From eab4d4c7565a2304a2f18bd79e5404581e1b57a6 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 23 Jul 2009 10:25:17 +0000 Subject: [PATCH] added options to bowtie_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@579 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/bowtie_seq | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq index c69d29c..849dbf2 100755 --- 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 }, ] ); -- 2.39.2