Updates to the usage message of the text2fvf binary

Not all short options for which long options were shown were mentioned
in the usage message. Also fix some grammar issues in the usage message.

Note: not all short options mentions in the options code have been
documented in the usage string yet. See Issue #3.

fvfutil/usage.cpp

@@ -7,21 +7,21 @@ void print_text2fvf_usage(char * progname)
     cout << "USAGE: " << progname << " -i INFILE -o OUTFILE [-r N2] "
          << "[--colnames[=CFILE]] [-t] [--datatype=TYPE]" << endl;
     cout << endl;
-    cout << "\t--infile=INFILE    : the name of the input file "
+    cout << "\t-i INFILE    --infile=INFILE    : the name of the input file "
          << "containing matrix in text format" << endl;
-    cout << "\t--outfile=OUTFILE  : name of the output file which "
+    cout << "\t-o OUTFILE   --outfile=OUTFILE  : name of the output file which "
          << "will containing matrix in FVF format" << endl;
-    cout << "\t--skipcols=N1      : skip N1 first columns when reading "
+    cout << "\t-c N1        --skipcols=N1      : skip N1 first columns when reading "
          << "from the input text file" << endl;
-    cout << "\t--rownames=N2      : row names are provided in the N2-th "
+    cout << "\t-r N2        --rownames=N2      : row names are provided in the N2-th "
          << "column of the text file" << endl;
     cout << "\t--colnames[=CFILE] : column names are provided either as "
          << "the first line of the text" << endl;
     cout << "\t                     matrix text file "
          << "(if no arguments supplied) or in a separate" << endl;
     cout << "\t                     text file CFILE" << endl;
-    cout << "\t--transpose        : should the matrix be transposed" << endl;
-    cout << "\t--datatype=TYPE    : specify destination data type, "
+    cout << "\t-t           --transpose        : should the matrix be transposed" << endl;
+    cout << "\t-d TYPE      --datatype=TYPE    : specify destination data type, "
          << "default is DOUBLE" << endl;
     cout << "\t-n STRING    --nanString=STRING : specify the string used to code NAs" << endl;
     cout << "\t-R           --Rmatrix          : if this option is set, the "
@@ -37,17 +37,17 @@ void print_text2fvf_usage(char * progname)
     cout << "By default, the columns of the text matrix are considered "
          << "as 'variables'" << endl;
     cout << "for which FVF will provide fast access. If you want it "
-         << "other way around," << endl;
-    cout << "please specify '-t' option." << endl;
+         << "the other way around," << endl;
+    cout << "please specify the '-t' option." << endl;
     cout << "" << endl;
     cout << "EXAMPLES: " << progname << " -i test.mldose -o test.mldose.fvf "
          << "-c 2 -r 1" << endl;
     cout << "          Text matrix file contains two starting columns, "
          << "first of which" << endl;
-    cout << "          contains subjects IDs." << endl;
-    cout << "          Command will convert text matrix provided "
+    cout << "          contains the subject IDs." << endl;
+    cout << "          The command will convert the text matrix provided "
          << "in 'test.mldose' to " << endl;
-    cout << "          FVF-formated file 'test.mldose.fvf'. "
+    cout << "          the FVF-formated file 'test.mldose.fvd and test.mldose.fvi'. "
          << "Columns will be stored as" << endl;
     cout << "          the fast-access FVF 'variables'" << endl;
     cout << "" << endl;
@@ -60,7 +60,7 @@ void print_text2fvf_usage(char * progname)
     cout << "          " << progname << " -i test.mldose "
          << "-o test.mldose.fvf -c 2 -r 1 --colnames=test.snplist" << endl;
     cout << "          Same as example 1, but we tell that column names "
-         << "are stored in file" << endl;
+         << "are stored in the file" << endl;
     cout << "          'test.snplist' (mind the full format "
          << "used: '--colnames=CFILE')" << endl;
     cout << "" << endl;