out2.fail()) {
 			cerr << "An error occurred writing the index to disk.  Please check if the disk is full." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		VMSG_NL("Returning from initFromVector");
 	}
@@ -2730,14 +2730,14 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 				if (stat(names[i], &sbuf) == -1) {
 					perror("stat");
 					cerr << "Error: Could not stat index file " << names[i] << " prior to memory-mapping" << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				mmFile[i] = (char*)mmap((void *)0, sbuf.st_size,
 										PROT_READ, MAP_SHARED, fds[i], 0);
 				if(mmFile == (void *)(-1)) {
 					perror("mmap");
 					cerr << "Error: Could not memory-map the index file " << names[i] << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				if(mmSweep) {
 					int sum = 0;
@@ -2793,7 +2793,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 	// or we might be setting up a race condition with other processes.
 	if(switchEndian && _useMm) {
 		cerr << "Error: Can't use memory-mapped files when the index is the opposite endianness" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	// Reads header entries one by one from primary stream
@@ -2860,7 +2860,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 	// into their own memory spaces.
 	if(_useMm && (offRateDiff || isaRateDiff)) {
 		cerr << "Error: Can't use memory-mapped files when the offrate or isarate is overridden" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	// Read nPat from primary stream
@@ -2894,7 +2894,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 				MM_READ_RET r = MM_READ(_in1, (void*)this->_plen, this->_nPat*4);
 				if(r != (MM_READ_RET)(this->_nPat*4)) {
 					cerr << "Error reading _plen[] array: " << r << ", " << (this->_nPat*4) << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 			}
 		} catch(bad_alloc& e) {
@@ -2939,7 +2939,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 			MM_READ_RET r = MM_READ(_in1, (void *)this->_rstarts, this->_nFrag*4*3);
 			if(r != (MM_READ_RET)(this->_nFrag*4*3)) {
 				cerr << "Error reading _rstarts[] array: " << r << ", " << (this->_nFrag*4*3) << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 	}
@@ -2972,7 +2972,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 					 << "Bowtie without the -z option, try adding the -z option to save memory.  If the" << endl
 					 << "-z option does not solve the problem, please try again on a computer with more" << endl
 					 << "memory." << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 		if(shmemLeader) {
@@ -2980,7 +2980,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 			MM_READ_RET r = MM_READ(_in1, (void *)this->_ebwt, eh->_ebwtTotLen);
 			if(r != (MM_READ_RET)eh->_ebwtTotLen) {
 				cerr << "Error reading _ebwt[] array: " << r << ", " << (eh->_ebwtTotLen) << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			if(switchEndian) {
 				uint8_t *side = this->_ebwt;
@@ -3042,7 +3042,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 				MM_READ_RET r = MM_READ(_in1, (void *)this->_ftab, eh->_ftabLen*4);
 				if(r != (MM_READ_RET)(eh->_ftabLen*4)) {
 					cerr << "Error reading _ftab[] array: " << r << ", " << (eh->_ftabLen*4) << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 			}
 		}
@@ -3066,7 +3066,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 				MM_READ_RET r = MM_READ(_in1, (void *)this->_eftab, eh->_eftabLen*4);
 				if(r != (MM_READ_RET)(eh->_eftabLen*4)) {
 					cerr << "Error reading _eftab[] array: " << r << ", " << (eh->_eftabLen*4) << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 			}
 		}
@@ -3082,7 +3082,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 		     << "If you ran Bowtie without the -z option, try adding the -z option to save" << endl
 		     << "memory.  If the -z option does not solve the problem, please try again on a" << endl
 		     << "computer with more memory." << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	// Read reference sequence names from primary index file (or not,
@@ -3121,7 +3121,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 					 << "If you ran Bowtie without the -z option, try adding the -z option to save" << endl
 					 << "memory.  If the -z option does not solve the problem, please try again on a" << endl
 					 << "computer with more memory." << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		} else {
 			shmemLeader = ALLOC_SHARED_U32(
@@ -3143,7 +3143,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 					MM_READ_RET r = MM_READ(_in2, (void *)buf, block << 2);
 					if(r != (MM_READ_RET)(block << 2)) {
 						cerr << "Error reading block of _offs[] array: " << r << ", " << (block << 2) << endl;
-						throw std::runtime_error("");
+						throw 1;
 					}
 					uint32_t idx = i >> offRateDiff;
 					for(uint32_t j = 0; j < block; j += (1 << offRateDiff)) {
@@ -3168,7 +3168,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 					if((offsLen & 0xc0000000) != 0) {
 						if(sizeof(char *) <= 4) {
 							cerr << "Sanity error: sizeof(char *) <= 4 but offsLen is " << hex << offsLen << endl;
-							throw std::runtime_error("");
+							throw 1;
 						}
 						// offsLen << 2 overflows, so do it in four reads
 						char *offs = (char *)this->_offs;
@@ -3176,7 +3176,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 							MM_READ_RET r = MM_READ(_in2, (void*)offs, offsLen);
 							if(r != (MM_READ_RET)(offsLen)) {
 								cerr << "Error reading block of _offs[] array: " << r << ", " << offsLen << endl;
-								throw std::runtime_error("");
+								throw 1;
 							}
 							offs += offsLen;
 						}
@@ -3185,7 +3185,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 						MM_READ_RET r = MM_READ(_in2, (void*)this->_offs, offsLen << 2);
 						if(r != (MM_READ_RET)(offsLen << 2)) {
 							cerr << "Error reading _offs[] array: " << r << ", " << (offsLen << 2) << endl;
-							throw std::runtime_error("");
+							throw 1;
 						}
 					}
 				}
@@ -3221,7 +3221,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 				 << "If you ran Bowtie without the -z option, try adding the -z option to save" << endl
 				 << "memory.  If the -z option does not solve the problem, please try again on a" << endl
 				 << "computer with more memory." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 	}
 	// Read _isa[]
@@ -3233,7 +3233,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 				MM_READ_RET r = MM_READ(_in2, (void *)tmp, 4);
 				if(r != (MM_READ_RET)4) {
 					cerr << "Error reading a word of the _isa[] array: " << r << ", 4" << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 			} else {
 				uint32_t idx = i >> isaRateDiff;
@@ -3252,7 +3252,7 @@ void Ebwt<TStr>::readIntoMemory(bool justHeader,
 			MM_READ_RET r = MM_READ(_in2, (void *)this->_isa, isaLen*4);
 			if(r != (MM_READ_RET)(isaLen*4)) {
 				cerr << "Error reading _isa[] array: " << r << ", " << (isaLen*4) << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 	}
diff --git a/ebwt_build.cpp b/ebwt_build.cpp
index cbe6bf8..f8eab0a 100644
--- a/ebwt_build.cpp
+++ b/ebwt_build.cpp
@@ -77,15 +77,18 @@ static void resetOptions() {
 }
 
 // Argument constants for getopts
-static const int ARG_BMAX      = 256;
-static const int ARG_BMAX_MULT = 257;
-static const int ARG_BMAX_DIV  = 258;
-static const int ARG_DCV       = 259;
-static const int ARG_SEED      = 260;
-static const int ARG_CUTOFF    = 261;
-static const int ARG_PMAP      = 262;
-static const int ARG_ISARATE   = 263;
-static const int ARG_NTOA      = 264;
+enum {
+	ARG_BMAX = 256,
+	ARG_BMAX_MULT,
+	ARG_BMAX_DIV,
+	ARG_DCV,
+	ARG_SEED,
+	ARG_CUTOFF,
+	ARG_PMAP,
+	ARG_ISARATE,
+	ARG_NTOA,
+	ARG_USAGE
+};
 
 /**
  * Print a detailed usage message to the provided output stream.
@@ -118,6 +121,7 @@ static void printUsage(ostream& out) {
 	    << "    -q/--quiet              verbose output (for debugging)" << endl
 	    //<< "    -s/--sanity             enable sanity checks (much slower/increased memory usage)" << endl
 	    << "    -h/--help               print detailed description of tool and its options" << endl
+	    << "    --usage                 print this usage message" << endl
 	    << "    --version               print version information and quit" << endl
 	    ;
 }
@@ -367,6 +371,7 @@ static struct option long_options[] = {
 	{(char*)"ntoa",         no_argument,       0,            ARG_NTOA},
 	{(char*)"justref",      no_argument,       0,            '3'},
 	{(char*)"noref",        no_argument,       0,            'r'},
+	{(char*)"usage",        no_argument,       0,            ARG_USAGE},
 	{(char*)0, 0, 0, 0} // terminator
 };
 
