--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy_core_wrapper.pl	Thu Jun 09 20:15:42 2016 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/env perl
+
+#--------------------------------------
+#
+#        snippy_core_wrapper.pl
+#
+# This is an intermediary script between snippy-core.xml and snippy-core
+# It:
+#   - Copys the supplied zipped snippy output files to the working dir
+#   - Untars them to their datafile name
+#   - Builds the snippy-core command and captures the stdout and stderr to files
+#   - Runs the snippy-core command
+#
+#--------------------------------------
+
+use warnings;
+use strict;
+use File::Copy;
+use File::Basename;
+
+my(@Options, $indirs, $mincov, $noref);
+setOptions();
+
+my @list_of_dirs = split /\s+/, $indirs;
+
+#The list of final directories to be passed to snippy-core will be stored here.
+my @snippy_outs;
+
+foreach my $d (@list_of_dirs){
+  #print STDERR "$d\n";
+  my $bn = basename($d);
+  my ($name, $dir, $ext) = fileparse($d, '\..*');
+  copy($d, $bn);
+  #print STDERR "$d, $bn, $name, $dir, $ext\n";
+  `tar -xf $bn`;
+  move("./out", "./$name");
+  unlink($bn);
+  push @snippy_outs, $name;
+}
+
+my $commandline = "snippy-core ";
+
+$commandline .= "--noref " if $noref;
+$commandline .= "--mincov $mincov " if $mincov;
+$commandline .= join(" ", @snippy_outs);
+print STDERR "snippy-core commandline: $commandline\n";
+
+my $ok = system($commandline);
+
+#----------------------------------------------------------------------
+# Option setting routines
+
+sub setOptions {
+  use Getopt::Long;
+
+  @Options = (
+    {OPT=>"help",    VAR=>\&usage,             DESC=>"This help"},
+    {OPT=>"mincov=i",  VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."},
+    {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."},
+    {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."},
+  );
+
+  &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();
+
+  # Now setup default values.
+  foreach (@Options) {
+    if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
+      ${$_->{VAR}} = $_->{DEFAULT};
+    }
+  }
+}
+
+sub usage {
+  print "Usage: $0 [options] -i inputfile > ... \n";
+  foreach (@Options) {
+    printf "  --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
+           defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
+  }
+  exit(1);
+}