disabled quality score conversion in FASTQ and Solexa

[biopieces.git] / bp_bin / align_pair_seq

diff --git a/bp_bin/align_pair_seq b/bp_bin/align_pair_seq
index ebe340d693a73f897a0ff1007c95f48aecb1f041..7f622f121d397cf0f124830860d3635935f94c5b 100755 (executable)
--- a/bp_bin/align_pair_seq
+++ b/bp_bin/align_pair_seq
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,15 +26,17 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::AlignTwoSeq;
+use Data::Dumper;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $count, $record, @records );
+my ( $options, $in, $out, $count, $record, @records, $space, $matches );
 
 $options = Maasha::Biopieces::parse_options();
 
@@ -53,11 +55,9 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
         if ( $count == 2 )
         {
-            $records[ 0 ]->{ 'SEQ' } = lc $records[ 0 ]->{ 'SEQ' };
-            $records[ 1 ]->{ 'SEQ' } = lc $records[ 1 ]->{ 'SEQ' };
-
-            my $matches = Maasha::AlignTwoSeq::align_two_seq( \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } );
+            $matches = Maasha::AlignTwoSeq::align_two_seq( { 'Q_SEQ' => \$records[ 0 ]->{ 'SEQ' } , 'S_SEQ' => \$records[ 1 ]->{ 'SEQ' } }, [] );
             
+            Maasha::AlignTwoSeq::shift_case( $matches, \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } );
             Maasha::AlignTwoSeq::insert_indels( $matches, \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } );
 
             map { Maasha::Biopieces::put_record( $_, $out ) } @records;