@@ -383,13 +388,13 @@ static int parseNumber(T lower, const char *errmsg) {
 		if (t < lower) {
 			cerr << errmsg << endl;
 			printUsage(cerr);
-			std::runtime_error("");
+			throw 1;
 		}
 		return t;
 	}
 	cerr << errmsg << endl;
 	printUsage(cerr);
-	std::runtime_error("");
+	throw 1;
 	return -1;
 }
 
@@ -431,11 +436,11 @@ static void parseOptions(int argc, const char **argv) {
 				break;
 			case 'h':
 				printLongUsage(cout);
-				throw std::runtime_error("");
+				throw 0;
 				break;
-			case '?':
-				printUsage(cerr);
-				throw std::runtime_error("");
+			case ARG_USAGE:
+				printUsage(cout);
+				throw 0;
 				break;
 			case ARG_BMAX:
 				bmax = parseNumber<uint32_t>(1, "--bmax arg must be at least 1");
@@ -473,9 +478,8 @@ static void parseOptions(int argc, const char **argv) {
 				if (long_options[option_index].flag != 0)
 					break;
 			default:
-				cerr << "Unknown option: " << (char)next_option << endl;
 				printUsage(cerr);
-				std::runtime_error("");
+				throw 1;
 		}
 	} while(next_option != -1);
 	if(bmax < 40) {
@@ -517,7 +521,7 @@ static void driver(const string& infile,
 			FILE *f = fopen(infiles[i].c_str(), "r");
 			if (f == NULL) {
 				cerr << "Error: could not open "<< infiles[i] << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 			FileBuf *fb = new FileBuf(f);
 			assert(fb != NULL);
@@ -549,7 +553,7 @@ static void driver(const string& infile,
 				cerr << "Could not open index file for writing: \"" << file3 << "\"" << endl
 					 << "Please make sure the directory exists and that permissions allow writing by" << endl
 					 << "Bowtie." << endl;
-				std::runtime_error("");
+				throw 1;
 			}
 			bool be = currentlyBigEndian();
 			writeU32(fout3, 1, be); // endianness sentinel
@@ -774,7 +778,17 @@ int bowtie_build(int argc, const char **argv) {
 		}
 		return 0;
 	} catch(std::exception& e) {
+		cerr << "Command: ";
+		for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+		cerr << endl;
 		return 1;
+	} catch(int e) {
+		if(e != 0) {
+			cerr << "Command: ";
+			for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+			cerr << endl;
+		}
+		return e;
 	}
 }
 }
diff --git a/ebwt_search.cpp b/ebwt_search.cpp
index fa954b6..76dc164 100644
--- a/ebwt_search.cpp
+++ b/ebwt_search.cpp
@@ -241,7 +241,7 @@ static void resetOptions() {
 
 // mating constraints
 
-static const char *short_options = "fF:qbzh?cu:rv:s:at3:5:o:e:n:l:w:p:k:m:1:2:I:X:x:B:yS";
+static const char *short_options = "fF:qbzhcu:rv:s:at3:5:o:e:n:l:w:p:k:m:1:2:I:X:x:B:yS";
 
 enum {
 	ARG_ORIG = 256,
@@ -317,7 +317,8 @@ enum {
 	ARG_REPORTSE,
 	ARG_HADOOPOUT,
 	ARG_FUZZY,
-	ARG_FULLREF
+	ARG_FULLREF,
+	ARG_USAGE
 };
 
 static struct option long_options[] = {
@@ -422,6 +423,7 @@ static struct option long_options[] = {
 	{(char*)"hadoopout",    no_argument,       0,            ARG_HADOOPOUT},
 	{(char*)"fuzzy",        no_argument,       0,            ARG_FUZZY},
 	{(char*)"fullref",      no_argument,       0,            ARG_FULLREF},
+	{(char*)"usage",        no_argument,       0,            ARG_USAGE},
 	{(char*)"sam",          no_argument,       0,            'S'},
 	{(char*)0, 0, 0, 0} // terminator
 };
@@ -503,6 +505,7 @@ static void printUsage(ostream& out) {
 	    << "  --verbose          verbose output (for debugging)" << endl
 	    << "  --version          print version information and quit" << endl
 	    << "  -h/--help          print detailed description of tool and its options" << endl
+	    << "  --usage            print this usage message" << endl
 	    ;
 }
 
@@ -1456,13 +1459,13 @@ static int parseInt(int lower, const char *errmsg) {
 		if (l < lower) {
 			cerr << errmsg << endl;
 			printUsage(cerr);
-			throw std::runtime_error("");
+			throw 1;
 		}
 		return (int32_t)l;
 	}
 	cerr << errmsg << endl;
 	printUsage(cerr);
-	throw std::runtime_error("");
+	throw 1;
 	return -1;
 }
 
@@ -1555,7 +1558,7 @@ static void parseOptions(int argc, const char **argv) {
 				     << "BOWTIE_MM defined.  Memory-mapped I/O is not supported under Windows.  If you" << endl
 				     << "would like to use memory-mapped I/O on a platform that supports it, please" << endl
 				     << "refrain from specifying BOWTIE_MM=0 when compiling Bowtie." << endl;
-				throw std::runtime_error("");
+				throw 1;
 #endif
 			}
 			case ARG_MMSWEEP: mmSweep = true; break;
@@ -1618,14 +1621,14 @@ static void parseOptions(int argc, const char **argv) {
 			case 'p':
 #ifndef BOWTIE_PTHREADS
 				cerr << "-p/--threads is disabled because bowtie was not compiled with pthreads support" << endl;
-				throw std::runtime_error("");
+				throw 1;
 #endif
 				nthreads = parseInt(1, "-p/--threads arg must be at least 1");
 				break;
 			case ARG_FILEPAR:
 #ifndef BOWTIE_PTHREADS
 				cerr << "--filepar is disabled because bowtie was not compiled with pthreads support" << endl;
-				throw std::runtime_error("");
+				throw 1;
 #endif
 				fileParallel = true;
 				break;
@@ -1634,7 +1637,7 @@ static void parseOptions(int argc, const char **argv) {
 				mismatches = parseInt(0, "-v arg must be at least 0");
 				if(mismatches > 3) {
 					cerr << "-v arg must be at most 3" << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				break;
 			case '3': trim3 = parseInt(0, "-3/--trim3 arg must be at least 0"); break;
@@ -1644,8 +1647,8 @@ static void parseOptions(int argc, const char **argv) {
 			case 'e': qualThresh = parseInt(1, "-e/--err arg must be at least 1"); break;
 			case 'n': seedMms = parseInt(0, "-n/--seedmms arg must be at least 0"); maqLike = 1; break;
 			case 'l': seedLen = parseInt(5, "-l/--seedlen arg must be at least 5"); break;
-			case 'h': printLongUsage(cout); throw std::runtime_error(""); break;
-			case '?': printUsage(cerr); throw std::runtime_error(""); break;
+			case 'h': printLongUsage(cout); throw 0; break;
+			case ARG_USAGE: printUsage(cout); throw 0; break;
 			case 'a': allHits = true; break;
 			case 'y': tryHard = true; break;
 			case ARG_RECAL: recal = true; break;
@@ -1678,7 +1681,7 @@ static void parseOptions(int argc, const char **argv) {
 				if(optarg == NULL || strlen(optarg) == 0) {
 					cerr << "--orig arg must be followed by a string" << endl;
 					printUsage(cerr);
-					throw std::runtime_error("");
+					throw 1;
 				}
 				origString = optarg;
 				break;
@@ -1687,9 +1690,8 @@ static void parseOptions(int argc, const char **argv) {
 				if (long_options[option_index].flag != 0)
 					break;
 			default:
-				cerr << "Unknown option: " << (char)next_option << endl;
 				printUsage(cerr);
-				throw std::runtime_error("");
+				throw 1;
 		}
 	} while(next_option != -1);
 	bool paired = mates1.size() > 0 || mates2.size() > 0 || mates12.size() > 0;
@@ -1710,7 +1712,7 @@ static void parseOptions(int argc, const char **argv) {
 		cerr << "Error: " << mates1.size() << " mate files/sequences were specified with -1, but " << mates2.size() << endl
 		     << "mate files/sequences were specified with -2.  The same number of mate files/" << endl
 		     << "sequences must be specified with -1 and -2." << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	// Check for duplicate mate input files
 	if(format != CMDLINE) {
@@ -1762,7 +1764,7 @@ static void parseOptions(int argc, const char **argv) {
 			cerr << "When -z/--phased is used, the --al option is unavailable" << endl;
 			error = true;
 		}
-		if(error) throw std::runtime_error("");
+		if(error) throw 1;
 	}
 	if(tryHard) {
 		// Increase backtracking limit to huge number
@@ -1772,15 +1774,15 @@ static void parseOptions(int argc, const char **argv) {
 	}
 	if(fullIndex && strata && !stateful && !oldBest) {
 		cerr << "--strata must be combined with --best" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if(strata && !allHits && khits == 1 && mhits == 0xffffffff) {
 		cerr << "--strata has no effect unless combined with -k, -m or -a" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if(fuzzy && (!stateful && !paired)) {
 		cerr << "--fuzzy must be combined with --best or paired-end alignment" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	// If both -s and -u are used, we need to adjust qUpto accordingly
 	// since it uses patid to know if we've reached the -u limit (and
@@ -1802,7 +1804,7 @@ static void parseOptions(int argc, const char **argv) {
 			cerr << "Error: --chainin cannot be combined with paired-end alignment; aborting..." << endl;
 			error = true;
 		}
-		if(error) throw std::runtime_error("");
+		if(error) throw 1;
 	}
 
