reworked usage and -h behaviour

bjmt · bjmt · commit a6cdb5904903 · 2019-05-02T23:34:17.000-04:00
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);
   }
 

Original file line number	Diff line number	Diff line change
`@@ -100,6 +100,7 @@ int main(int argc, char **argv) {`
`100`	`100`	`seqfile.open(optarg);`
`101`	`101`	`if (seqfile.bad()) {`
`102`	`102`	`cerr << "Error: file not found" << endl;`
	`103`	`+ cerr << "Run countlets -h to see usage." << endl;`
`103`	`104`	`exit(EXIT_FAILURE);`
`104`	`105`	`}`
`105`	`106`	`has_file = true;`
`@@ -117,6 +118,7 @@ int main(int argc, char **argv) {`
`117`	`118`	`outfile.open(optarg);`
`118`	`119`	`if (outfile.bad()) {`
`119`	`120`	`cerr << "Error: could not create outfile" << endl;`
	`121`	`+ cerr << "Run countlets -h to see usage." << endl;`
`120`	`122`	`exit(EXIT_FAILURE);`
`121`	`123`	`}`
`122`	`124`	`has_out = true;`
`@@ -134,12 +136,14 @@ int main(int argc, char **argv) {`
`134`	`136`
`135`	`137`	`if (k < 1) {`
`136`	`138`	`cerr << "Error: k must be greater than 0" << endl;`
	`139`	`+ cerr << "Run countlets -h to see usage." << endl;`
`137`	`140`	`exit(EXIT_FAILURE);`
`138`	`141`	`}`
`139`	`142`
`140`	`143`	`if (!has_file) {`
`141`	`144`	`if (isatty(STDIN_FILENO)) {`
`142`		`- usage();`
	`145`	`+ cerr << "Error: missing input" << endl;`
	`146`	`+ cerr << "Run countlets -h to see usage." << endl;`
`143`	`147`	`exit(EXIT_FAILURE);`
`144`	`148`	`}`
`145`	`149`	`}`
`@@ -180,6 +184,7 @@ int main(int argc, char **argv) {`
`180`	`184`
`181`	`185`	`if (alph.length() < 1) {`
`182`	`186`	`cerr << "Error: could not parse -a option" << endl;`
	`187`	`+ cerr << "Run countlets -h to see usage." << endl;`
`183`	`188`	`exit(EXIT_FAILURE);`
`184`	`189`	`}`
`185`	`190`
Original file line number	Diff line number	Diff line change
`@@ -102,6 +102,7 @@ int main(int argc, char **argv) {`
`102`	`102`	`infile.open(optarg);`
`103`	`103`	`if (infile.bad()) {`
`104`	`104`	`cerr << "Error: file not found" << endl;`
	`105`	`+ cerr << "Run countwin -h to see usage." << endl;`
`105`	`106`	`exit(EXIT_FAILURE);`
`106`	`107`	`}`
`107`	`108`	`has_file = true;`
`@@ -112,6 +113,7 @@ int main(int argc, char **argv) {`
`112`	`113`	`outfile.open(optarg);`
`113`	`114`	`if (outfile.bad()) {`
`114`	`115`	`cerr << "Error: could not create outfile" << endl;`
	`116`	`+ cerr << "Run countwin -h to see usage." << endl;`
`115`	`117`	`exit(EXIT_FAILURE);`
`116`	`118`	`}`
`117`	`119`	`has_out = true;`
`@@ -150,12 +152,14 @@ int main(int argc, char **argv) {`
`150`	`152`
`151`	`153`	`if (k < 1) {`
`152`	`154`	`cerr << "Error: k must be greater than 0" << endl;`
	`155`	`+ cerr << "Run countwin -h to see usage." << endl;`
`153`	`156`	`exit(EXIT_FAILURE);`
`154`	`157`	`}`
`155`	`158`
`156`	`159`	`if (!has_file) {`
