From 158b5df5074ce53313349c9420a5235f36d47d0c Mon Sep 17 00:00:00 2001
From: Migun Shakya <microbeatic@gmail.com>
Date: Wed, 1 Apr 2020 22:26:08 -0600
Subject: [PATCH] added print statement that describes the run

---
 src/phame                              | 18 +++++++-----------
 test/ctl_files/t7_ebola_cmp_preads.ctl |  2 +-
 test/ctl_files/t9_ebola_ctg_preads.ctl |  2 +-
 3 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/src/phame b/src/phame
index e4d0d4d..c2db213 100755
--- a/src/phame
+++ b/src/phame
@@ -313,27 +313,23 @@ print "\tproject = $project\n";
 print "\tcdsSNPS = $gsignal\n";
 print "\tbuildSNPdb:\t$buildSNPdb\n";
 print "\tdata:\t$data\n";
-print "\ttree:\t$tree\n";
 if ( $tree == 1){
     print "\tTrees will be made using FastTree.\n"
-}
-if ( $tree == 2){
+} elsif ( $tree == 2){
     print "\tTrees will be made using RaxML.\n"
-}
-
-if ( $tree == 3){
+} elsif ( $tree == 3){
     print "\tTrees will be made using iqtree.\n"
-}
-
-if ( $tree == 4){
+} elsif ( $tree == 4){
     print "\tTrees will be made using all three methods.\n"
+} elsif ($tree == 0){
+    print "\tNo Trees to be made.\n"
 }
 
-if ( $bsignal == 0){
+if ( $bsignal == 0 and $tree > 0 ){
     print "\tNo bootstraps.\n"
 }
 
-if ( $bsignal == 1){
+if ( $bsignal == 1 and $tree > 0 ){
     print "\t$bootstrap bootstraps!\n"
 }
 
diff --git a/test/ctl_files/t7_ebola_cmp_preads.ctl b/test/ctl_files/t7_ebola_cmp_preads.ctl
index d47c60f..f2823c7 100644
--- a/test/ctl_files/t7_ebola_cmp_preads.ctl
+++ b/test/ctl_files/t7_ebola_cmp_preads.ctl
@@ -2,7 +2,7 @@
       workdir = ../workdirs/t7_ebola_complete_pread # directory where contigs/reads files are located and output is stored
 
     reference = 1  # 0:pick a random reference; 1:use given reference; 2: use ANI based reference
-      reffile = KJ660347.fasta  # reference filename 
+      reffile = KJ660347.ref_genome.fasta  # reference filename 
 
       project = t7  # main alignment file name
 
diff --git a/test/ctl_files/t9_ebola_ctg_preads.ctl b/test/ctl_files/t9_ebola_ctg_preads.ctl
index 5d3e5f1..38c5434 100644
--- a/test/ctl_files/t9_ebola_ctg_preads.ctl
+++ b/test/ctl_files/t9_ebola_ctg_preads.ctl
@@ -2,7 +2,7 @@
       workdir = ../workdirs/t9_ebola_contigs_pread # directory where contigs/reads files are located and output is stored
 
     reference = 1  # 0:pick a random reference; 1:use given reference; 2: use ANI based reference
-      reffile = KJ660347.fasta  # reference filename 
+      reffile = KJ660347.ref_genome.fasta  # reference filename 
 
       project = t9  # main alignment file name