finishm 0.0.1

data/spec/priner_spec.rb

@@ -0,0 +1,7 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Priner" do
+  it "fails" do
+    fail "hey buddy, you should probably rename this file and start specing for real"
+  end
+end

data/spec/read_input_spec.rb

@@ -0,0 +1,23 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'tempfile'
+
+Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm'); Bio::Log::CLI.configure('bio-velvet')
+
+
+describe "ReadInput" do
+  it 'should output correct fasta velvet singles' do
+    input = Bio::FinishM::ReadInput.new
+    input.fasta_singles = ['my.fasta']
+    input.velvet_read_arguments.should == ' -fasta -short my.fasta'
+    input.fasta_singles = ['my.fasta','another.fasta']
+    input.velvet_read_arguments.should == ' -fasta -short my.fasta another.fasta'
+  end
+
+#   it 'should handle interleaved pairs' do
+#     input = Bio::FinishM::ReadInput.new
+#     input.interleaved_fastq = ['my.fastq']
+#     input.velvet_read_arguments.should == ' -fastq -shortPaired my.fastq'
+#     input.interleaved_fastq_gz = ['my.fastq','fq2']
+#     input.velvet_read_arguments.should == ' -fastq -shortPaired my.fastq -fastq.gz -shortPaired my.fastq fq2'
+#   end
+end

data/spec/read_selection_by_kmer_spec.rb

@@ -0,0 +1,166 @@
+require 'tempfile'
+require 'rspec'
+require 'pp'
+require 'systemu'
+
+# To run this test:
+# $ rspec /path/to/test_script_being_tested.rb
+
+# Assumes that the name of the file being tested is ../something.rb relative to the directory containing this test scripts, and the name of this tes script is test_something.rb
+$:.unshift File.join(File.dirname(__FILE__),'..')
+script_under_test = File.basename(__FILE__).gsub(/^test_/,'')
+base = File.join File.dirname(__FILE__),'..'
+path_to_script = "rdmd -I#{base}/../BioD/ #{base}/bin/read_selection_by_kmer.d --quiet"
+
+# Re-build at the start
+status, stdout, stderr = systemu "rdmd --build-only -I#{base}/../BioD/ #{base}/bin/read_selection_by_kmer.d"
+raise stderr unless stderr == ""
+
+describe script_under_test do
+  it 'should scripting test ok' do
+    reads = %w(>whitelist_me ATGCCCC >blacklist_me ATGCATGG >ignore_me AAAAAAAA)
+    whitelist = %w(ATGC)
+    blacklist = %w(ATGG)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+    status, stdout, stderr = systemu "#{path_to_script} --whitelist #{whitelist_file.path} --blacklist #{blacklist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCC).join("\n")+"\n")
+  end
+
+  it 'should work without blacklist' do
+    reads = %w(>whitelist_me ATGCCCC >blacklist_me ATGCATGG >ignore_me AAAAAAAA)
+    whitelist = %w(ATGC)
+    blacklist = %w()
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+    status, stdout, stderr = systemu "#{path_to_script} --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCC >blacklist_me ATGCATGG).join("\n")+"\n")
+  end
+
+  it 'should default to a low kmer coverage' do
