diff --git a/src/Common.hpp b/src/Common.hpp
index f67ee5c..bdfaffa 100644
--- a/src/Common.hpp
+++ b/src/Common.hpp
@@ -75,6 +75,7 @@ struct Bustools_opt
   std::string dump;
   bool dump_bool = false;
   bool split_correct = false;
+  bool parse_error = false;
 
   /* predict */
   std::string predict_input; //specified the same way as the output for count - count and histogram filenames will be created from this
diff --git a/src/bustools_main.cpp b/src/bustools_main.cpp
index ab954a8..857eb71 100644
--- a/src/bustools_main.cpp
+++ b/src/bustools_main.cpp
@@ -172,6 +172,9 @@ void parse_ProgramOptions_sort(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -213,6 +216,9 @@ void parse_ProgramOptions_merge(int argc, char **argv, Bustools_opt &opt)
     case 'e':
       opt.count_ecs = optarg;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -245,6 +251,9 @@ void parse_ProgramOptions_mash(int argc, char **argv, Bustools_opt &opt)
     case 'o':
       opt.output = optarg;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -312,6 +321,9 @@ void parse_ProgramOptions_capture(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -375,6 +387,9 @@ void parse_ProgramOptions_count(int argc, char **argv, Bustools_opt &opt)
     case 'm':
       opt.count_gene_multimapping = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -446,6 +461,9 @@ void parse_ProgramOptions_umicorrect(int argc, char **argv, Bustools_opt& opt) {
     case 'e':
       opt.count_ecs = optarg;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -480,6 +498,9 @@ void parse_ProgramOptions_predict(int argc, char **argv, Bustools_opt& opt) {
     case 't':
       opt.predict_t = atof(optarg);
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -521,6 +542,9 @@ void parse_ProgramOptions_dump(int argc, char **argv, Bustools_opt &opt)
     case 'd':
       opt.text_dumppad = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -560,6 +584,9 @@ void parse_ProgramOptions_fromtext(int argc, char **argv, Bustools_opt& opt) {
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -608,6 +635,9 @@ void parse_ProgramOptions_correct(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -650,12 +680,15 @@ void parse_ProgramOptions_whitelist(int argc, char **argv, Bustools_opt &opt)
     case 'f':
       opt.threshold = atoi(optarg);
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
   }
   
-  /* All other argumuments are (sorted) BUS files. */
+  /* All other arguments are (sorted) BUS files. */
   while (optind < argc)
     opt.files.push_back(argv[optind++]);
   
@@ -717,12 +750,15 @@ void parse_ProgramOptions_project(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
   }
   
-  /* All other argumuments are (sorted) BUS files. */
+  /* All other arguments are (sorted) BUS files. */
   while (optind < argc)
     opt.files.push_back(argv[optind++]);
   
@@ -763,12 +799,15 @@ void parse_ProgramOptions_inspect(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
   }
   
-  /* All other argumuments are (sorted) BUS files. */
+  /* All other arguments are (sorted) BUS files. */
   while (optind < argc)
     opt.files.push_back(argv[optind++]);
   
@@ -809,12 +848,15 @@ void parse_ProgramOptions_linker(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
   }
   
-  /* All other argumuments are (sorted) BUS files. */
+  /* All other arguments are (sorted) BUS files. */
   while (optind < argc)
     opt.files.push_back(argv[optind++]);
   
@@ -856,6 +898,9 @@ void parse_ProgramOptions_collapse(int argc, char** argv, Bustools_opt& opt) {
     case 'e':
       opt.count_ecs = optarg;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -904,6 +949,9 @@ void parse_ProgramOptions_clusterhist(int argc, char** argv, Bustools_opt& opt)
     case 'c':
       opt.cluster_input_file = optarg;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -947,12 +995,15 @@ void parse_ProgramOptions_extract(int argc, char **argv, Bustools_opt &opt)
     case 'p':
       opt.stream_out = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
   }
   
-  /* All other argumuments are (sorted) BUS files. */
+  /* All other arguments are (sorted) BUS files. */
   while (optind < argc)
     opt.files.push_back(argv[optind++]);
   
@@ -994,6 +1045,9 @@ bool parse_ProgramOptions_inflate(int argc, char **argv, Bustools_opt &opt)
     case 'h':
       print_usage = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -1074,6 +1128,9 @@ bool parse_ProgramOptions_compress(int argc, char **argv, Bustools_opt &opt)
     case 'h':
       print_usage = true;
       break;
+    case '?':
+      opt.parse_error = true;
+      break;
     default:
       break;
     }
@@ -1093,7 +1150,11 @@ bool check_ProgramOptions_sort(Bustools_opt &opt)
 {
   
