Provide proper help output for all tools of last

[Andreas Tille]

Hi,

when preparing the latest version of last as Debian package (here named
last-align) I tried to provide man pages for all tools provided in the
package to comply with Debian policy.  The easiest way to do this is
simply using the help2man tool which produces more or less reasonable
manpages from the output you give when using the help option
(-h/--help).

When doing so I stumbled upon the fact that not all tools direct the
help output to stdout but rather stderr.  This is not conform to GNU
coding standards and thus intentionally not supported by help2man[1].
So I did a small patch (attached) to enable output to stdout (and
defining a -h option for lastdb which was missing).  Please feel free
to apply this patch in your next version.

I would also be really happy if
    last-map-probs, last-reduce-alignments, last-remove-dominated,
    maf-join, maf2tab
would get a -/--help option as well to be able to provide rudimentary
manpages also for these tools.

IMHO this would be in the interest of your users - properly maintained
manpages with real text would be even better.

Hope this helps a bit enhancing your fine software.

Kind regards and thanks for maintaining last

    Andreas.

[1] http://bugs.debian.org/138752

-- 
http://fam-tille.de

Author: Andreas Tille <ti...@debian.org>
Description: According to GNU coding standards help messages should go to stdout
 not to stderr.  THis patch ensures that help2man will work correctly
--- last-62.orig/src/LastalArguments.cc
+++ last-62/src/LastalArguments.cc
@@ -4,6 +4,8 @@
 #include "stringify.hh"
 #include <unistd.h>  // getopt
 #include <sstream>
+#include <cstdlib>
+#include <iostream>
 #include <vector>
 #include <stdexcept>
 #include <cstring>  // strtok
@@ -108,7 +110,8 @@
 	 != -1 ){
     switch(c){
     case 'h':
-      throw std::runtime_error(help);
+      std::cout << help ;
+      exit(1);
     case 'o':
       outFile = optarg;
       break;
--- last-62.orig/src/LastdbArguments.cc
+++ last-62/src/LastdbArguments.cc
@@ -2,6 +2,8 @@
 
 #include "LastdbArguments.hh"
 #include "stringify.hh"
+#include <cstdlib>
+#include <iostream>
 #include <unistd.h>  // getopt
 #include <stdexcept>
 
@@ -27,6 +29,7 @@
 usage: lastdb [options] output-name fasta-sequence-file(s)\n\
 \n\
 Main Options (default settings):\n\
+-h: show all options and their default settings\n\
 -p: interpret the sequences as proteins\n\
 -c: read the sequences case-sensitively\n\
 -m: periodic spaced-seed pattern (" + maskPattern + ")\n\
@@ -40,8 +43,11 @@
 ";
 
   int c;
-  while( (c = getopt(argc, argv, "pcm:w:s:a:b:v")) != -1 ) {
+  while( (c = getopt(argc, argv, "hpcm:w:s:a:b:v")) != -1 ) {
     switch(c){
+    case 'h':
+      std::cout << usage;
+      exit(1);
     case 'p':
       isProtein = true;
       break;