+    reads = %w(>whitelist_me ATGCCCC >blacklist_me ATGCATGG >ignore_me AAAAAAAA)
+    whitelist = %w(ATGC)
+    blacklist = %w()
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+    status, stdout, stderr = systemu "#{path_to_script} --whitelist #{whitelist_file.path} --reads #{reads_file.path}"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCC).join("\n")+"\n")
+  end
+
+  it 'should handle multiple whitelisted components' do
+    reads = %w(>whitelist_me ATGCCCC >blacklist_me ATGCATGG >ignore_me AAAAAAAA)
+    whitelist = %w(ATGC AAAA)
+    blacklist = %w(ATGG)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+    status, stdout, stderr = systemu "#{path_to_script} --whitelist #{whitelist_file.path} --blacklist #{blacklist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCC >ignore_me AAAAAAAA).join("\n")+"\n")
+  end
+
+  it 'should handle multiple whitelisted components in the same sequence' do
+    reads = %w(>whitelist_me ATGCCCCAAAA >blacklist_me ATGCATGG >ignore_me AAAAAAAA)
+    whitelist = %w(ATGC AAAA)
+    blacklist = %w(ATGG)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+    status, stdout, stderr = systemu "#{path_to_script} --whitelist #{whitelist_file.path} --blacklist #{blacklist_file.path} --reads #{reads_file.path}"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCCAAAA).join("\n")+"\n")
+  end
+
+  it 'should handle multiple whitelisted components in the same sequence and one in revcomp' do
+    reads = %w(>whitelist_me ATGCCCCTTTT >blacklist_me ATGCATGG >ignore_me AAAAAAAA)
+    whitelist = %w(ATGC AAAA)
+    blacklist = %w(ATGG)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+    status, stdout, stderr = systemu "#{path_to_script} --whitelist #{whitelist_file.path} --blacklist #{blacklist_file.path} --reads #{reads_file.path}"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCCTTTT).join("\n")+"\n")
+  end
+
+  it 'should handle min leftover length' do
+    reads = %w(>whitelist_me ATGCCCCTTTT >blacklist_me ATGCATGG)
+    whitelist = %w(ATGC)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 4 --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCCTTTT >blacklist_me ATGCATGG).join("\n")+"\n")
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 6 --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCCTTTT).join("\n")+"\n")
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 7 --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCCTTTT).join("\n")+"\n")
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 8 --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w().join("\n"))
+  end
+
+  it 'should handle min leftover length when kmer is on reverse strand' do
+    reads = %w(>whitelist_me ATGCCCCTTTT >blacklist_me ATGCATGG)
+    whitelist = %w(GCAT)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 6 --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>whitelist_me ATGCCCCTTTT).join("\n")+"\n")
+  end
+
+