 	if(outType == OUTPUT_CHAIN) {
@@ -1819,7 +1821,7 @@ static void parseOptions(int argc, const char **argv) {
 			cerr << "Error: --chainout cannot be combined with paired-end alignment; aborting..." << endl;
 			error = true;
 		}
-		if(error) throw std::runtime_error("");
+		if(error) throw 1;
 	}
 
 	if(mate1fw && trim5 > 0) {
@@ -2221,7 +2223,7 @@ static void exactSearch(PairedPatternSource& _patsrc,
 	if((mates1.size() > 0 || mates12.size() > 0) && mixedThresh < 0xffffffff) {
 		Timer _t(cerr, "Time loading reference: ", timing);
 		refs = new BitPairReference(adjustedEbwtFileBase, sanityCheck, NULL, &os, false, useMm, useShmem, mmSweep, verbose, startVerbose);
-		if(!refs->loaded()) throw std::runtime_error("");
+		if(!refs->loaded()) throw 1;
 	}
 	exactSearch_refs   = refs;
 
@@ -2253,7 +2255,7 @@ static void exactSearch(PairedPatternSource& _patsrc,
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -2443,7 +2445,7 @@ static void mismatchSearch(PairedPatternSource& _patsrc,
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -2478,7 +2480,7 @@ static void mismatchSearch(PairedPatternSource& _patsrc,
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -2660,7 +2662,7 @@ static void mismatchSearchFull(PairedPatternSource& _patsrc,
 	if((mates1.size() > 0 || mates12.size() > 0) && mixedThresh < 0xffffffff) {
 		Timer _t(cerr, "Time loading reference: ", timing);
 		refs = new BitPairReference(adjustedEbwtFileBase, sanityCheck, NULL, &os, false, useMm, useShmem, mmSweep, verbose, startVerbose);
-		if(!refs->loaded()) throw std::runtime_error("");
+		if(!refs->loaded()) throw 1;
 	}
 	mismatchSearch_refs = refs;
 
@@ -2693,7 +2695,7 @@ static void mismatchSearchFull(PairedPatternSource& _patsrc,
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -3031,7 +3033,7 @@ static void twoOrThreeMismatchSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -3052,7 +3054,7 @@ static void twoOrThreeMismatchSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -3072,7 +3074,7 @@ static void twoOrThreeMismatchSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -3280,7 +3282,7 @@ static void twoOrThreeMismatchSearchFull(
 	if((mates1.size() > 0 || mates12.size() > 0) && mixedThresh < 0xffffffff) {
 		Timer _t(cerr, "Time loading reference: ", timing);
 		refs = new BitPairReference(adjustedEbwtFileBase, sanityCheck, NULL, &os, false, useMm, useShmem, mmSweep, verbose, startVerbose);
-		if(!refs->loaded()) throw std::runtime_error("");
+		if(!refs->loaded()) throw 1;
 	}
 	twoOrThreeMismatchSearch_refs     = refs;
 	twoOrThreeMismatchSearch_patsrc   = &_patsrc;
@@ -3319,7 +3321,7 @@ static void twoOrThreeMismatchSearchFull(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -3949,7 +3951,7 @@ static void seededQualCutoffSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -3962,7 +3964,7 @@ static void seededQualCutoffSearch(
 	} catch(bad_alloc& ba) {
 		cerr << "Could not reserve space for PartialAlignmentManager" << endl;
 		cerr << "Please subdivide the read set and invoke bowtie separately for each subdivision" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	seededQualSearch_pamRc = pamRc;
 	{
@@ -3985,7 +3987,7 @@ static void seededQualCutoffSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -4004,7 +4006,7 @@ static void seededQualCutoffSearch(
 	} catch(bad_alloc& ba) {
 		cerr << "Could not reserve space for PartialAlignmentManager" << endl;
 		cerr << "Please subdivide the read set and invoke bowtie separately for each subdivision" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	seededQualSearch_pamFw = pamFw;
 	{
@@ -4023,7 +4025,7 @@ static void seededQualCutoffSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -4051,7 +4053,7 @@ static void seededQualCutoffSearch(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -4114,7 +4116,7 @@ static void seededQualCutoffSearchFull(
 	if((mates1.size() > 0 || mates12.size() > 0) && mixedThresh < 0xffffffff) {
 		Timer _t(cerr, "Time loading reference: ", timing);
 		refs = new BitPairReference(adjustedEbwtFileBase, sanityCheck, NULL, &os, false, useMm, useShmem, mmSweep, verbose, startVerbose);
-		if(!refs->loaded()) throw std::runtime_error("");
+		if(!refs->loaded()) throw 1;
 	}
 	seededQualSearch_refs = refs;
 
@@ -4156,7 +4158,7 @@ static void seededQualCutoffSearchFull(
 			int ret;
 			if((ret = pthread_join(threads[i], NULL)) != 0) {
 				cerr << "Error: pthread_join returned non-zero status: " << ret << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 #endif
@@ -4231,7 +4233,7 @@ patsrcFromStrings(int format, const vector<string>& qs) {
 			                               verbose, seed);
 		default: {
 			cerr << "Internal error; bad patsrc format: " << format << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 	}
 }
@@ -4293,7 +4295,7 @@ static void driver(const char * type,
 	for(size_t i = 0; i < mates12.size(); i++) {
 		if(mates12[i] == "-" && !fullIndex) {
 			cerr << "Input file \"-\" is not compatible with -z/--phased" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		const vector<string>* qs = &mates12;
 		vector<string> tmp;
@@ -4313,7 +4315,7 @@ static void driver(const char * type,
 	for(size_t i = 0; i < mates1.size(); i++) {
 		if(mates1[i] == "-" && !fullIndex) {
 			cerr << "Input file \"-\" is not compatible with -z/--phased" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		const vector<string>* qs = &mates1;
 		vector<string> tmp;
@@ -4333,7 +4335,7 @@ static void driver(const char * type,
 	for(size_t i = 0; i < mates2.size(); i++) {
 		if(mates2[i] == "-" && !fullIndex) {
 			cerr << "Input file \"-\" is not compatible with -z/--phased" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		const vector<string>* qs = &mates2;
 		vector<string> tmp;
@@ -4358,7 +4360,7 @@ static void driver(const char * type,
 	for(size_t i = 0; i < queries.size(); i++) {
 		if(queries[i] == "-" && !fullIndex) {
 			cerr << "Input file \"-\" is not compatible with -z/--phased" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		const vector<string>* qs = &queries;
 		PatternSource* patsrc = NULL;
@@ -4405,11 +4407,11 @@ static void driver(const char * type,
 	} else {
 		if(outType == OUTPUT_BINARY && !refOut) {
 			cerr << "Error: Must specify an output file when output mode is binary" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		else if(outType == OUTPUT_CHAIN) {
 			cerr << "Error: Must specify an output file when output mode is --chain" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		fout = new OutFileBuf();
 	}
@@ -4569,7 +4571,7 @@ static void driver(const char * type,
 				break;
 			default:
 				cerr << "Invalid output type: " << outType << endl;
-				throw std::runtime_error("");
+				throw 1;
 		}
     	if(verbose || startVerbose) {
     		cerr << "Dispatching to search driver: "; logTime(cerr, true);
@@ -4611,7 +4613,7 @@ static void driver(const char * type,
 				}
 			} else {
 				cerr << "Error: " << mismatches << " is not a supported number of mismatches" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		} else {
 			// Search without mismatches
@@ -4743,7 +4745,7 @@ int bowtie(int argc, const char **argv) {
 					cerr << "Note that if <mates> files are specified using -1/-2, a <singles> file cannot" << endl
 						 << "also be specified.  Please run bowtie separately for mates and singles." << endl;
 				}
-				throw std::runtime_error("");
+				throw 1;
 			}
 
