reworked usage and -h behaviour

bjmt · May 3, 2019 · a6cdb59 · a6cdb59
1 parent efa6caa
commit a6cdb59
Show file tree

Hide file tree

Showing 6 changed files with 28 additions and 5 deletions.
diff --git a/README b/README
@@ -17,7 +17,7 @@ The following binaries are created:
     bin/seqgen        Generate a random string
     bin/shuffler      Shuffle a string or sequences inside a fasta file
 
-Run these without any arguments or with the -h flag to see usage.
+Run these with the -h flag to see usage.
 
 
 countfa

diff --git a/src/countfa.cpp b/src/countfa.cpp
@@ -128,6 +128,7 @@ int main(int argc, char **argv) {
                   seqfile.open(optarg);
                   if (seqfile.bad()) {
                     cerr << "Error: file not found" << endl;
+                    cerr << "Run countfa -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_file = true;
@@ -140,7 +141,8 @@ int main(int argc, char **argv) {
 
   if (!has_file) {
     if (isatty(STDIN_FILENO)) {
-      usage();
+      cerr << "Error: missing input" << endl;
+      cerr << "Run countfa -h to see usage." << endl;
       exit(EXIT_FAILURE);
     }
     do_countfa(cin);

diff --git a/src/countlets.cpp b/src/countlets.cpp
@@ -100,6 +100,7 @@ int main(int argc, char **argv) {
                   seqfile.open(optarg);
                   if (seqfile.bad()) {
                     cerr << "Error: file not found" << endl;
+                    cerr << "Run countlets -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_file = true;
@@ -117,6 +118,7 @@ int main(int argc, char **argv) {
                   outfile.open(optarg);
                   if (outfile.bad()) {
                     cerr << "Error: could not create outfile" << endl;
+                    cerr << "Run countlets -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_out = true;
@@ -134,12 +136,14 @@ int main(int argc, char **argv) {
 
   if (k < 1) {
     cerr << "Error: k must be greater than 0" << endl;
+    cerr << "Run countlets -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 
   if (!has_file) {
     if (isatty(STDIN_FILENO)) {
-      usage();
+      cerr << "Error: missing input" << endl;
+      cerr << "Run countlets -h to see usage." << endl;
       exit(EXIT_FAILURE);
     }
   }
@@ -180,6 +184,7 @@ int main(int argc, char **argv) {
 
     if (alph.length() < 1) {
       cerr << "Error: could not parse -a option" << endl;
+      cerr << "Run countlets -h to see usage." << endl;
       exit(EXIT_FAILURE);
     }
 

diff --git a/src/countwin.cpp b/src/countwin.cpp
@@ -102,6 +102,7 @@ int main(int argc, char **argv) {
                   infile.open(optarg);
                   if (infile.bad()) {
                     cerr << "Error: file not found" << endl;
+                    cerr << "Run countwin -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_file = true;
@@ -112,6 +113,7 @@ int main(int argc, char **argv) {
                   outfile.open(optarg);
                   if (outfile.bad()) {
                     cerr << "Error: could not create outfile" << endl;
+                    cerr << "Run countwin -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_out = true;
@@ -150,12 +152,14 @@ int main(int argc, char **argv) {
 
   if (k < 1) {
     cerr << "Error: k must be greater than 0" << endl;
+    cerr << "Run countwin -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 
   if (!has_file) {
     if (isatty(STDIN_FILENO)) {
       cerr << "Error: missing input" << endl;
+      cerr << "Run countwin -h to see usage." << endl;
       exit(EXIT_FAILURE);
     }
   }
@@ -170,6 +174,7 @@ int main(int argc, char **argv) {
   } else {
     if (window < k) {
       cerr << "Error: window size must be equal to or greater than k" << endl;
+      cerr << "Run countwin -h to see usage." << endl;
       exit(EXIT_FAILURE);
     }
   }
@@ -178,6 +183,7 @@ int main(int argc, char **argv) {
 
   if (step < 1 || step > window) {
     cerr << "Error: step size must be between 1 and window size" << endl;
+    cerr << "Run countwin -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 
@@ -204,6 +210,7 @@ int main(int argc, char **argv) {
   STOP = START + seq.length() - 1;
   if (seq.length() < k) {
     cerr << "Error: sequence cannot be smaller than k" << endl;
+    cerr << "Run countwin -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
   counts = count_klets(vector<char>(seq.begin(), seq.end()), klets, lets_uniq, k, alphlen);

diff --git a/src/seqgen.cpp b/src/seqgen.cpp
@@ -60,7 +60,8 @@ int main(int argc, char **argv) {
   size_t last, next;
 
   if (argc == 1) {
-    usage();
+    cerr << "Error: missing alphabet and sequence length" << endl;
+    cerr << "Run seqgen -h to see usage." << endl;
     return 0;
   }
 
@@ -70,6 +71,7 @@ int main(int argc, char **argv) {
                   outfile.open(optarg);
                   if (outfile.bad()) {
                     cerr << "Error: could not create outfile" << endl;
+                    cerr << "Run seqgen -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_out = true;
@@ -95,6 +97,7 @@ int main(int argc, char **argv) {
 
   if (seqlen < 1) {
     cerr << "Error: please input a desired sequence length above 0" << endl;;
+    cerr << "Run seqgen -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 
@@ -113,6 +116,7 @@ int main(int argc, char **argv) {
 
   if (alphlen < 1) {
     cerr << "Error: could not parse sequence alphabet" << endl;
+    cerr << "Run seqgen -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 

diff --git a/src/shuffler.cpp b/src/shuffler.cpp
@@ -210,6 +210,7 @@ int main(int argc, char **argv) {
                   seqfile.open(optarg);
                   if (seqfile.bad()) {
                     cerr << "Error: file not found" << endl;
+                    cerr << "Run shuffler -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_file = true;
@@ -226,6 +227,7 @@ int main(int argc, char **argv) {
                   outfile.open(optarg);
                   if (outfile.bad()) {
                     cerr << "Error: could not create outfile" << endl;
+                    cerr << "Run shuffler -h to see usage." << endl;
                     exit(EXIT_FAILURE);
                   }
                   has_out = true;
@@ -254,17 +256,20 @@ int main(int argc, char **argv) {
   }
 
   if (!has_file && isatty(STDIN_FILENO)) {
-    usage();
+    cerr << "Error: missing input" << endl;
+    cerr << "Run shuffler -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 
   if (k < 1) {
     cerr << "Error: k must be greater than 0" << endl;
+    cerr << "Run shuffler -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }
 
   if (use_linear && use_markov) {
     cerr << "Error: only use one of -l and -m flags" << endl;
+    cerr << "Run shuffler -h to see usage." << endl;
     exit(EXIT_FAILURE);
   }