updating contact info, and making recurrence as the default vertex type

README.md

@@ -38,7 +38,7 @@ Usage
 Support
 -------
 
-For user support please email adamscott@wustl.edu
+For user support please email amila@wustl.edu
 
 
 Update

lib/TGI/Mutpro/Main/Cluster.pm

@@ -80,7 +80,7 @@ sub new {
     $this->{'linear_cutoff'} = 0;
 	$this->{'max_radius'} = 10;
     $this->{'length_scale'} = $MAXGEODESIC;
-	$this->{'vertex_type'} = $SITE;
+	$this->{'vertex_type'} = $RECURRENCE;
 	$this->{'distance_measure'} = $AVERAGEDISTANCE;
     $this->{'amino_acid_header'} = "amino_acid_change";
     $this->{'transcript_id_header'} = "transcript_name";
@@ -411,7 +411,7 @@ sub setOptions {
 	if ( $this->{'vertex_type'} eq $SITE or $this->{'clustering'} eq $DENSITY ) {
 		if ( $this->{'JSON_status'} == 0 ) {
 			if ( not defined $this->{'hup_file'} or not -e $this->{'hup_file'} ) {
-				warn "If you're using SITE and/or DENSITY, you must provide a valid hugo.uniprot.pdb.csv file location using --hup-file option\n";
+				warn "If you're using SITE and/or DENSITY, you must provide a valid hugo.uniprot.pdb.csv(generated by preprocess step) file location using --hup-file option\n";
 				die $this->help_text();
 			}
 		}
@@ -2002,7 +2002,7 @@ Usage: hotspot3d cluster [options]
 
                              OPTIONAL (General)
 --clustering                 Cluster using network or density-based methods (network or density), default: network
---vertex-type                Graph vertex type for network-based clustering (recurrence, unique, site or weight), default: site
+--vertex-type                Graph vertex type for network-based clustering (recurrence, unique, site or weight), default: recurrence
                                  recurrence vertices are the genomic mutations for each sample from the given .maf
                                  unique vertices are the specific genomic changes
                                  site vertices are the affected protein positions