refactoring of assemble_pairs

[biopieces.git] / bp_bin / extract_seq

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index d5760d5a76f7cf31b8e91e3f409f7921dd254af0..40260cc9e490b3629fb131f8435b8f6c3c81144c 100755 (executable)
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -69,23 +69,34 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     {
         if ( defined $beg and defined $end )
         {
-            if ( $end - $beg + 1 > length $record->{ "SEQ" } ) {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
-            } else {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
+            if ( $end - $beg + 1 > length $record->{ "SEQ" } )
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
+                $record->{ "SCORES" } = substr $record->{ "SEQ" }, $beg if $record->{ "SCORES" };
+            }
+            else
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
+                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $end - $beg + 1 if $record->{ "SCORES" };
             }
         }
         elsif ( defined $beg and defined $len )
         {
-            if ( $len > length $record->{ "SEQ" } ) {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
-            } else {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
+            if ( $len > length $record->{ "SEQ" } )
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
+                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
+            }
+            else
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg, $len;
+                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $len if $record->{ "SCORES" };
             }
         }
         elsif ( defined $beg )
         {
-            $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+            $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
+            $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
         }
 
         $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };