fixed seq qual length check

[biopieces.git] / bp_bin / read_mysql

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index 8abc9087434cb1a0a49598515d7d15fbfa535981..2d8f7b1674c3704cb2bb554554fb703a70505a8a 100755 (executable)
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::SQL;
@@ -35,17 +36,17 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
+my ( $user, $password, $options, $in, $out, $record, $dbh, $results );
 
-$default_user     = Maasha::UCSC::ucsc_get_user();
-$default_password = Maasha::UCSC::ucsc_get_password();
+$user     = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
+$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef,             allowed => undef, disallowed => undef },
-        { long => 'query',    short => 'q', type => 'string', mandatory => 'yes', default => undef,             allowed => undef, disallowed => undef },
-        { long => 'user',     short => 'u', type => 'string', mandatory => 'no',  default => $default_user,     allowed => undef, disallowed => undef },
-        { long => 'password', short => 'p', type => 'string', mandatory => 'no',  default => $default_password, allowed => undef, disallowed => undef },
+        { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef,     allowed => undef, disallowed => undef },
+        { long => 'query',    short => 'q', type => 'string', mandatory => 'yes', default => undef,     allowed => undef, disallowed => undef },
+        { long => 'user',     short => 'u', type => 'string', mandatory => 'no',  default => $user,     allowed => undef, disallowed => undef },
+        { long => 'password', short => 'p', type => 'string', mandatory => 'no',  default => $password, allowed => undef, disallowed => undef },
     ]   
 );