+  it 'should handle min leftover length with blacklist in the middle' do
+    reads = %w(>blacklist_me ATGCCCCTTTT >blacklist_me2 ATGCATGG)
+    whitelist = %w(GCAT)
+    blacklist = %w(CCCT)
+
+    reads_file = Tempfile.new('reads'); reads_file.puts reads.join("\n"); reads_file.close
+    whitelist_file = Tempfile.new('whitelist'); whitelist_file.puts whitelist.join("\n"); whitelist_file.close
+    blacklist_file = Tempfile.new('blacklist'); blacklist_file.puts blacklist.join("\n"); blacklist_file.close
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 6 --whitelist #{whitelist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq(%w(>blacklist_me ATGCCCCTTTT).join("\n")+"\n")
+
+    status, stdout, stderr = systemu "#{path_to_script} --min-leftover-length 6 --whitelist #{whitelist_file.path} --blacklist #{blacklist_file.path} --reads #{reads_file.path} --kmer-coverage-target 10"
+    raise stderr unless stderr == ""
+    status.exitstatus.should eq(0)
+    stdout.should eq("")
+  end
+end

data/spec/read_to_node_spec.rb

@@ -0,0 +1,35 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "ReadToNode" do
+  it 'should work with postive and negative node IDs' do
+    rtn = Bio::FinishM::ReadToNode.new(File.join(TEST_DATA_DIR, 'read_to_node/1_a_graph/ReadToNode.bin'))
+    rtn[1].should == [1]
+    rtn[2].should == [1]
+    rtn[256].should == [7]
+    rtn[6002].should == [18]
+  end
+
+  it 'should be able to deal with reads that are not contained in the graph at all' do
+    rtn = Bio::FinishM::ReadToNode.new(File.join(TEST_DATA_DIR, 'read_to_node/2_no_read256_or_259/ReadToNode.bin'))
+
+    # Originally: read, node
+    # 255, -3
+    # 256, -7 => removed
+    # 257, -1
+    # 258, 2
+    # 259, 1 => removed
+    # 260, -1
+    rtn[255].should == [3]
+    rtn[256].should == []
+    rtn[257].should == [1]
+    rtn[258].should == [2]
+    rtn[259].should == []
+    rtn[260].should == [1]
+  end
+
+  it 'should be able to deal with there being no last read' do
+    rtn = Bio::FinishM::ReadToNode.new(File.join(TEST_DATA_DIR, 'read_to_node/3_no_last_read/ReadToNode.bin'))
+    rtn[6002].should == []
+    rtn[6001].should == [3]
+  end
+end

data/spec/roundup_spec.rb

@@ -0,0 +1,366 @@
+require 'tempfile'
+require 'bio'
+require 'bio-commandeer'
+require 'spec_helper'
+
+describe 'finishm tweak' do
+  path_to_script = File.join(File.dirname(__FILE__),'..','bin','finishm roundup')
+
+  it 'should scripting test ok two scaffolds, one with a gap' do
+    Dir.mktmpdir do |tmpdir|
+      command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/1_gap_then_unscaffolded/reads.fa.gz "+
+        "--genomes #{TEST_DATA_DIR}/tweak/1_gap_then_unscaffolded/scaffolds.fa --output-directory #{tmpdir}"
+      Bio::Commandeer.run(command).should == ''
+      output_file = File.join(tmpdir,'scaffolds.fa.scaffolds.fasta')
+      File.exist?(output_file).should == true
+      File.open(output_file).read.should == <<EOF
