From 5b9b9fe5bdae753a380e9883ad503a6a1adea82e Mon Sep 17 00:00:00 2001
From: Shujun Ou <shujun.ou.1@gmail.com>
Date: Fri, 3 Apr 2020 13:21:53 -0500
Subject: [PATCH] correct genome sequence number in the TEanno.sum file #73

---
 EDTA.pl              | 2 +-
 util/buildSummary.pl | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/EDTA.pl b/EDTA.pl
index e953596..faed9f7 100755
--- a/EDTA.pl
+++ b/EDTA.pl
@@ -607,7 +607,7 @@
 	`perl $make_masked -genome $genome -rmout $genome.out -maxdiv 30 -minscore 1000 -minlen 1000 -hardmask 1 -misschar N -threads $threads -exclude $exclude`;
 	`mv $genome.new.masked $genome.MAKER.masked`;
 	my $maker_TE = `perl $count_base $genome.MAKER.masked`;
-	$maker_TE = (split /\s+/, $maker_TE)[-1];
+	$maker_TE = (split /\s+/, $maker_TE)[3];
 	$maker_TE = sprintf("%.2f%%", $maker_TE*100);
 
 	# check results and report status
diff --git a/util/buildSummary.pl b/util/buildSummary.pl
index f6d77a9..6512028 100755
--- a/util/buildSummary.pl
+++ b/util/buildSummary.pl
@@ -691,7 +691,7 @@ sub usage {
 ##
 print "Repeat Stats\n";
 print "============\n";
-print "Total Sequences: " . scalar( keys( %seqs ) ) . "\n";
+print "Total Sequences: " . $totalSeqNum . "\n";
 print "Total Length: $totalSeqLen bp\n";
 if ( $taxDB ) {
   print "Ancestral Repeats: $ancestralCount ( $ancestralBPMasked bp )\n";