refactoring of assemble_pairs

[biopieces.git] / bp_bin / align_seq

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index 469a97abd7910fe5e6db8a5de884f594c7c4ea2b..632d732f21fe47bcdc054061bcc210f9fbdae8fe 100755 (executable)
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -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;
 use Maasha::Align;
@@ -48,7 +49,7 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
-    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {  # TODO use biopieces2fasta() instead
         push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
     } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
         push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];