allow for inflation factor for MCL to be changed

dist.ini

@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.8.0
+version = 3.8.1
 author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute

lib/Bio/Roary.pm

@@ -47,6 +47,7 @@ has 'group_limit'                 => ( is => 'rw', isa => 'Num',      default  =
 has 'core_definition'             => ( is => 'rw', isa => 'Num',      default  => 1.0 );
 has 'verbose'                     => ( is => 'rw', isa => 'Bool',     default  => 0 );
 has 'mafft'                       => ( is => 'ro', isa => 'Bool',     default  => 0 );
+has 'inflation_value'             => ( is => 'rw', isa => 'Num',      default  => 1.5 );
 
 has 'output_multifasta_files' => ( is => 'ro', isa => 'Bool', default => 0 );
 
@@ -108,6 +109,7 @@ sub run {
         mcl_exec        => $self->mcl_exec,
         job_runner      => $self->job_runner,
         cpus            => $self->cpus,
+	inflation_value => $self->inflation_value,
         output_file     => $output_mcl_filename
     );
     $mcl->run();

lib/Bio/Roary/CommandLine/Roary.pm

@@ -54,6 +54,8 @@ has 'kraken_db' => ( is => 'rw', isa => 'Str',  default => '/lustre/scratch118/i
 has 'run_qc'    => ( is => 'rw', isa => 'Bool', default => 0 );
 has '_working_directory' => ( is => 'rw', isa => 'File::Temp::Dir', lazy => 1, builder => '_build__working_directory' );
 
+has 'inflation_value'             => ( is => 'rw', isa => 'Num',      default  => 1.5 );
+
 sub _build__working_directory
 {
 	my ($self) = @_;
@@ -69,7 +71,7 @@ sub BUILD {
         $job_runner,            $makeblastdb_exec,  $mcxdeblast_exec,         $mcl_exec,      $blastp_exec,
         $apply_unknowns_filter, $cpus,              $output_multifasta_files, $verbose_stats, $translation_table,
         $run_qc,                $core_definition,   $help,                    $kraken_db,     $cmd_version,
-        $mafft,                 $output_directory,  $check_dependancies,
+        $mafft,                 $output_directory,  $check_dependancies, $inflation_value,
     );
 
     GetOptionsFromArray(
@@ -99,6 +101,7 @@ sub BUILD {
         'k|kraken_db=s'             => \$kraken_db,
         'w|version'                 => \$cmd_version,
         'a|check_dependancies'      => \$check_dependancies,
+	'inflation_value=f'         => \$inflation_value,
         'h|help'                    => \$help,
     );
 
@@ -143,6 +146,7 @@ sub BUILD {
     $self->mcxdeblast_exec($mcxdeblast_exec)   if ( defined($mcxdeblast_exec) );
     $self->mcl_exec($mcl_exec)                 if ( defined($mcl_exec) );
     $self->cpus($cpus)                         if ( defined($cpus) );
+    $self->inflation_value($inflation_value)   if ( defined($inflation_value));
 
     if ( defined($perc_identity) ) {
         $self->perc_identity($perc_identity);
@@ -298,6 +302,7 @@ sub run {
         core_definition         => $self->core_definition,
         verbose                 => $self->verbose,
         mafft                   => $self->mafft,
+	inflation_value         => $self->inflation_value,
     );
     $pan_genome_obj->run();
 

lib/Bio/Roary/External/Mcl.pm

@@ -31,7 +31,7 @@ has 'output_file'     => ( is => 'ro', isa => 'Str', default  => 'output_groups'
 
 has '_score'     => ( is => 'ro', isa => 'Str', default  => 'r' );
 
-has '_inflation_value' => ( is => 'ro', isa => 'Num', default => 1.5 );
+has 'inflation_value' => ( is => 'ro', isa => 'Num', default => 1.5 );
 has '_logging'         => ( is => 'ro', isa => 'Str', default  => '> /dev/null 2>&1' );
 
 has 'memory_in_mb'  => ( is => 'ro', isa => 'Int',  lazy => 1, builder => '_build_memory_in_mb' );
@@ -84,7 +84,7 @@ sub _command_to_run {
             $self->_full_mcxdeblast_exec, '-m9', '--score='.$self->_score,
             '--line-mode=abc', $self->blast_results, '2> /dev/null',
             '|', $self->mcl_exec, '-', '--abc',
-            '-I', $self->_inflation_value, '-o', $self->output_file, 
+            '-I', $self->inflation_value, '-o', $self->output_file, 
             $self->_logging
         )
     );