*** empty log message ***

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;

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);

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

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
 	;
 }
 
@@ -108,43 +113,46 @@ 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;
 }
 
 /**
  * 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. */
 			case 0:
 				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;
 	}
 }

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;
 }