 			// Optionally summarize
@@ -4778,6 +4780,13 @@ int bowtie(int argc, const char **argv) {
 		for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
 		cerr << endl;
 		return 1;
+	} catch(int e) {
+		if(e != 0) {
+			cerr << "Command: ";
+			for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+			cerr << endl;
+		}
+		return e;
 	}
 } // bowtie()
 } // extern "C"
diff --git a/ebwt_search_backtrack.h b/ebwt_search_backtrack.h
index 3d1a23e..038a67f 100644
--- a/ebwt_search_backtrack.h
+++ b/ebwt_search_backtrack.h
@@ -115,7 +115,7 @@ class GreedyDFSRangeSource {
 				cerr << "Unable to allocate memory for depth-first "
 				     << "backtracking search; new length = " << length(*_qry)
 				     << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		} else {
 			// New length is less than old length, so there's no need
@@ -3202,7 +3202,7 @@ class EbwtRangeSourceDriver :
 		if(cext == PIN_TO_BEGINNING)    return 0;
 		if(cext == PIN_TO_LEN)          return len;
 		cerr << "Bad SearchConstraintExtent: " << cext;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	bool seed_;
diff --git a/filebuf.h b/filebuf.h
index 24e6090..6d3bbcc 100644
--- a/filebuf.h
+++ b/filebuf.h
@@ -277,7 +277,7 @@ class BitpairOutFileBuf {
 		out_ = fopen(in, "wb");
 		if(out_ == NULL) {
 			std::cerr << "Error: Could not open bitpair-output file " << in << std::endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 	}
 
@@ -296,7 +296,7 @@ class BitpairOutFileBuf {
 				// Flush the buffer
 				if(!fwrite((const void *)buf_, BUF_SZ, 1, out_)) {
 					std::cerr << "Error writing to the reference index file (.4.ebwt)" << std::endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				// Reset to beginning of the buffer
 				cur_ = 0;
@@ -316,7 +316,7 @@ class BitpairOutFileBuf {
 			if(bpPtr_ == 0) cur_--;
 			if(!fwrite((const void *)buf_, cur_ + 1, 1, out_)) {
 				std::cerr << "Error writing to the reference index file (.4.ebwt)" << std::endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 		fclose(out_);
@@ -348,7 +348,7 @@ class OutFileBuf {
 		out_ = fopen(out, binary ? "wb" : "w");
 		if(out_ == NULL) {
 			std::cerr << "Error: Could not open alignment output file " << out << std::endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 	}
 
@@ -407,7 +407,7 @@ class OutFileBuf {
 	void flush() {
 		if(!fwrite((const void *)buf_, cur_, 1, out_)) {
 			std::cerr << "Error while flushing and closing output" << std::endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		cur_ = 0;
 	}
diff --git a/hit.h b/hit.h
index b85868e..c8db9dd 100644
--- a/hit.h
+++ b/hit.h
@@ -87,27 +87,27 @@ class Hit {
 		if(seqan::length(patName) > 0xffff) {
 			cerr << "Error: One or more read names are 2^16 characters or longer.  Please truncate" << endl
 			     << "read names and re-run bowtie." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(mms.count() > 0xff) {
 			cerr << "Error: The alignment contains 256 or more mismatches.  bowtie cannot handle" << endl
 			     << "alignments with this many alignments.  Please provide smaller reads or consider" << endl
 			     << "using a different tool." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(seqan::length(quals) > 0xffff) {
 			cerr << "Error: One or more quality strings are 2^16 characters or longer.  Please" << endl
 			     << "truncate reads and re-run bowtie." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(seqan::length(patSeq) > 0xffff) {
 			cerr << "Error: One or more read sequences are 2^16 characters or longer.  Please" << endl
 			     << "truncate reads and re-run bowtie." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(stratum < 0 || stratum >= 4) {
 			cerr << "Error: Stratum is out of bounds: " << stratum << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 	}
 
@@ -277,7 +277,7 @@ class RecalTable {
 				memset(ents_, 0, len_ << 2);
 			} catch(std::bad_alloc& e) {
 				cerr << "Error allocating recalibration table with " << len_ << " entries" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 	}
@@ -1075,7 +1075,7 @@ class HitSink {
     			s = name.substr(0, dotoff) + "_2" + s.substr(dotoff);
     		}
     	} else if(mateType != 0) {
-    		cerr << "Bad mate type " << mateType << endl; throw std::runtime_error("");
+    		cerr << "Bad mate type " << mateType << endl; throw 1;
     	}
     	std::ofstream* tmp = new ofstream(s.c_str(), ios::out);
     	if(tmp->fail()) {
@@ -1084,7 +1084,7 @@ class HitSink {
     		} else {
     			cerr << "Could not open paired-end aligned/unaligned-read file for writing: " << name << endl;
     		}
-    		throw std::runtime_error("");
+    		throw 1;
     	}
     	return tmp;
     }
@@ -1339,7 +1339,7 @@ class HitSinkPerThread {
 	virtual bool setHits(HitSet& hs) {
 		if(!hs.empty()) {
 			cerr << "Error: default setHits() called with non-empty HitSet" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		return false;
 	}
@@ -2730,11 +2730,11 @@ class VerboseHitSink : public HitSink {
 		}
 		if(in.bad()) {
 			cerr << "Alignment file set \"bad\" bit" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(in.fail()) {
 			cerr << "A line from the alignment file was longer than 4K" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		in.getline(buf, 4096);
 		size_t len = in.gcount();
@@ -2830,7 +2830,7 @@ class VerboseHitSink : public HitSink {
 			if(!found) {
 				cerr << "Could not find an id to map reference name \"" << refName << "\" to." << endl
 				     << "Try using -n to specify the index used to generate the alignments." << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 
@@ -3446,7 +3446,7 @@ class ChainingHitSink : public HitSink {
 	 */
 	virtual void append(ostream& o, const Hit& h) {
 		cerr << "Error: ChainingHitSink::append() not implemented" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	/**
diff --git a/map_tool.cpp b/map_tool.cpp
index 9c5624b..4b299c8 100644
--- a/map_tool.cpp
+++ b/map_tool.cpp
@@ -127,6 +127,7 @@ static void printUsage(ostream& out) {
 	    << "  -n/--names <ebwt>  if needed, get ref names from index w/ basename <ebwt> " << endl
 	    << "  -v/--verbose       verbose output (for debugging)" << endl
 	    << "  -h/--help          print detailed description of tool and its options" << endl
+	    << "  --usage            print detailed description of tool and its options" << endl
 	    << "  --version          print version information and quit" << endl
 	    ;
 }
@@ -135,7 +136,8 @@ static const char *short_options = "hvsdbsDBCQFn:";
 
 enum {
 	ARG_VERSION = 256,
-	ARG_REFIDX
+	ARG_REFIDX,
+	ARG_USAGE
 };
 
 static struct option long_options[] = {
@@ -152,6 +154,7 @@ static struct option long_options[] = {
 	{(char*)"help",       no_argument, 0, 'h'},
 	{(char*)"refidx",     no_argument, 0, ARG_REFIDX},
 	{(char*)"version",    no_argument, 0, ARG_VERSION},
+	{(char*)"usage",      no_argument, 0, ARG_USAGE},
 	{(char*)0, 0, 0, 0} // terminator
 };
 