+>scaffold1 scaffold random_sequence_length_5000_chopped_1-600_then_N_then_chopped_700-2000:random_sequence_length_5000_chopped_3000-5000$
+TTCCGGGTGTTATGGTGTCGCCGTGTTAACTAATAACTTTGTCCGTGTCAATTGATAACGTAAACTGCCTATCTCACGTACGATCCACTACGCGCACCCGAACTTCGGAGAATTAGCAAAGGAAAGTGTATCAAGCATTTGGTAAAACAGATGGTATTCCTCAATACTGGGCTGACGCGGAAATAGCGCGAACTTATTTATCGGTACGTTAGGTGTATCTACTAAGTAAGATTTCTGATAGTTATCAGGGCGTTCTAAATTTAGTCTCACAGACCCCTGCGTATGCAGCCGCACAGCCAATGCCGATCCTTTCTAAGATAACTCCCGCAGGAAACGTGTAGATCCAAGCTTGTTCCTCGGAGTAGCAAGCTAACTTCAAGCTTACTCAAAGCAGACAAGTTTTAATAGTGCACGCCGTAACGTTCCCCGCAACGAGTATGTGATCCGGATGCGATAAACAAGCTGAGTCACCGTGACGGGGTACTAAGTAATGACATATTGCGAGCATATGCTCCACAAGAAATGTCATACAATAGCACCAATGAGCAAGTTCATATCTGTTATTATTCAGTTACTAAAAATATACTAGTAACTCGACCTGTTAGGTTATCTGCAAATCACTAGCTACTGTATCTCATAAGATTGTCAATCGCGTCATGTCCGCAACCAGGTGCGAACGTCTTGTCCCGGTATCTTGGAATTGAAAGGGACTTGCCAGTCATTAGGACACTAAACCGGATAAACCAGAAAAAAGGAATGCGCGCCGCGGAGGTGCACGATGCCAGCGCAGACAATAACGCCGGACCTTCCAGGGTTCATGGTCAAGTTAAGCGTGCGGCTGCAGCGCAAAATCGTTATCCCACCTCTTATATGCAACACCGTCGACGAAGCGAAGGATTATGAGGGTAGCTCGATAGAATGAAAGCACGTCTTGGGCGGAGGTTCGTTATGATGAAGGCGGTCTGGAGGTACGAGCCGAAAGAGGAGCCGCGTGCGACTCCGACTCGCGTAGTTGAAATCAGGGGGTTTAAACTCTACTTGCCAATTCACCTGATGTGTAACCTGAGGCTATGAGTTGCCAGAGGTCCAATATTTGCTAGTCTGGCTGAGGTTAAGCTAGTAGTTCTAACTACAGGCGGCAGGCCAATTGTGAGCCAACGCACTAGATCACGTGCATACAACCACAACACATAAACTCGCTTTAAAGTGCGGGGTGCCCCCGGTCGAACTAAGCTCTCGTCCACGTTTTGGGGGAAAAGTCCTATGGATCCTGAGACAGCGCGCCTCCACGGAGCAAAAGTTGTTGACCAATAGTCTGACCATAACAACATGTGACTGGGTAGCCCCTGGTCATCCCCCCACATTGCCGATTTGTCAACAGTTGCACTGCCTGGAGGATCATGCGTCAGGATCAAGTCTATCGCCCACGACATATGAATTTCCACTGTCCGTGCGTCGAACCACGACAGTATGTGAGACGTGTCGAAGTCCCCCCCTTAGTGAAACGGCACTTTCTTAACCAAAGATTAAGCGGCGCCTTGGAATGGTTATCCTACGAGGAGTATGTCATACTCACTCTGTTTCTAGAACAAGTCCGTGAGAATTAGGCTGTCGGAGTAGTTTAGATAAGTGTATTTTATCTTCCGAGGCTATGGCTGGTGTGAACAATTCCCCAGACTTCCGAATTTGACTTCCTCAGTTCCGGGGCTCCCCATGACCAAACTAGATGGAATAACCTACATGACCAAACTGTCGCTTCCTGTATTGTGCTCTCAAGACTATATGAGTCGAATTCCAAGGCGCTATATCGCCTATTAAGGCAAGGCAGCCTCTAGCGCTATGCATTTCGTAACGGAATTAACGCCCACACCATCCTCAATTAACGTTAGGTACTCATATCCCCCTCATATTGGGGCCAATACCCCAAGGAGTTCGGACACGATCAACCAGCGGCGTCACCGCCCCCAGTGTGCAACGTTGTGGGGGAACACGAAATATATAGTGTAAAGTTGATCTCCATTGCCCCGCAGACGAATTCGTACGAGAACAATGAGTATGGATAGCTAGACACAAACGTTGCATAAAATTCTTTAACTTAAAGAAAAAACAATCTCAGGCTACAATCTTCGTTCACAACTAACTTACCGGTCCTCCCTCAAAACATCAGGTGGACGCTTCTTCAACTTCCTCCCCATATTATCGGGCGTATGTCTATCAAAGTGCTCCGCTAGCACTCGGGAAGGACTTATGATAACTACTGATGCCACTCGGAGTCGCGTTCACATCGTTCCCTCGGTTAAGAAGCAGAGGGCGTCATTAGCATTCAGCACGATCACCTATCCTAGTCTGATGGGACATAGGTGCTTCAAGCACTCGCACATATTAGATTTGCTGCCGCTTATAGCCAATAAATTGTCTATGATATAACGTTCATAGCCATGTGCGTTACCCTAATGTTGAAGGCGTGGTGTAAAGGCCATCCGACAACGCACTTTCTGGGTGTTTCGGCTTGCTGCAACTCCCATATTCATCCCTCGCGATGTGCCCTTAACGCTGTGTCCTATGAACCGGAAGAGCTCTTGCTTTCCCTGATTAGTTTCGAAGCAGTCGTCAGGACTACCACTCTGTATGGGGGCCTGGAGGAGCTTGGGTACAGGGTACTGTCGAGGGTAAAACTCGTAGGCAAAGGAGCAATTCGCGGACCATTCAGGGCATGCTTCTCCGGCTCCTTAGCGGAGATTAAGTAGACTAAATAGAGAGTAATGATGGGTTTCAATTTGGTTTGCCGATGTTTTGGTGTGTGCTAGCGACTTGCAATCTTCAGTTCACTAAACAGATCGGGTCGCGGACTATACTTTATCCGACGAACAGTTCTCCGCCGTATATACGGGGCGAAGCGTGGCTATCGTGAGCACCAGATACAGAGATAGCGATTGGGGACACATATAAATTCAAATACGTACGGGTAGCTCACAAATGTAGGTCCCCAGGGTGCGTCGTAACCACCAGCGCTAACCGCCCGGGAGTTAGAGAGTCCAGTGGTGTGTGATCAAAGACCCGTTTAGCCGATGCCTACCACACCCGAACGGCAAACAGCGGTGTTCAACTACCGTGGCCGCCGCGTGCTTCCAGTCTTATAGTCCCTGTACCTACGGAGTGATCTACATCGAATAGGTTGTGATTGAACCGCGGCTCTCGGCACCCTAAGGCCTCTTCATTAATACCTCAATTTGGCATGAGGAGCGCTTCGCCATTCTGCTTATACATGTACCGGCTTGGGTGAGGTTGGAGAAAAAGCGACCTGTGGCGCCACGTGATGTCCTCCTAAGAGGCAGAATCCCCTCGCTTGTGGTTTTGCCGTAATCCTGGTGTAAGGTTAGGTGTACAATATCGCTGGTACTCTGATCGCCGAGATCCAGTATCGGCCCTGTGCAAAATCACACCATATTGTATAGTCAGGCCGTACAGAAATGACACCATTCGAGAGAGCCTTTCCACAAGAAATATCGGTTCTACTGTCGAGATTCCCGCCGGACTCGATCTCACGCCCGGAGGTCGGGGAACGTTTCCTTTGTGATTAGCATATGGAGACTATTTATGACTGGCGATGCTGTGGAGTCACTTAGTGGAAAGACACCTAATCGTGAGGGTACTATCAACGTGGCTGAGCCAATACATTGGATGAGTGTCCCCCCTGTCCCCCTTTCTATGTTCGTCCCGGAGGTCCCGATGTGTTTGATAGCCGCGAGGGATGATCGATGAGTACTGCCGCTGTCTTTCTGCGAGGTGCCAGCTTCCAAAAATGTGTCGGAGTCGTATCTTTCTTACGAAGGTTAGAAGTCTGAGCGCTAGATTTCTTAAATTTGCCGAGATAAAGCGCCGTGACTTTAATATGAGGATGGGAGCAACTACCTTCGCGCTCAGCATCCGTACCTTCGTGCGTTACCACAACCCCGAAGGCGTACAGGTAACCGTTCGAATTGACTACCCAAGGGCCCGGAAGTTAAATAGTAGGTTAGTGCAATGTGCGACTACTGTGGGTGTAAGTATATAATCGCCGGGACGTACAACCCTGGCAGCTTGTAGTCCAATTTCGCACATGTCGGTATAATTCTCGCTTAATCAGCATCATGGAGATCCCTTCGAGGCCAAGGGCCTAGAGAAACTAACGCGTAAACTACGCACTCTAAGGTACAGGGGTGAATCCGTAGCGACTACATTATCGCTGAAACCTCGGATCGTCGCTTTTTTCCAATCCTCAGGCGGCGAAACTTCGTAAATTGTACCAACCTGTGGCCGTGGCTAGGGTCGGTAAGATAGCGGGGAAACATGGTAAGTTACGATCGGGATGTCTGTAAGAACCAACCACGGACGCGACCGAAACCCCTACGCCATTAAAATCGGTTCTAATCCAGATTTATTCTATAATGCGCCTGTTGATCGTCGGCGGAACGAGCACGGCTGATCGACGTAGTACTCGCTTAGGTGCCCTCGGCCGTCCCCAACTTGTTTTATAGTTGTCTAAATTCTCCGTCTAGGACGTGGCCATCCGAGAGTTTTTACAACGAGAATTAGGAAACTATCGTCGCCGATTCCTTACCCTTATTGGAATGATGGGGCCGGGCTATAGTATCAGGACAGACCTGTTGACAATTAATATCTACTAGGATTGAAGCGACAGAACTCGGGTTATGACTTAACTATGTCTTCTTTATAATGACGAGACCTCAATTTGGGCGTAATGTGAGGAGCATAAGGATGTTCGTCACAAAAACAGTATGTCCGTCACACATATTCCTTATGGGTGGGTAAGCGGCTAAAATGTCTCGATCACAAACAAAGAACTGGATATCGGGGTGTATTACGGGGGGTATGCAATGTAAGCGCTGAGTAATCGCAAGAGGCTTAAAATGACGAATCTAAGTTCATTGCCTACCCTTAACGAGTATGGCTAATCGGTAGCCCTTCGCTGATGACTAAAACCTAAGCGCCGCCACAGA
+EOF
+    end
+  end
+
+  it 'should scripting test ok with reverse order of scaffolds' do
+    answer = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/1_gap_then_unscaffolded/answer.fa").entries[0].to_biosequence.to_s
+    Dir.mktmpdir do |tmpdir|
+      #File.open('/tmp/in2','w') do |t|
+      Tempfile.open('testing_scaffolds') do |t|
+        t.puts '>seq1'
+        t.puts answer[2000..-1]
+        t.puts '>seq2'
+        t.puts answer[0..1500]
+        t.close
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/1_gap_then_unscaffolded/reads.fa.gz "+
+          "--genomes #{t.path} --output-directory #{tmpdir}"
+        Bio::Commandeer.run command
+        output_file = File.join(tmpdir,File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file).should == true
