refactoring of assemble_pairs

[biopieces.git] / bp_bin / add_ident

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
index 16bde7abc886bd719452c467dc08f27d4183b765..b15a86dbf7d6aa63f117574b36f756ca2a8c1e38 100755 (executable)
--- a/bp_bin/add_ident
+++ b/bp_bin/add_ident
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 
@@ -39,6 +40,7 @@ $options = Maasha::Biopieces::parse_options(
     [
         { long => 'key',    short => 'k', type => 'string', mandatory => 'no', default => 'ID', allowed => undef, disallowed => undef },
         { long => 'prefix', short => 'p', type => 'string', mandatory => 'no', default => 'ID', allowed => undef, disallowed => undef },
+        { long => 'offset', short => 'o', type => 'uint',   mandatory => 'no', default => '0',  allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -48,7 +50,7 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 $key    = $options->{ "key" };
 $prefix = $options->{ "prefix" };
 
-$i = 0;
+$i = $options->{ "offset" };
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
@@ -82,4 +84,3 @@ END
 
 
 __END__
-