@@ -165,9 +168,12 @@ static void parseOptions(int argc, char **argv) {
 		next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
 		switch (next_option) {
 			case 'h':
-			case '?':
 				printLongUsage(cout);
-				throw std::runtime_error("");
+				throw 0;
+				break;
+			case ARG_USAGE:
+				printUsage(cout);
+				throw 0;
 				break;
 			case 'v': verbose = true; break;
 			case 's': sorthits = true; break;
@@ -184,9 +190,8 @@ static void parseOptions(int argc, char **argv) {
 			case -1: /* Done with options. */ break;
 			case 0: if (long_options[option_index].flag != 0) break;
 			default:
-				cerr << "Unknown option: " << (char)next_option << endl;
 				printUsage(cerr);
-				throw runtime_error("");
+				throw 1;
 		}
 	} while(next_option != -1);
 }
@@ -262,7 +267,7 @@ int main(int argc, char **argv) {
 			out = new ofstream(argv[optind]);
 		} else if(outformat == FORMAT_BIN) {
 			cerr << "If -B/--outbin is specified, <align_out> must also be specified" << endl;
-			throw runtime_error("");
+			throw 1;
 		}
 
 		// Read in reference names, if requested
@@ -364,6 +369,16 @@ int main(int argc, char **argv) {
 
 		return 0;
 	} catch(std::exception& e) {
+		cerr << "Command: ";
+		for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+		cerr << endl;
 		return 1;
+	} catch(int e) {
+		if(e != 0) {
+			cerr << "Command: ";
+			for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+			cerr << endl;
+		}
+		return e;
 	}
 }
diff --git a/maq_convert/bfa.cpp b/maq_convert/bfa.cpp
index ced9914..7f545ad 100644
--- a/maq_convert/bfa.cpp
+++ b/maq_convert/bfa.cpp
@@ -14,7 +14,7 @@ nst_bfa1_t *nst_new_bfa1()
 	bfa1 = (nst_bfa1_t*)malloc(sizeof(nst_bfa1_t));
 	if(bfa1 == NULL) {
 		cerr << "Exhausted memory allocating space for the .bfa file" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	bfa1->name = 0;
 	bfa1->seq = bfa1->mask = 0;
@@ -31,7 +31,7 @@ void nst_delete_bfa1(nst_bfa1_t *bfa1)
 }
 static void bfa_read_error() {
 	fprintf(stderr, "Error reading from .bfa file\n");
-	throw std::runtime_error("");
+	throw 1;
 }
 nst_bfa1_t *nst_load_bfa1(FILE *fp)
 {
@@ -42,7 +42,7 @@ nst_bfa1_t *nst_load_bfa1(FILE *fp)
 	bfa1->name = (char*)malloc(sizeof(char) * len);
 	if(bfa1->name == NULL) {
 		cerr << "Exhausted memory allocating space for the .bfa file name" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	/*
 	 * BTL: I had to add in these return-value checks to keep gcc 4.3.2
@@ -60,7 +60,7 @@ nst_bfa1_t *nst_load_bfa1(FILE *fp)
 	bfa1->seq = (bit64_t*)malloc(sizeof(bit64_t) * bfa1->len);
 	if(bfa1->seq == NULL) {
 		cerr << "Exhausted memory allocating space for the .bfa file sequence" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if(fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp) != (size_t)bfa1->len) {
 		bfa_read_error();
@@ -68,7 +68,7 @@ nst_bfa1_t *nst_load_bfa1(FILE *fp)
 	bfa1->mask = (bit64_t*)malloc(sizeof(bit64_t) * bfa1->len);
 	if(bfa1->mask == NULL) {
 		cerr << "Exhausted memory allocating space for the .bfa file mask" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if(fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp) != (size_t)bfa1->len) {
 		bfa_read_error();
diff --git a/maq_convert/bowtie_convert.cpp b/maq_convert/bowtie_convert.cpp
index f431b37..da09541 100644
--- a/maq_convert/bowtie_convert.cpp
+++ b/maq_convert/bowtie_convert.cpp
@@ -86,7 +86,7 @@ static void printLongUsage(ostream& out) {
 	"\n"
 	"    -v            Print verbose output (for debugging).\n"
 	"\n"
-	"    -h/-?         Print detailed description of tool and its options\n"
+	"    -h            Print detailed description of tool and its options\n"
 	"                  (from MANUAL).\n"
 	"\n"
 	;
@@ -102,7 +102,7 @@ static void printUsage(ostream& out) {
 	"Options:\n"
 	"    -o            output Maq map in old (pre Maq 0.7.0) format\n"
 	"    -v            verbose output\n"
-	"    -h/-?         print detailed description of tool and its options\n"
+	"    -h            print detailed description of tool and its options\n"
 	"\n"
 	;
 }
@@ -196,14 +196,14 @@ int convert_bwt_to_maq(const string& bwtmap_fname,
 	if (!bwtf)
 	{
 		fprintf(stderr, "Error: could not open Bowtie mapfile %s for reading\n", bwtmap_fname.c_str());
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	void* maqf = gzopen(maqmap_fname.c_str(), "w");
 	if (!maqf)
 	{
 		fprintf(stderr, "Error: could not open Maq mapfile %s for writing\n", maqmap_fname.c_str());
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	std::map<string, int> seqid_to_name;
@@ -287,7 +287,7 @@ int convert_bwt_to_maq(const string& bwtmap_fname,
 				(aln_t<MAXLEN>*)malloc(sizeof(aln_t<MAXLEN>) * (next_max));
 			if(tmp == NULL) {
 				cerr << "Memory exhausted allocating space for alignments." << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			memcpy(tmp, mm->mapped_reads, sizeof(aln_t<MAXLEN>) * (max));
 			free(mm->mapped_reads);
@@ -420,7 +420,7 @@ int convert_bwt_to_maq(const string& bwtmap_fname,
 	mm->ref_name = (char**)malloc(sizeof(char*) * mm->n_ref);
 	if(mm->ref_name == NULL) {
 		cerr << "Exhausted memory allocating reference name" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	for (map<string, unsigned int>::const_iterator i = names_to_ids.begin();
@@ -463,7 +463,7 @@ void get_names_from_bfa(const string& bfa_filename,
 	if (!bfaf)
 	{
 		fprintf(stderr, "Error: could not open Binary FASTA file %s for reading\n", bfa_filename.c_str());
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	unsigned int next_id = 0;
@@ -485,7 +485,7 @@ int main(int argc, char **argv)
 		string bwtmap_filename;
 		string maqmap_filename;
 		string bfa_filename;
-		const char *short_options = "voh?";
+		const char *short_options = "voh";
 		int next_option;
 		do {
 			next_option = getopt(argc, argv, short_options);
@@ -497,14 +497,13 @@ int main(int argc, char **argv)
 					short_map_format = true;
 					break;
 				case 'h':
-				case '?':
 					printLongUsage(cout);
-					throw std::runtime_error("");
+					throw 0;
 				case -1: /* Done with options. */
 					break;
 				default:
 					printUsage(cerr);
-					throw std::runtime_error("");
+					throw 1;
 			}
 		} while(next_option != -1);
 