+        File.open(output_file).read.should == <<EOF
+>scaffold1 scaffold seq1:seq2
+TCTGTGGCGGCGCTTAGGTTTTAGTCATCAGCGAAGGGCTACCGATTAGCCATACTCGTTAAGGGTAGGCAATGAACTTAGATTCGTCATTTTAAGCCTCTTGCGATTACTCAGCGCTTACATTGCATACCCCCCGTAATACACCCCGATATCCAGTTCTTTGTTTGTGATCGAGACATTTTAGCCGCTTACCCACCCATAAGGAATATGTGTGACGGACATACTGTTTTTGTGACGAACATCCTTATGCTCCTCACATTACGCCCAAATTGAGGTCTCGTCATTATAAAGAAGACATAGTTAAGTCATAACCCGAGTTCTGTCGCTTCAATCCTAGTAGATATTAATTGTCAACAGGTCTGTCCTGATACTATAGCCCGGCCCCATCATTCCAATAAGGGTAAGGAATCGGCGACGATAGTTTCCTAATTCTCGTTGTAAAAACTCTCGGATGGCCACGTCCTAGACGGAGAATTTAGACAACTATAAAACAAGTTGGGGACGGCCGAGGGCACCTAAGCGAGTACTACGTCGATCAGCCGTGCTCGTTCCGCCGACGATCAACAGGCGCATTATAGAATAAATCTGGATTAGAACCGATTTTAATGGCGTAGGGGTTTCGGTCGCGTCCGTGGTTGGTTCTTACAGACATCCCGATCGTAACTTACCATGTTTCCCCGCTATCTTACCGACCCTAGCCACGGCCACAGGTTGGTACAATTTACGAAGTTTCGCCGCCTGAGGATTGGAAAAAAGCGACGATCCGAGGTTTCAGCGATAATGTAGTCGCTACGGATTCACCCCTGTACCTTAGAGTGCGTAGTTTACGCGTTAGTTTCTCTAGGCCCTTGGCCTCGAAGGGATCTCCATGATGCTGATTAAGCGAGAATTATACCGACATGTGCGAAATTGGACTACAAGCTGCCAGGGTTGTACGTCCCGGCGATTATATACTTACACCCACAGTAGTCGCACATTGCACTAACCTACTATTTAACTTCCGGGCCCTTGGGTAGTCAATTCGAACGGTTACCTGTACGCCTTCGGGGTTGTGGTAACGCACGAAGGTACGGATGCTGAGCGCGAAGGTAGTTGCTCCCATCCTCATATTAAAGTCACGGCGCTTTATCTCGGCAAATTTAAGAAATCTAGCGCTCAGACTTCTAACCTTCGTAAGAAAGATACGACTCCGACACATTTTTGGAAGCTGGCACCTCGCAGAAAGACAGCGGCAGTACTCATCGATCATCCCTCGCGGCTATCAAACACATCGGGACCTCCGGGACGAACATAGAAAGGGGGACAGGGGGGACACTCATCCAATGTATTGGCTCAGCCACGTTGATAGTACCCTCACGATTAGGTGTCTTTCCACTAAGTGACTCCACAGCATCGCCAGTCATAAATAGTCTCCATATGCTAATCACAAAGGAAACGTTCCCCGACCTCCGGGCGTGAGATCGAGTCCGGCGGGAATCTCGACAGTAGAACCGATATTTCTTGTGGAAAGGCTCTCTCGAATGGTGTCATTTCTGTACGGCCTGACTATACAATATGGTGTGATTTTGCACAGGGCCGATACTGGATCTCGGCGATCAGAGTACCAGCGATATTGTACACCTAACCTTACACCAGGATTACGGCAAAACCACAAGCGAGGGGATTCTGCCTCTTAGGAGGACATCACGTGGCGCCACAGGTCGCTTTTTCTCCAACCTCACCCAAGCCGGTACATGTATAAGCAGAATGGCGAAGCGCTCCTCATGCCAAATTGAGGTATTAATGAAGAGGCCTTAGGGTGCCGAGAGCCGCGGTTCAATCACAACCTATTCGATGTAGATCACTCCGTAGGTACAGGGACTATAAGACTGGAAGCACGCGGCGGCCACGGTAGTTGAACACCGCTGTTTGCCGTTCGGGTGTGGTAGGCATCGGCTAAACGGGTCTTTGATCACACACCACTGGACTCTCTAACTCCCGGGCGGTTAGCGCTGGTGGTTACGACGCACCCTGGGGACCTACATTTGTGAGCTACCCGTACGTATTTGAATTTATATGTGTCCCCAATCGCTATCTCTGTATCTGGTGCTCACGATAGCCACGCTTCGCCCCGTATATACGGCGGAGAACTGTTCGTCGGATAAAGTATAGTCCGCGACCCGATCTGTTTAGTGAACTGAAGATTGCAAGTCGCTAGCACACACCAAAACATCGGCAAACCAAATTGAAACCCATCATTACTCTCTATTTAGTCTACTTAATCTCCGCTAAGGAGCCGGAGAAGCATGCCCTGAATGGTCCGCGAATTGCTCCTTTGCCTACGAGTTTTACCCTCGACAGTACCCTGTACCCAAGCTCCTCCAGGCCCCCATACAGAGTGGTAGTCCTGACGACTGCTTCGAAACTAATCAGGGAAAGCAAGAGCTCTTCCGGTTCATAGGACACAGCGTTAAGGGCACATCGCGAGGGATGAATATGGGAGTTGCAGCAAGCCGAAACACCCAGAAAGTGCGTTGTCGGATGGCCTTTACACCACGCCTTCAACATTAGGGTAACGCACATGGCTATGAACGTTATATCATAGACAATTTATTGGCTATAAGCGGCAGCAAATCTAATATGTGCGAGTGCTTGAAGCACCTATGTCCCATCAGACTAGGATAGGTGATCGTGCTGAATGCTAATGACGCCCTCTGCTTCTTAACCGAGGGAACGATGTGAACGCGACTCCGAGTGGCATCAGTAGTTATCATAAGTCCTTCCCGAGTGCTAGCGGAGCACTTTGATAGACATACGCCCGATAATATGGGGAGGAAGTTGAAGAAGCGTCCACCTGATGTTTTGAGGGAGGACCGGTAAGTTAGTTGTGAACGAAGATTGTAGCCTGAGATTGTTTTTTCTTTAAGTTAAAGAATTTTATGCAACGTTTGTGTCTAGCTATCCATACTCATTGTTCTCGTACGAATTCGTCTGCGGGGCAATGGAGATCAACTTTACACTATATATTTCGTGTTCCCCCACAACGTTGCACACTGGGGGCGGTGACGCCGCTGGTTGATCGTGTCCGAACTCCTTGGGGTATTGGCCCCAATATGAGGGGGATATGAGTACCTAACGTTAATTGAGGATGGTGTGGGCGTTAATTCCGTTACGAAATGCATAGCGCTAGAGGCTGCCTTGCCTTAATAGGCGATATAGCGCCTTGGAATTCGACTCATATAGTCTTGAGAGCACAATACAGGAAGCGACAGTTTGGTCATGTAGGTTATTCCATCTAGTTTGGTCATGGGGAGCCCCGGAACTGAGGAAGTCAAATTCGGAAGTCTGGGGAATTGTTCACACCAGCCATAGCCTCGGAAGATAAAATACACTTATCTAAACTACTCCGACAGCCTAATTCTCACGGACTTGTTCTAGAAACAGAGTGAGTATGACATACTCCTCGTAGGATAACCATTCCAAGGCGCCGCTTAATCTTTGGTTAAGAAAGTGCCGTTTCACTAAGGGGGGGACTTCGACACGTCTCACATACTGTCGTGGTTCGACGCACGGACAGTGGAAATTCATATGTCGTGGGCGATAGACTTGATCCTGACGCATGATCCTCCAGGCAGTGCAACTGTTGACAAATCGGCAATGTGGGGGGATGACCAGGGGCTACCCAGTCACATGTTGTTATGGTCAGACTATTGGTCAACAACTTTTGCTCCGTGGAGGCGCGCTGTCTCAGGATCCATAGGACTTTTCCCCCAAAACGTGGACGAGAGCTTAGTTCGACCGGGGGCACCCCGCACTTTAAAGCGAGTTTATGTGTTGTGGTTGTATGCACGTGATCTAGTGCGTTGGCTCACAATTGGCCTGCCGCCTGTAGTTAGAACTACTAGCTTAACCTCAGCCAGACTAGCAAATATTGGACCTCTGGCAACTCATAGCCTCAGGTTACACATCAGGTGAATTGGCAAGTAGAGTTTAAACCCCCTGATTTCAACTACGCGAGTCGGAGTCGCACGCGGCTCCTCTTTCGGCTCGTACCTCCAGACCGCCTTCATCATAACGAACCTCCGCCCAAGACGTGCTTTCATTCTATCGAGCTACCCTCATAATCCTTCGCTTCGTCGACGGTGTTGCATATAAGAGGTGGGATAACGATTTTGCGCTGCAGCCGCACGCTTAACTTGACCATGAACCCTGGAAGGTCCGGCGTTATTGTCTGCGCTGGCATCGTGCACCTCCGCGGCGCGCATTCCTTTTTTCTGGTTTATCCGGTTTAGTGTCCTAATGACTGGCAAGTCCCTTTCAATTCCAAGATACCGGGACAAGACGTTCGCACCTGGTTGCGGACATGACGCGATTGACAATCTTATGAGATACAGTAGCTAGTGATTTGCAGATAACCTAACAGGTCGAGTTACTAGTATATTTTTAGTAACTGAATAATAACAGATATGAACTTGCTCATTGGTGCTATTGTATGACATTTCTTGTGGAGCATATGCTCGCAATATGTCATTACTTAGTACCCCGTCACGGTGACTCAGCTTGTTTATCGCATCCGGATCACATACTCGTTGCGGGGAACGTTACGGCGTGCACTATTAAAACTTGTCTGCTTTGAGTAAGCTTGAAGTTAGCTTGCTACTCCGAGGAACAAGCTTGGATCTACACGTTTCCTGCGGGAGTTATCTTAGAAAGGATCGGCATTGGCTGTGCGGCTGCATACGCAGGGGTCTGTGAGACTAAATTTAGAACGCCCTGATAACTATCAGAAATCTTACTTAGTAGATACACCTAACGTACCGATAAATAAGTTCGCGCTATTTCCGCGTCAGCCCAGTATTGAGGAATACCATCTGTTTTACCAAATGCTTGATACACTTTCCTTTGCTAATTCTCCGAAGTTCGGGTGCGCGTAGTGGATCGTACGTGAGATAGGCAGTTTACGTTATCAATTGACACGGACAAAGTTATTAGTTAACACGGCGACACCATAACACCCGGAA
+EOF
+      end
+    end
+  end
+
+  it 'should work at wandering and fixing multiple genomes' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+        t.puts '>seq1'
+        t.puts answer2[0..1000]
+        t.puts '>seq2'
+        t.puts answer2[1000..-1]
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/1_gap_then_unscaffolded/reads.fa.gz,#{TEST_DATA_DIR}/tweak/2_second_genome/reads.fa.gz "+
+          "--genomes #{TEST_DATA_DIR}/tweak/1_gap_then_unscaffolded/scaffolds.fa,#{t.path} --output-directory #{tmpdir}"
+        Bio::Commandeer.run(command).should == ''
+        output_file = File.join(tmpdir,'scaffolds.fa.scaffolds.fasta')
+        File.exist?(output_file).should == true
+        File.open(output_file).read.should == <<EOF
