more soap_seq debugging

git-svn-id: http://biopieces.googlecode.com/svn/trunk@182 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 4e30438ce13ce08e8a9d54a52781aa6cd8f3f34c..039536eb3b4efbc55f09f60adb8e0f3103d11817 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -575,6 +575,8 @@ sub get_options
         @options = qw(
             in_file|i=s
             genome|g=s
+            mismatches|m=s
+            gap_size|G=s
             cpus|c=s
         );
     }
@@ -3584,7 +3586,9 @@ sub script_soap_seq
 
     my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields );
 
-    $options->{ "cpus" } ||= 1;
+    $options->{ "mismatches" } ||= 2;
+    $options->{ "gap_size" }   ||= 0;
+    $options->{ "cpus" }       ||= 1;
 
     $options->{ "in_file" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna" if $options->{ 'genome' };
 
@@ -3604,7 +3608,7 @@ sub script_soap_seq
 
     close $fh_out;
 
-    Maasha::Common::run( "soap", "-r 2 -a $tmp_in -p $options->{ 'cpus' } -d $options->{ 'in_file' } -o $tmp_out > /dev/null 2>&1", 1 );
+    Maasha::Common::run( "soap", "-r 2 -a $tmp_in -v $options->{ 'mismatches' } -g $options->{ 'gap_size'} -p $options->{ 'cpus' } -d $options->{ 'in_file' } -o $tmp_out > /dev/null 2>&1", 1 );
 
     unlink $tmp_in;