@@ -554,6 +553,16 @@ int main(int argc, char **argv)
 
 		return ret;
 	} catch(std::exception& e) {
+		cerr << "Command: ";
+		for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+		cerr << endl;
 		return 1;
+	} catch(int e) {
+		if(e != 0) {
+			cerr << "Command: ";
+			for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
+			cerr << endl;
+		}
+		return e;
 	}
 }
diff --git a/maq_convert/maqmap.h b/maq_convert/maqmap.h
index 0cadf64..f61397d 100644
--- a/maq_convert/maqmap.h
+++ b/maq_convert/maqmap.h
@@ -50,7 +50,7 @@ header_t<MAXLEN>* maq_init_header()
 	header_t<MAXLEN>* mm = (header_t<MAXLEN>*)calloc(1, sizeof(header_t<MAXLEN>));
 	if(mm == NULL) {
 		std::cerr << "Exhausted memory allocating maqmap header" << std::endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	mm->format = MAQMAP_FORMAT_NEW;
 	return mm;
@@ -96,14 +96,14 @@ header_t<MAXLEN>* maq_read_header(gzFile fp)
 	mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
 	if(mm->ref_name == NULL) {
 		std::cerr << "Exhausted memory allocating reference name list" << std::endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	for (k = 0; k != mm->n_ref; ++k) {
 		gzread(fp, &len, 4);
 		mm->ref_name[k] = (char*)malloc(len);
 		if(mm->ref_name[k] == NULL) {
 			std::cerr << "Exhausted memory allocating reference name" << std::endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		gzread(fp, mm->ref_name[k], len);
 	}
diff --git a/maq_convert/read_bfq.h b/maq_convert/read_bfq.h
index 327cfd7..03f76ef 100644
--- a/maq_convert/read_bfq.h
+++ b/maq_convert/read_bfq.h
@@ -30,8 +30,8 @@ static bool ma_load_1read(gzFile fp, TStr& ret) {
 	// Read name length
 	if (gzread(fp, &len, sizeof(int)) != sizeof(int)) return false;
 	if(len > 2047) {
-		throw std::runtime_error(
-			"One or more .bfq read names are longer than 2047 characters");
+		cerr << "One or more .bfq read names are longer than 2047 characters" << endl;
+		throw 1;
 	}
 	// Read name
 	gzread(fp, name, sizeof(char) * len);
@@ -39,8 +39,8 @@ static bool ma_load_1read(gzFile fp, TStr& ret) {
 	// Read sequence length
 	if(gzread(fp, &len, sizeof(int)) != sizeof(int)) return false;
 	if(len > 2048) {
-		throw std::runtime_error(
-			"One or more .bfq read sequences are longer than 2048 bases");
+		cerr << "One or more .bfq read sequences are longer than 2048 bases" << endl;
+		throw 1;
 	}
 	seqan::reserve(ret, len, seqan::Exact());
 	gzread(fp, seq, sizeof(char) * len);
diff --git a/pat.cpp b/pat.cpp
index 49cd734..e57138a 100644
--- a/pat.cpp
+++ b/pat.cpp
@@ -13,25 +13,25 @@ void wrongQualityFormat(const String<char>& read_name) {
 	     << "If this is a FASTQ file with integer (non-ASCII-encoded) qualities, please" << endl
 	     << "re-run Bowtie with the --integer-quals option.  If this is a FASTQ file with" << endl
 	     << "alternate basecall information, please re-run Bowtie with the --fuzzy option." << endl;
-	throw std::runtime_error("");
+	throw 1;
 }
 
 void tooFewQualities(const String<char>& read_name) {
 	cerr << "Too few quality values for read: " << read_name << endl
 		 << "\tare you sure this is a FASTQ-int file?" << endl;
-	throw std::runtime_error("");
+	throw 1;
 }
 
 void tooManyQualities(const String<char>& read_name) {
 	cerr << "Reads file contained a pattern with more than 1024 quality values." << endl
 		 << "Please truncate reads and quality values and and re-run Bowtie" << endl;
-	throw std::runtime_error("");
+	throw 1;
 }
 
 void tooManySeqChars(const String<char>& read_name) {
 	cerr << "Reads file contained a pattern with more than 1024 sequence characters." << endl
 		 << "Please truncate reads and quality values and and re-run Bowtie" << endl;
-	throw std::runtime_error("");
+	throw 1;
 }
 
 /**
diff --git a/pat.h b/pat.h
index cf5e7c1..cc15e3d 100644
--- a/pat.h
+++ b/pat.h
@@ -356,7 +356,7 @@ class PatternSource {
 			out_.open(dumpfile_, ios_base::out);
 			if(!out_.good()) {
 				cerr << "Could not open pattern dump file \"" << dumpfile_ << "\" for writing" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 		MUTEX_INIT(lock_);
@@ -1060,7 +1060,7 @@ class RandomPatternSource : public PatternSource {
 	{
 		if(length_ > 1024) {
 			cerr << "Read length for RandomPatternSource may not exceed 1024; got " << length_ << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		rand_.init(seed_);
 	}
@@ -1155,7 +1155,7 @@ class RandomPatternSourcePerThread : public PatternSourcePerThread {
 		patid_ = thread_;
 		if(length_ > 1024) {
 			cerr << "Read length for RandomPatternSourcePerThread may not exceed 1024; got " << length_ << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		rand_.init(thread_);
 	}
@@ -1595,7 +1595,7 @@ class BufferedFilePatternSource : public TrimmingPatternSource {
 			filebuf_.newFile(in);
 			return;
 		}
-		throw std::runtime_error("");
+		throw 1;
 	}
 	vector<string> infiles_; /// filenames for read files
 	vector<bool> errs_; /// whether we've already printed an error for each file
@@ -1673,7 +1673,7 @@ class FastaPatternSource : public BufferedFilePatternSource {
 			}
 			if(c != '>') {
 				cerr << "Error: reads file does not look like a FASTA file" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			assert(c == '>' || c == '#');
 			first_ = false;
@@ -1711,7 +1711,7 @@ class FastaPatternSource : public BufferedFilePatternSource {
 				if(dstLen + 1 > 1024) {
 					cerr << "Input file contained a pattern more than 1024 characters long.  Please truncate" << endl
 						 << "reads and re-run Bowtie" << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				r.patBufFw [dstLen] = charToDna5[c];
 				r.qualBuf[dstLen]   = 'I';
@@ -1748,7 +1748,7 @@ class FastaPatternSource : public BufferedFilePatternSource {
 	virtual void readPair(ReadBuf& ra, ReadBuf& rb, uint32_t& patid) {
 		// (For now, we shouldn't ever be here)
 		cerr << "In FastaPatternSource.readPair()" << endl;
-		throw std::runtime_error("");
+		throw 1;
 		read(ra, patid);
 		readCnt_--;
 		read(rb, patid);
@@ -2027,7 +2027,7 @@ class TabbedPatternSource : public BufferedFilePatternSource {
 					if(dstLen + 1 > 1024) {
 						cerr << "Input file contained a pattern more than 1024 characters long.  Please truncate" << endl
 							 << "reads and re-run Bowtie" << endl;
-						throw std::runtime_error("");
+						throw 1;
 					}
 					r.patBufFw[dstLen] = charToDna5[c];
 					dstLen++;
@@ -2229,7 +2229,7 @@ class FastaContinuousPatternSource : public BufferedFilePatternSource {
 	// from a continuous input.
 	virtual void readPair(ReadBuf& ra, ReadBuf& rb, uint32_t& patid) {
 		cerr << "In FastaContinuousPatternSource.readPair()" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	/**
@@ -2371,7 +2371,7 @@ class FastqPatternSource : public BufferedFilePatternSource {
 			}
 			if(c != '@') {
 				cerr << "Error: reads file does not look like a FASTQ file" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			assert_eq('@', c);
 			first_ = false;
@@ -2405,7 +2405,7 @@ class FastqPatternSource : public BufferedFilePatternSource {
 				_setLength(r.name, nameLen);
 				cerr << "FASTQ read name is too long; read names must be " << (bufSz-2) << " characters or fewer." << endl;
 				cerr << "Beginning of bad read name: " << r.name << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		}
 		_setBegin(r.name, r.nameBuf);
@@ -2440,7 +2440,7 @@ class FastqPatternSource : public BufferedFilePatternSource {
 				charsRead = 0;
 				if(altBufIdx >= 3) {
 					cerr << "At most 3 alternate sequence strings permitted; offending read: " << r.name << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				// Move on to the next alternate-sequence buffer
 				sbuf = r.altPatBufFw[altBufIdx++];
@@ -2505,7 +2505,7 @@ class FastqPatternSource : public BufferedFilePatternSource {
 					if((*qualsReadCur) == 0) continue;
 					if(altBufIdx >= 3) {
 						cerr << "At most 3 alternate quality strings permitted; offending read: " << r.name << endl;
-						throw std::runtime_error("");
+						throw 1;
 					}
 					qbuf = r.altQualBuf[altBufIdx++];
 					qualsReadCur = &qualsRead[altBufIdx];
@@ -2602,7 +2602,7 @@ class FastqPatternSource : public BufferedFilePatternSource {
 	virtual void readPair(ReadBuf& ra, ReadBuf& rb, uint32_t& patid) {
 		// (For now, we shouldn't ever be here)
 		cerr << "In FastqPatternSource.readPair()" << endl;
-		throw std::runtime_error("");
+		throw 1;
 		read(ra, patid);
 		readCnt_--;
 		read(rb, patid);
@@ -2670,7 +2670,7 @@ class RawPatternSource : public BufferedFilePatternSource {
 				if(c == '@') {
 					cerr << "Reads file looks like a FASTQ file; please use -q" << endl;
 				}
-				throw std::runtime_error("");
+				throw 1;
 			}
 			first_ = false;
 		}
@@ -2715,7 +2715,7 @@ class RawPatternSource : public BufferedFilePatternSource {
 	virtual void readPair(ReadBuf& ra, ReadBuf& rb, uint32_t& patid) {
 		// (For now, we shouldn't ever be here)
 		cerr << "In RawPatternSource.readPair()" << endl;
-		throw std::runtime_error("");
+		throw 1;
 		read(ra, patid);
 		readCnt_--;
 		read(rb, patid);
@@ -2793,10 +2793,7 @@ class ChainPatternSource : public BufferedFilePatternSource {
 	virtual void readPair(ReadBuf& ra, ReadBuf& rb, uint32_t& patid) {
 		// (For now, we shouldn't ever be here)
 		cerr << "In ChainPatternSource.readPair()" << endl;
-		throw std::runtime_error("");
-		read(ra, patid);
-		readCnt_--;
-		read(rb, patid);
+		throw 1;
 	}
 };
 
