From b9669489749d627874b5c1ab29a0b3150ec95a87 Mon Sep 17 00:00:00 2001
From: Lee Katz - Aspen <gzu2@cdc.gov>
Date: Fri, 27 Mar 2020 13:24:28 -0400
Subject: [PATCH] fixed version number; added bootstrapping test for fofn
 option

---
 lib/Mashtree.pm  |  2 +-
 t/08_bootstrap.t | 33 +++++++++++++++++++++++++++++++--
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/lib/Mashtree.pm b/lib/Mashtree.pm
index c2e99ba..a6c2e9e 100644
--- a/lib/Mashtree.pm
+++ b/lib/Mashtree.pm
@@ -26,7 +26,7 @@ local $0=basename $0;
 ######
 # CONSTANTS
 
-our $VERSION = "1.0.4";
+our $VERSION = "1.1.2";
 our $MASHTREE_VERSION=$VERSION;
 our @fastqExt=qw(.fastq.gz .fastq .fq .fq.gz);
 our @fastaExt=qw(.fasta .fna .faa .mfa .fas .fsa .fa);
diff --git a/t/08_bootstrap.t b/t/08_bootstrap.t
index 773a653..936db45 100644
--- a/t/08_bootstrap.t
+++ b/t/08_bootstrap.t
@@ -11,13 +11,13 @@ use Bio::TreeIO;
 use IO::String;
 use Scalar::Util qw/looks_like_number/;
 
-use Test::More tests => 4;
+use Test::More tests => 5;
 
 use_ok 'Mashtree';
 use Mashtree;
 use Mashtree::Db;
 
-$ENV{PATH}="./bin:$ENV{PATH}";
+$ENV{PATH}="$RealBin/../bin:$ENV{PATH}";
 
 my $correctMashtree="((sample2:0.0020443525,sample1:0.0021037373)66:0.0000540274,sample3:0.0019622177,sample4:0.0020673526)83;";
 $correctMashtree=~s/(\d+\.)(\d+)/$1 . substr($2,0,4)/ge; # global and expression
@@ -61,3 +61,32 @@ subtest "Parts of the tree file intact" => sub{
   is $correctNodeString, $nodeString, "Taxon names in the tree: $nodeString";
 };
 
+# Address the bug fix https://github.com/lskatz/mashtree/issues/51#issuecomment-604495598
+subtest "file-of-filenames" => sub{
+  plan tests=>2;
+
+  # Make the file of filenames
+  my $fofn = "$RealBin/lambda/lambda.fofn";
+  my @file = glob("$RealBin/lambda/*.fastq.gz");
+  open(my $fh, ">", $fofn) or die "ERROR: could not write to $fofn: $!";
+  for my $f(@file){
+    print $fh "$f\n";
+  }
+  close $fh;
+
+  my $mashtreeFofn = `mashtree_bootstrap.pl --tempdir $RealBin/lambda/jackknife.tmp --reps 100 --numcpus 2 -- --file-of-files $fofn 2>$RealBin/lambda/jackknife.log`;
+  note $mashtreeFofn;
+  
+  my $treeFh = IO::String->new($mashtree);
+  my $tree = Bio::TreeIO->new(-fh=>$treeFh, -format=>"newick")->next_tree;
+  $passed = is(ref($tree),"Bio::Tree::Tree","Produced a BioPerl tree object");
+  if(!$passed){
+    diag "Tree string produced was $mashtree";
+    BAIL_OUT("Tree object was not produced out of the tree string");
+  }
+
+  my @leaf = sort map{$_->id} grep{$_->is_Leaf} $tree->get_nodes;
+  is(scalar(@leaf), 4, "correct number of nodes");
+  note "@leaf";
+};
+