bleh blah

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

diff --git a/code_perl/Maasha/UCSC.pm b/code_perl/Maasha/UCSC.pm
index 7445807a42029c8940cd36716b7aa2349406b84c..fad1401a38d6744cbcffea9736b0dae50ae54c90 100644 (file)
--- a/code_perl/Maasha/UCSC.pm
+++ b/code_perl/Maasha/UCSC.pm
@@ -1216,6 +1216,11 @@ sub phastcons_parse_entry
     # Given a PhastCons entry converts this to a
     # list of super blocks.
 
+#    $options->{ "min" }       ||= 10;
+#    $options->{ "dist" }      ||= 25;
+#    $options->{ "threshold" } ||= 0.8;
+#    $options->{ "gap" }       ||= 5;
+
     my ( $lines,   # list of lines
          $args,    # argument hash
        ) = @_;
@@ -1638,9 +1643,13 @@ sub ucsc_get_user
 
     # Returns a string.
 
-    my ( $fh, $line, $user );
+    my ( $file, $fh, $line, $user );
+
+    $file = "$ENV{ 'HOME' }/.hg.conf";
+
+    return if not -f $file;
 
-    $fh = Maasha::Common::read_open( "$ENV{ 'HOME' }/.hg.conf" );
+    $fh = Maasha::Common::read_open( $file );
 
     while ( $line = <$fh> )
     {
@@ -1669,9 +1678,13 @@ sub ucsc_get_password
 
     # Returns a string.
 
-    my ( $fh, $line, $password );
+    my ( $file, $fh, $line, $password );
+
+    $file = "$ENV{ 'HOME' }/.hg.conf";
+
+    return if not -f $file;
 
-    $fh = Maasha::Common::read_open( "$ENV{ 'HOME' }/.hg.conf" );
+    $fh = Maasha::Common::read_open( $file );
 
     while ( $line = <$fh> )
     {