diff --git a/pool.h b/pool.h
index e9854c8..cd0f168 100644
--- a/pool.h
+++ b/pool.h
@@ -39,7 +39,7 @@ class ChunkPool {
 			std::cerr << "Error: Could not allocate ChunkPool of "
 			          << totSz << " bytes" << std::endl;
 			exhausted();
-			throw std::runtime_error(""); // Exit if we haven't already
+			throw 1; // Exit if we haven't already
 		}
 	}
 
@@ -148,7 +148,7 @@ class ChunkPool {
 		}
 		if(exhaustCrash_) {
 			std::cerr << "Please try specifying a larger --chunkmbs <int> (default is 32)" << std::endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		lastSkippedRead_ = patid;
 	}
diff --git a/qual.h b/qual.h
index 7930bf8..832c70a 100644
--- a/qual.h
+++ b/qual.h
@@ -85,7 +85,7 @@ inline static char charToPhred33(char c, bool solQuals, bool phred64Quals) {
 	if(c == ' ') {
 		cerr << "Saw a space but expected an ASCII-encoded quality value." << endl
 		     << "Are quality values formatted as integers?  If so, try --integer-quals." << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if (solQuals) {
 		// Convert solexa-scaled chars to phred
@@ -96,7 +96,7 @@ inline static char charToPhred33(char c, bool solQuals, bool phred64Quals) {
 			     << ((int)c)
 			     << " but expected 64-based Solexa qual (converts to " << (int)cc << ")." << endl
 			     << "Try not specifying --solexa-quals." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		c = cc;
 	}
@@ -106,7 +106,7 @@ inline static char charToPhred33(char c, bool solQuals, bool phred64Quals) {
 			     << ((int)c)
 			     << " but expected 64-based Phred qual." << endl
 			     << "Try not specifying --solexa1.3-quals/--phred64-quals." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		// Convert to 33-based phred
 		c -= (64-33);
@@ -117,7 +117,7 @@ inline static char charToPhred33(char c, bool solQuals, bool phred64Quals) {
 			cerr << "Saw ASCII character "
 			     << ((int)c)
 			     << " but expected 33-based Phred qual." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 	}
 	return c;
@@ -141,7 +141,7 @@ inline static char intToPhred33(int iQ, bool solQuals) {
 	}
 	if (pQ < 33) {
 		cerr << "Saw negative Phred quality " << ((int)pQ-33) << "." << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	assert_geq(pQ, 0);
 	return (int)pQ;
diff --git a/range_cache.h b/range_cache.h
index 1ed590d..447ae38 100644
--- a/range_cache.h
+++ b/range_cache.h
@@ -43,7 +43,7 @@ class RangeCacheMemPool {
 			} catch(std::bad_alloc& e) {
 				cerr << "Allocation error allocating " << lim
 					 << " words of range-cache memory" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			assert(buf_ != NULL);
 			// Fill with 1s to signal that these elements are
diff --git a/range_source.h b/range_source.h
index ddf7bf6..6a45498 100644
--- a/range_source.h
+++ b/range_source.h
@@ -1917,7 +1917,7 @@ class StubRangeSourceDriver : public RangeSourceDriver<TRangeSource> {
 	virtual void advanceImpl(int until) { }
 
 	/// Return the last valid range found
-	virtual Range& range() { throw std::runtime_error(""); }
+	virtual Range& range() { throw 1; }
 