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   size_t max_threads = std::thread::hardware_concurrency();
   
   if (opt.threads <= 0)
@@ -1220,7 +1281,11 @@ bool check_ProgramOptions_sort(Bustools_opt &opt)
 bool check_ProgramOptions_merge(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   // check for output directory
   if (!opt.stream_out)
   {
@@ -1309,7 +1374,11 @@ bool check_ProgramOptions_merge(Bustools_opt &opt)
 bool check_ProgramOptions_mash(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (opt.output.empty())
   {
     std::cerr << "Error: missing output directory" << std::endl;
@@ -1378,7 +1447,11 @@ bool check_ProgramOptions_mash(Bustools_opt &opt)
 bool check_ProgramOptions_dump(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out)
   {
     if (opt.output.empty())
@@ -1416,7 +1489,11 @@ bool check_ProgramOptions_dump(Bustools_opt &opt)
 bool check_ProgramOptions_fromtext(Bustools_opt& opt) 
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out) 
   {
     if (opt.output.empty()) 
@@ -1455,7 +1532,11 @@ bool check_ProgramOptions_fromtext(Bustools_opt& opt)
 bool check_ProgramOptions_capture(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (opt.filter)
   {
     // check if output directory exists or if we can create it
@@ -1567,7 +1648,11 @@ bool check_ProgramOptions_capture(Bustools_opt &opt)
 bool check_ProgramOptions_correct(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out)
   {
     if (opt.output.empty())
@@ -1630,6 +1715,10 @@ bool check_ProgramOptions_correct(Bustools_opt &opt)
 bool check_ProgramOptions_count(Bustools_opt &opt)
 {
   bool ret = true;
+
+  if (opt.parse_error) {
+      ret = false;
+  }
   
   // check for output directory
   if (opt.output.empty())
@@ -1775,7 +1864,11 @@ bool check_ProgramOptions_count(Bustools_opt &opt)
 
 bool check_ProgramOptions_predict(Bustools_opt& opt) {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   // check for output directory
   if (opt.output.empty()) {
     std::cerr << "Error: Missing output directory" << std::endl;
@@ -1846,7 +1939,11 @@ bool check_ProgramOptions_predict(Bustools_opt& opt) {
 
 bool check_ProgramOptions_umicorrect(Bustools_opt& opt) {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out) {
     if (opt.output.empty()) {
       std::cerr << "Error: missing output file" << std::endl;
@@ -1907,7 +2004,11 @@ bool check_ProgramOptions_umicorrect(Bustools_opt& opt) {
 bool check_ProgramOptions_whitelist(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (opt.output.empty())
   {
     std::cerr << "Error: missing output file" << std::endl;
@@ -1956,7 +2057,11 @@ bool check_ProgramOptions_whitelist(Bustools_opt &opt)
 bool check_ProgramOptions_project(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (opt.output.empty())
   {
     std::cerr << "Error: Missing output file" << std::endl;
@@ -2068,7 +2173,11 @@ bool check_ProgramOptions_project(Bustools_opt &opt)
 bool check_ProgramOptions_inspect(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (opt.output.size() && !checkOutputFileValid(opt.output))
   {
     std::cerr << "Error: unable to open output file" << std::endl;
@@ -2124,7 +2233,11 @@ bool check_ProgramOptions_inspect(Bustools_opt &opt)
 bool check_ProgramOptions_linker(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out)
   {
     if (opt.output.empty())
@@ -2164,7 +2277,11 @@ bool check_ProgramOptions_linker(Bustools_opt &opt)
 
 bool check_ProgramOptions_collapse(Bustools_opt& opt) {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   // check for output directory
   if (opt.output.empty()) {
     std::cerr << "Error: Missing output directory" << std::endl;
@@ -2245,7 +2362,11 @@ bool check_ProgramOptions_collapse(Bustools_opt& opt) {
 
 bool check_ProgramOptions_clusterhist(Bustools_opt& opt) {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   // check for output directory
   if (opt.output.empty()) {
     std::cerr << "Error: Missing output directory" << std::endl;
@@ -2343,7 +2464,11 @@ bool check_ProgramOptions_clusterhist(Bustools_opt& opt) {
 bool check_ProgramOptions_extract(Bustools_opt &opt)
 {
   bool ret = true;
-  
+
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (opt.output.empty())
   {
     std::cerr << "Error: missing output directory" << std::endl;
@@ -2434,9 +2559,12 @@ bool check_ProgramOptions_extract(Bustools_opt &opt)
 
 bool check_ProgramOptions_inflate(Bustools_opt &opt)
 {
-
   bool ret = true;
 
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out)
   {
     if (opt.output.empty())
@@ -2479,6 +2607,10 @@ bool check_ProgramOptions_compress(Bustools_opt &opt)
 {
   bool ret = true;
 
+  if (opt.parse_error) {
+    ret = false;
+  }
+
   if (!opt.stream_out)
   {
     if (opt.output.empty())
@@ -2656,7 +2788,7 @@ void Bustools_count_Usage()
             << "    --genecounts      Aggregate counts to genes only" << std::endl
             << "    --umi-gene        Perform gene-level collapsing of UMIs" << std::endl
             << "    --em              Estimate gene abundances using EM algorithm" << std::endl
-            << "    --cm              Count multiplicites instead of UMIs" << std::endl
+            << "    --cm              Count multiplicities instead of UMIs" << std::endl
             << "-m, --multimapping    Include bus records that pseudoalign to multiple genes" << std::endl
             << "    --hist            Output copy per UMI histograms for all genes" << std::endl 
             << "-d  --downsample      Specify a factor between 0 and 1 specifying how much to downsample" << std::endl