migrated blat_seq

[biopieces.git] / code_perl / Maasha / UCSC / PSL.pm

diff --git a/code_perl/Maasha/UCSC/PSL.pm b/code_perl/Maasha/UCSC/PSL.pm
index a45006ec0bfbb85967cf31d33bb38b1ac71c16df..4dfaf841f8dc7155d0b439ffc1ec3bf33c5b15dd 100644 (file)
--- a/code_perl/Maasha/UCSC/PSL.pm
+++ b/code_perl/Maasha/UCSC/PSL.pm
@@ -120,7 +120,7 @@ sub psl_entry_get
 }
 
 
-sub psl2record
+sub psl2biopiece
 {
     # Martin A. Hansen, November 2008
 
@@ -179,11 +179,11 @@ sub psl_calc_score
 
     my ( $score );
 
-    $score = $psl_entry[ MATCHES ] +
-             int( $psl_entry[ REPMATCHES ] / 2 ) - 
-             $psl_entry[ MISMATCHES ] - 
-             $psl_entry[ QNUMINSERT ] - 
-             $psl_entry[ SNUMINSERT ];
+    $score = $psl_entry->[ MATCHES ] +
+             int( $psl_entry->[ REPMATCHES ] / 2 ) - 
+             $psl_entry->[ MISMATCHES ] - 
+             $psl_entry->[ QNUMINSERT ] - 
+             $psl_entry->[ SNUMINSERT ];
 
     return $score;
 }