From 5a72e59723846a89b73db70d7976b1d61fa4c32a Mon Sep 17 00:00:00 2001
From: eead-csic-compbio <compbio@eead.csic.es>
Date: Wed, 3 Feb 2016 17:51:28 +0100
Subject: [PATCH] fixed bug in get_homologues.pl which meant pan genome was
 overestimated with -c

---
 CHANGES.txt       | 1 +
 get_homologues.pl | 7 +++----
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGES.txt b/CHANGES.txt
index d34cce0..38a6261 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -90,3 +90,4 @@
 25012016: fixed bug in _cluster_makeHomolog.pl,_cluster_makeInparalog.pl,_cluster_makeOrtholog.pl reported by Maliha Aziz, which did not affect results, but produce them slower
 01022016: updated download_genomes_ncbi.pl and sample_genome_list.txt to fit current NCBI repositories, and manual
 01022016: removed estimate_RAM from get_homologues.pl, as RAM consumption has been reduced
+03022016: fixed bug in get_homologues.pl which meant pan genome was overestimated with -c; EST not affected, thanks Joaquim Martins Jr!
diff --git a/get_homologues.pl b/get_homologues.pl
index d09f43e..10efce9 100755
--- a/get_homologues.pl
+++ b/get_homologues.pl
@@ -1719,7 +1719,6 @@
       $LSE_reference = cluster_lineage_expansions($ref_inparalogues);
     }
 
-
     for($t=1;$t<$n_of_taxa;$t++)
     {
       $coregenome[$s][$t] = 0;
@@ -1835,7 +1834,7 @@
         my $ref_homol = makeHomolog($saveRAM,$tmptaxa[$t],$tmptaxa[$t2],$evalue_cutoff,
           $MIN_PERSEQID_HOM,$MIN_COVERAGE_HOM,$redo_orth);
 
-        foreach $gene ($gindex{$tmptaxa[$t]}[0] .. $gindex{$tmptaxa[0]}[1])
+        foreach $gene ($gindex{$tmptaxa[$t]}[0] .. $gindex{$tmptaxa[$t]}[1])
         {
           if($ref_homol->{$gene}){ $n_of_homs_in_genomes{$gene}++; }
         }
@@ -1858,13 +1857,13 @@
       }
 
       # update pan total
-      foreach $gene ($gindex{$tmptaxa[$t]}[0] .. $gindex{$tmptaxa[0]}[1])
+      foreach $gene ($gindex{$tmptaxa[$t]}[0] .. $gindex{$tmptaxa[$t]}[1])
       {
         next if($n_of_homs_in_genomes{$gene} || $inparalogues{$gene});
         $pangenome[$s][$t]++;
       }
 
-      print "# adding $tmptaxa[$t]: core=$coregenome[$s][$t] pan=$pangenome[$s][$t]\n";
+      print "# adding $tmptaxa[$t]: core=$coregenome[$s][$t] pan=$pangenome[$s][$t]\n"; 
     }
   }