Possible p-value bug

[rmashl]

$ hotspot3d

Version: V0.6.3

$ hotspot3d search --maf-file=$maf --prep-dir=$dir --output-prefix=$prefix 1>t.out 2>t.err

resulted in a lot of

Use of uninitialized value $threed_cut in numeric le (<=) at /mypath/perl5/lib/perl5/TGI/Mutpro/Main/Proximity.pm line 502, line 2835.

Observed in Proximity.pm that both keys 'pvalue_cutoff' and 'p_value_cutoff' are used. This patch works for me:

--- Proximity.pm.orig   2016-10-04 16:14:08.000000000 -0500
+++ Proximity.pm    2016-10-09 21:06:56.707320000 -0500
@@ -63,13 +63,13 @@
     );
     if ( $help ) { print STDERR help_text(); exit 0; }
     unless( $options ) { die $this->help_text(); }
-   if ( not defined $this->{'p_value_cutoff'} ) {
+   if ( not defined $this->{'pvalue_cutoff'} ) {
         if ( not defined $this->{'3d_distance_cutoff'} and not defined $this->{'pvalue_cutoff'} ) {
             warn "HotSpot3D::Cluster warning: no pair distance limit given, setting to default p-value cutoff = 0.05\n";
-            $this->{'p_value_cutoff'} = $PVALUEDEFAULT;
+            $this->{'pvalue_cutoff'} = $PVALUEDEFAULT;
             $this->{'3d_distance_cutoff'} = $MAXDISTANCE;
         } else {
-            $this->{'p_value_cutoff'} = 1;
+            $this->{'pvalue_cutoff'} = 1;
         }
     } else {
         if ( not defined $this->{'3d_distance_cutoff'} ) {

[kuanlinhuang]

I got the same problem at the search step and this patch also worked for me.

[AdamDS]

good catch. updated code for v0.6.3.