`157`	`160`	`if (isatty(STDIN_FILENO)) {`
`158`	`161`	`cerr << "Error: missing input" << endl;`
	`162`	`+ cerr << "Run countwin -h to see usage." << endl;`
`159`	`163`	`exit(EXIT_FAILURE);`
`160`	`164`	`}`
`161`	`165`	`}`
`@@ -170,6 +174,7 @@ int main(int argc, char **argv) {`
`170`	`174`	`} else {`
`171`	`175`	`if (window < k) {`
`172`	`176`	`cerr << "Error: window size must be equal to or greater than k" << endl;`
	`177`	`+ cerr << "Run countwin -h to see usage." << endl;`
`173`	`178`	`exit(EXIT_FAILURE);`
`174`	`179`	`}`
`175`	`180`	`}`
`@@ -178,6 +183,7 @@ int main(int argc, char **argv) {`
`178`	`183`
`179`	`184`	`if (step < 1 \|\| step > window) {`
`180`	`185`	`cerr << "Error: step size must be between 1 and window size" << endl;`
	`186`	`+ cerr << "Run countwin -h to see usage." << endl;`
`181`	`187`	`exit(EXIT_FAILURE);`
`182`	`188`	`}`
`183`	`189`
`@@ -204,6 +210,7 @@ int main(int argc, char **argv) {`
`204`	`210`	`STOP = START + seq.length() - 1;`
`205`	`211`	`if (seq.length() < k) {`
`206`	`212`	`cerr << "Error: sequence cannot be smaller than k" << endl;`
	`213`	`+ cerr << "Run countwin -h to see usage." << endl;`
`207`	`214`	`exit(EXIT_FAILURE);`
`208`	`215`	`}`
`209`	`216`	`counts = count_klets(vector<char>(seq.begin(), seq.end()), klets, lets_uniq, k, alphlen);`
Original file line number	Diff line number	Diff line change
`@@ -210,6 +210,7 @@ int main(int argc, char **argv) {`
`210`	`210`	`seqfile.open(optarg);`
`211`	`211`	`if (seqfile.bad()) {`
`212`	`212`	`cerr << "Error: file not found" << endl;`
	`213`	`+ cerr << "Run shuffler -h to see usage." << endl;`
`213`	`214`	`exit(EXIT_FAILURE);`
`214`	`215`	`}`
`215`	`216`	`has_file = true;`
`@@ -226,6 +227,7 @@ int main(int argc, char **argv) {`
`226`	`227`	`outfile.open(optarg);`
`227`	`228`	`if (outfile.bad()) {`
`228`	`229`	`cerr << "Error: could not create outfile" << endl;`
	`230`	`+ cerr << "Run shuffler -h to see usage." << endl;`
`229`	`231`	`exit(EXIT_FAILURE);`
`230`	`232`	`}`
`231`	`233`	`has_out = true;`
`@@ -254,17 +256,20 @@ int main(int argc, char **argv) {`
`254`	`256`	`}`
`255`	`257`
`256`	`258`	`if (!has_file && isatty(STDIN_FILENO)) {`
`257`		`- usage();`
	`259`	`+ cerr << "Error: missing input" << endl;`
	`260`	`+ cerr << "Run shuffler -h to see usage." << endl;`
`258`	`261`	`exit(EXIT_FAILURE);`
`259`	`262`	`}`
`260`	`263`
`261`	`264`	`if (k < 1) {`
`262`	`265`	`cerr << "Error: k must be greater than 0" << endl;`
	`266`	`+ cerr << "Run shuffler -h to see usage." << endl;`
`263`	`267`	`exit(EXIT_FAILURE);`
`264`	`268`	`}`
`265`	`269`
`266`	`270`	`if (use_linear && use_markov) {`
`267`	`271`	`cerr << "Error: only use one of -l and -m flags" << endl;`
	`272`	`+ cerr << "Run shuffler -h to see usage." << endl;`
`268`	`273`	`exit(EXIT_FAILURE);`
`269`	`274`	`}`
`270`	`275`