removed debug message

[biopieces.git] / bp_bin / mate_pair_dist

diff --git a/bp_bin/mate_pair_dist b/bp_bin/mate_pair_dist
index d6526799e16200f8b0bc052ff47971fe3db05b72..0475f7d275a5fda9cf3b4a07e81ac1bce07d0d34 100755 (executable)
--- a/bp_bin/mate_pair_dist
+++ b/bp_bin/mate_pair_dist
@@ -52,16 +52,19 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     {
         ( $q_id, $mate ) = split "/", $record->{ 'Q_ID' }, 2;
 
-        if ( $mate == 2 )
+        if ( $mate )
         {
-            if ( $record->{ 'STRAND' } eq '+' ) {
-                $record->{ 'STRAND' } = '-';
-            } else {
-                $record->{ 'STRAND' } = '+';
+            if ( $mate == 2 )
+            {
+                if ( $record->{ 'STRAND' } eq '+' ) {
+                    $record->{ 'STRAND' } = '-';
+                } else {
+                    $record->{ 'STRAND' } = '+';
+                }
             }
-        }
 
-        push @{ $data{ $record->{ 'S_ID' } }{ $record->{ 'STRAND' } }{ $q_id }{ $mate } }, $record; 
+            push @{ $data{ $record->{ 'S_ID' } }{ $record->{ 'STRAND' } }{ $q_id }{ $mate } }, $record; 
+        }
     }
 
     Maasha::Biopieces::put_record( $record, $out );
@@ -89,9 +92,16 @@ foreach $contig ( keys %data )
                 foreach $mate2 ( @mates2 )
                 {
                     $new_record = {
-                        S_ID   => $contig,
-                        Q_ID1  => $mate1->{ 'Q_ID' },
-                        Q_ID2  => $mate2->{ 'Q_ID' },
+                        S_ID     => $contig,
+                        Q_ID1    => $mate1->{ 'Q_ID' },
+                        Q_ID2    => $mate2->{ 'Q_ID' },
+                        S_BEG1   => $mate1->{ 'S_BEG' },
+                        S_BEG2   => $mate2->{ 'S_BEG' },
+                        S_END1   => $mate1->{ 'S_END' },
+                        S_END2   => $mate2->{ 'S_END' },
+                        SEQ_LEN1 => $mate1->{ 'SEQ_LEN' },
+                        SEQ_LEN2 => $mate2->{ 'SEQ_LEN' },
+                        STRAND   => $mate1->{ 'STRAND' },
                         DIST   => abs( $mate2->{ 'S_BEG' } - $mate1->{ 'S_BEG' } ),
                     };
 
@@ -125,41 +135,3 @@ END
 
 
 __END__
-
-
-@records = sort { $a->{ 'S_ID' }   cmp $b->{ 'S_ID' }   or 
-                  $a->{ 'STRAND' } cmp $b->{ 'STRAND' } or
-                  $a->{ 'Q_ID' }   cmp $b->{ 'Q_ID' }   or
-                  $a->{ 'S_BEG' }  <=> $b->{ 'S_BEG' } } @records;
-
-print STDERR "done.\n" if $options->{ 'verbose' };
-
-# map { print join( "\t", $_->{ 'S_ID' }, $_->{ 'STRAND' }, $_->{ 'Q_ID' }, $_->{ 'S_BEG' } ), "\n" } @records; # DEBUG
-print Dumper( \@records );
-
-$i = 0;
-
-while ( $i < @records - 1 )
-{
-    $j = $i + 1;
-
-    while ( $j < @records and 
-            $records[ $i ]->{ 'S_ID' }   eq $records[ $j ]->{ 'S_ID' } and
-            $records[ $i ]->{ 'STRAND' } eq $records[ $j ]->{ 'STRAND' }
-    )
-    {
-        ( $id1, $mate1 ) = split "/", $records[ $i ]->{ 'Q_ID' }, 2;
-        ( $id2, $mate2 ) = split "/", $records[ $j ]->{ 'Q_ID' }, 2;
-
-         print Dumper( $i, $j, $id1, $mate1, $id1, $mate2 );
-
-        if ( $id1 eq $id2 and $mate1 == 1 and $mate2 == 2 )
-        {
-            print "Dist: " . ( $records[ $j ]->{ 'S_BEG' } - $records[ $i ]->{ 'S_BEG' } ) . "\n";
-        }
-
-        $j++;
-    }
-
-    $i = $j;
-}