added --no_gaps switch in blast_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@625 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index 55d05308ce6a7ef8d1ee9bf942c9bfbd9102dfa2..e567e77954050b9566ca44e22d0cd43e363d7af7 100755 (executable)
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -48,6 +48,7 @@ $options = Maasha::Biopieces::parse_options(
         { long => 'e_val',    short => 'e', type => 'float',  mandatory => 'no', default => 10,    allowed => undef,                                  disallowed => undef },
         { long => 'filter',   short => 'f', type => 'string', mandatory => 'no', default => 'no',  allowed => 'yes,no',                               disallowed => undef },
         { long => 'cpus',     short => 'c', type => 'uint',   mandatory => 'no', default => 1,     allowed => undef,                                  disallowed => 0 },
+        { long => 'no_gaps',  short => 'G', type => 'flag',   mandatory => 'no', default => undef, allowed => undef,                                  disallowed => undef },
     ]   
 );
 
@@ -89,6 +90,12 @@ if ( $options->{ 'filter' } eq 'yes' ) {
      $options->{ 'filter' } = 'F';
 }
 
+if ( $options->{ 'no_gaps' } ) {
+    $options->{ 'gapped' } = 'F';
+} else {
+    $options->{ 'gapped' } = 'T';
+}
+
 if ( $options->{ 'verbose' } )
 {
     Maasha::Common::run(
@@ -97,6 +104,7 @@ if ( $options->{ 'verbose' } )
             "-p $program",
             "-e $options->{ 'e_val' }",
             "-a $options->{ 'cpus' }",
+            "-g $options->{ 'gapped' }",
             "-m 8",
             "-i $tmp_in",
             "-d $options->{ 'database' }",