added options to bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@579 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index c69d29c9f8d71560c94c911351320aeb90cc97ec..849dbf28deaf6c34968b50d53aea75709f66bcae 100755 (executable)
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -42,9 +42,11 @@ my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out,
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'genome',     short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef,     disallowed => undef },
-        { long => 'mismatches', short => 'm', type => 'uint',   mandatory => 'no',  default => 2,     allowed => "0,1,2,3", disallowed => undef },
-        { long => 'max_hits',   short => 'h', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef,     disallowed => 0     },
+        { long => 'genome',      short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef,     disallowed => undef },
+        { long => 'mismatches',  short => 'm', type => 'uint',   mandatory => 'no',  default => 0,     allowed => "0,1,2,3", disallowed => undef },
+        { long => 'max_hits',    short => 'h', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef,     disallowed => 0     },
+        { long => 'seed_length', short => 's', type => 'uint',   mandatory => 'no',  default => 28,    allowed => undef,     disallowed => 0     },
+        { long => 'cpus',        short => 'c', type => 'uint',   mandatory => 'no',  default => 1,     allowed => undef,     disallowed => 0     },
     ]   
 );