 	/**
 	 * Return whether we're generating ranges for the first or the
diff --git a/ref_aligner.h b/ref_aligner.h
index b787af5..2161e3e 100644
--- a/ref_aligner.h
+++ b/ref_aligner.h
@@ -138,7 +138,7 @@ class RefAligner {
 			if(refbuf_ == NULL) throw std::bad_alloc();
 		} catch(std::bad_alloc& e) {
 			cerr << "Error: Could not allocate reference-space alignment buffer of " << newsz << "B" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		refbufSz_ = newsz;
 		freeRefbuf_ = true;
diff --git a/ref_read.cpp b/ref_read.cpp
index 1e96f52..57c9eae 100644
--- a/ref_read.cpp
+++ b/ref_read.cpp
@@ -179,7 +179,7 @@ size_t fastaRefReadSizes(vector<FileBuf*>& in,
 				cerr << "Error: Reference sequence has more than 2^32-1 characters!  Please divide the" << endl
 				     << "reference into batches or chunks of about 3.6 billion characters or less each" << endl
 				     << "and index each independently." << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			tot += rec.len;
 			first = false;
diff --git a/ref_read.h b/ref_read.h
index 4e3d7ed..e1d0862 100644
--- a/ref_read.h
+++ b/ref_read.h
@@ -43,12 +43,12 @@ struct RefRecord {
 		assert(in != NULL);
 		if(!fread(&off, 4, 1, in)) {
 			cerr << "Error reading RefRecord offset from FILE" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(swap) off = endianSwapU32(off);
 		if(!fread(&len, 4, 1, in)) {
 			cerr << "Error reading RefRecord offset from FILE" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(swap) len = endianSwapU32(len);
 		first = fgetc(in) ? true : false;
@@ -60,7 +60,7 @@ struct RefRecord {
 		char c;
 		if(!read(in, &c, 1)) {
 			cerr << "Error reading RefRecord 'first' flag" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		first = (c ? true : false);
 	}
@@ -139,7 +139,7 @@ static RefRecord fastaRefReadAppend(FileBuf& in,
 		c = skipWhitespace(in);
 		if(c != '>') {
 			cerr << "Reference file does not seem to be a FASTA file" << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		lastc = c;
 	}
diff --git a/reference.h b/reference.h
index 026728d..37c9eb9 100644
--- a/reference.h
+++ b/reference.h
@@ -77,14 +77,14 @@ class BitPairReference {
 			if (stat(s4.c_str(), &sbuf) == -1) {
 				perror("stat");
 				cerr << "Error: Could not stat index file " << s4.c_str() << " prior to memory-mapping" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			mmFile = (char*)mmap((void *)0, sbuf.st_size,
 			                     PROT_READ, MAP_SHARED, f4, 0);
 			if(mmFile == (void *)(-1) || mmFile == NULL) {
 				perror("mmap");
 				cerr << "Error: Could not memory-map the index file " << s4.c_str() << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			if(mmSweep) {
 				int sum = 0;
@@ -121,7 +121,7 @@ class BitPairReference {
 		if(one != 1) {
 			if(useMm_) {
 				cerr << "Error: Can't use memory-mapped files when the index is the opposite endianness" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			assert_eq(0x1000000, one);
 			swap = true; // have to endian swap U32s
@@ -132,7 +132,7 @@ class BitPairReference {
 		sz = readU32(f3, swap);
 		if(sz == 0) {
 			cerr << "Error: number of reference records is 0 in " << s3 << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 
 		// Read records
@@ -159,7 +159,7 @@ class BitPairReference {
 				nrefs_++;
 			} else if(i == 0) {
 				cerr << "First record in reference index file was not marked as 'first'" << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 			cumsz += recs_.back().len;
 			cumlen += recs_.back().off;
@@ -192,7 +192,7 @@ class BitPairReference {
 				size_t ret = fread(sanityBuf_, 1, cumsz >> 2, ftmp);
 				if(ret != (cumsz >> 2)) {
 					cerr << "Only read " << ret << " bytes (out of " << (cumsz >> 2) << ") from reference index file " << s4 << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				fclose(ftmp);
 				for(size_t i = 0; i < (cumsz >> 2); i++) {
@@ -201,7 +201,7 @@ class BitPairReference {
 			}
 #else
 			cerr << "Shouldn't be at " << __FILE__ << ":" << __LINE__ << " without BOWTIE_MM defined" << endl;
-			throw std::runtime_error("");
+			throw 1;
 #endif
 		} else {
 			bool shmemLeader = true;
@@ -213,7 +213,7 @@ class BitPairReference {
 				} catch(std::bad_alloc& e) {
 					cerr << "Error: Ran out of memory allocating space for the bitpacked reference.  Please" << endl
 						 << "re-run on a computer with more memory." << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 			} else {
 				shmemLeader = ALLOC_SHARED_U8(
@@ -236,7 +236,7 @@ class BitPairReference {
 				// Didn't read all of it?
 				if(ret != (cumsz >> 2)) {
 					cerr << "Only read " << ret << " bytes (out of " << (cumsz >> 2) << ") from reference index file " << s4 << endl;
-					throw std::runtime_error("");
+					throw 1;
 				}
 				// Make sure there's no more
 				char c;
diff --git a/refmap.cpp b/refmap.cpp
index b254e00..025d563 100644
--- a/refmap.cpp
+++ b/refmap.cpp
@@ -21,7 +21,7 @@ void ReferenceMap::map(U32Pair& h) const {
 		cerr << "Could not find a reference-map entry for reference "
 				  << h.first << " in map file \"" << fname_ << "\""
 				  << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	h.second += map_[h.first].second;
 	h.first = map_[h.first].first;
@@ -34,7 +34,7 @@ void ReferenceMap::parse() {
 	ifstream in(fname_);
 	if(!in.good() || !in.is_open()) {
 		cerr << "Could not open reference map file " << fname_ << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	int c;
 	while((c = in.peek()) != EOF) {
@@ -60,8 +60,5 @@ void ReferenceMap::parse() {
 		while(isspace(in.peek())) in.get();
 	}
 	assert_eq(EOF, c);
-	if(map_.empty()) {
-		throw std::runtime_error("");
-	}
 	in.close();
 }
diff --git a/sam.cpp b/sam.cpp
index 6696bfa..98457a3 100644
--- a/sam.cpp
+++ b/sam.cpp
@@ -29,6 +29,11 @@ void SAMHitSink::appendAligned(ostream& ss,
 	ss << h.patName << "\t";
 	// FLAG
 	int flags = 0;
+	if(h.mate == 1) {
+		flags |= SAM_FLAG_PAIRED | SAM_FLAG_SECOND_IN_PAIR;
+	} else if(h.mate == 2) {
+		flags |= SAM_FLAG_PAIRED | SAM_FLAG_FIRST_IN_PAIR;
+	}
 	if(!h.fw) flags |= SAM_FLAG_QUERY_STRAND;
 	ss << flags << "\t";
 	// RNAME
diff --git a/search_1mm_phase1.c b/search_1mm_phase1.c
index f6ac90a..8614947 100644
--- a/search_1mm_phase1.c
+++ b/search_1mm_phase1.c
@@ -11,7 +11,7 @@
 
 	if(plen < 2) {
 		cerr << "Error: Reads must be at least 2 characters long in 1-mismatch mode" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 
 	if(!nofw) {
diff --git a/search_23mm_phase1.c b/search_23mm_phase1.c
index 9288555..494d920 100644
--- a/search_23mm_phase1.c
+++ b/search_23mm_phase1.c
@@ -12,11 +12,11 @@
 
 	if(plen < 3 && two) {
 		cerr << "Error: Read (" << name << ") is less than 3 characters long" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	else if(plen < 4) {
 		cerr << "Error: Read (" << name << ") is less than 4 characters long" << endl;
-		throw std::runtime_error("");
+		throw 1;
 	}
 	if(!nofw) {
 		// Do an exact-match search on the forward pattern, just in
diff --git a/sequence_io.h b/sequence_io.h
index 255f0a1..09b4366 100644
--- a/sequence_io.h
+++ b/sequence_io.h
@@ -30,11 +30,13 @@ static void readSequenceFile(const std::string& infile,
 	if(baseCutoff <= 0) return;
 	FILE *in = fopen(infile.c_str(), "r");
 	if(in == NULL) {
-		throw runtime_error("Could not open sequence file");
+		cerr << "Could not open sequence file" << endl;
+		throw 1;
 	}
 	// Associate large input buffer with FILE *in
 	if(setvbuf(in, buf, _IOFBF, 256 * 1024) != 0) {
-		throw runtime_error("Could not create input buffer for sequence file");
+		cerr << "Could not create input buffer for sequence file" << endl;
+		throw 1;
 	}
 	// Read entries using SeqAn
 	int cnt = 0;
diff --git a/shmem.h b/shmem.h
index c991696..5e5145d 100644
--- a/shmem.h
+++ b/shmem.h
@@ -70,7 +70,7 @@ bool allocSharedMem(std::string fname,
 					cerr << "shmctl returned " << ret
 						 << " for IPC_RMID, errno is " << errno
 						 << ", shmid is " << shmid << endl;
-					throw std::runtime_error("");
+					throw 1;
 				} else {
 					cerr << "Deleted shared mem chunk with shmid " << shmid << endl;
 				}
@@ -82,22 +82,22 @@ bool allocSharedMem(std::string fname,
 			} else {
 				cerr << "shmget returned " << shmid << " for and errno is " << errno << endl;
 			}
-			throw std::runtime_error("");
+			throw 1;
 		}
 		ptr = (T*)shmat(shmid, 0, 0);
 		if(ptr == (void*)-1) {
 			cerr << "Failed to attach " << memName << " to shared memory with shmat()." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(ptr == NULL) {
 			cerr << memName << " pointer returned by shmat() was NULL." << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		// Did I create it, or did I just attach to one created by
 		// another process?
 		if((ret = shmctl(shmid, IPC_STAT, &ds)) < 0) {
 			cerr << "shmctl returned " << ret << " for IPC_STAT and errno is " << errno << endl;
-			throw std::runtime_error("");
+			throw 1;
 		}
 		if(ds.shm_segsz != shmemLen) {
 			cerr << "Warning: shared-memory chunk's segment size (" << ds.shm_segsz
@@ -105,7 +105,7 @@ bool allocSharedMem(std::string fname,
 				 << "Deleteing old shared memory block and trying again." << endl;
 			if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
 				cerr << "shmctl returned " << ret << " for IPC_RMID and errno is " << errno << endl;
-				throw std::runtime_error("");
+				throw 1;
 			}
 		} else {
 			break;