+>scaffold1 scaffold random_sequence_length_5000_chopped_1-600_then_N_then_chopped_700-2000:random_sequence_length_5000_chopped_3000-5000$
+TTCCGGGTGTTATGGTGTCGCCGTGTTAACTAATAACTTTGTCCGTGTCAATTGATAACGTAAACTGCCTATCTCACGTACGATCCACTACGCGCACCCGAACTTCGGAGAATTAGCAAAGGAAAGTGTATCAAGCATTTGGTAAAACAGATGGTATTCCTCAATACTGGGCTGACGCGGAAATAGCGCGAACTTATTTATCGGTACGTTAGGTGTATCTACTAAGTAAGATTTCTGATAGTTATCAGGGCGTTCTAAATTTAGTCTCACAGACCCCTGCGTATGCAGCCGCACAGCCAATGCCGATCCTTTCTAAGATAACTCCCGCAGGAAACGTGTAGATCCAAGCTTGTTCCTCGGAGTAGCAAGCTAACTTCAAGCTTACTCAAAGCAGACAAGTTTTAATAGTGCACGCCGTAACGTTCCCCGCAACGAGTATGTGATCCGGATGCGATAAACAAGCTGAGTCACCGTGACGGGGTACTAAGTAATGACATATTGCGAGCATATGCTCCACAAGAAATGTCATACAATAGCACCAATGAGCAAGTTCATATCTGTTATTATTCAGTTACTAAAAATATACTAGTAACTCGACCTGTTAGGTTATCTGCAAATCACTAGCTACTGTATCTCATAAGATTGTCAATCGCGTCATGTCCGCAACCAGGTGCGAACGTCTTGTCCCGGTATCTTGGAATTGAAAGGGACTTGCCAGTCATTAGGACACTAAACCGGATAAACCAGAAAAAAGGAATGCGCGCCGCGGAGGTGCACGATGCCAGCGCAGACAATAACGCCGGACCTTCCAGGGTTCATGGTCAAGTTAAGCGTGCGGCTGCAGCGCAAAATCGTTATCCCACCTCTTATATGCAACACCGTCGACGAAGCGAAGGATTATGAGGGTAGCTCGATAGAATGAAAGCACGTCTTGGGCGGAGGTTCGTTATGATGAAGGCGGTCTGGAGGTACGAGCCGAAAGAGGAGCCGCGTGCGACTCCGACTCGCGTAGTTGAAATCAGGGGGTTTAAACTCTACTTGCCAATTCACCTGATGTGTAACCTGAGGCTATGAGTTGCCAGAGGTCCAATATTTGCTAGTCTGGCTGAGGTTAAGCTAGTAGTTCTAACTACAGGCGGCAGGCCAATTGTGAGCCAACGCACTAGATCACGTGCATACAACCACAACACATAAACTCGCTTTAAAGTGCGGGGTGCCCCCGGTCGAACTAAGCTCTCGTCCACGTTTTGGGGGAAAAGTCCTATGGATCCTGAGACAGCGCGCCTCCACGGAGCAAAAGTTGTTGACCAATAGTCTGACCATAACAACATGTGACTGGGTAGCCCCTGGTCATCCCCCCACATTGCCGATTTGTCAACAGTTGCACTGCCTGGAGGATCATGCGTCAGGATCAAGTCTATCGCCCACGACATATGAATTTCCACTGTCCGTGCGTCGAACCACGACAGTATGTGAGACGTGTCGAAGTCCCCCCCTTAGTGAAACGGCACTTTCTTAACCAAAGATTAAGCGGCGCCTTGGAATGGTTATCCTACGAGGAGTATGTCATACTCACTCTGTTTCTAGAACAAGTCCGTGAGAATTAGGCTGTCGGAGTAGTTTAGATAAGTGTATTTTATCTTCCGAGGCTATGGCTGGTGTGAACAATTCCCCAGACTTCCGAATTTGACTTCCTCAGTTCCGGGGCTCCCCATGACCAAACTAGATGGAATAACCTACATGACCAAACTGTCGCTTCCTGTATTGTGCTCTCAAGACTATATGAGTCGAATTCCAAGGCGCTATATCGCCTATTAAGGCAAGGCAGCCTCTAGCGCTATGCATTTCGTAACGGAATTAACGCCCACACCATCCTCAATTAACGTTAGGTACTCATATCCCCCTCATATTGGGGCCAATACCCCAAGGAGTTCGGACACGATCAACCAGCGGCGTCACCGCCCCCAGTGTGCAACGTTGTGGGGGAACACGAAATATATAGTGTAAAGTTGATCTCCATTGCCCCGCAGACGAATTCGTACGAGAACAATGAGTATGGATAGCTAGACACAAACGTTGCATAAAATTCTTTAACTTAAAGAAAAAACAATCTCAGGCTACAATCTTCGTTCACAACTAACTTACCGGTCCTCCCTCAAAACATCAGGTGGACGCTTCTTCAACTTCCTCCCCATATTATCGGGCGTATGTCTATCAAAGTGCTCCGCTAGCACTCGGGAAGGACTTATGATAACTACTGATGCCACTCGGAGTCGCGTTCACATCGTTCCCTCGGTTAAGAAGCAGAGGGCGTCATTAGCATTCAGCACGATCACCTATCCTAGTCTGATGGGACATAGGTGCTTCAAGCACTCGCACATATTAGATTTGCTGCCGCTTATAGCCAATAAATTGTCTATGATATAACGTTCATAGCCATGTGCGTTACCCTAATGTTGAAGGCGTGGTGTAAAGGCCATCCGACAACGCACTTTCTGGGTGTTTCGGCTTGCTGCAACTCCCATATTCATCCCTCGCGATGTGCCCTTAACGCTGTGTCCTATGAACCGGAAGAGCTCTTGCTTTCCCTGATTAGTTTCGAAGCAGTCGTCAGGACTACCACTCTGTATGGGGGCCTGGAGGAGCTTGGGTACAGGGTACTGTCGAGGGTAAAACTCGTAGGCAAAGGAGCAATTCGCGGACCATTCAGGGCATGCTTCTCCGGCTCCTTAGCGGAGATTAAGTAGACTAAATAGAGAGTAATGATGGGTTTCAATTTGGTTTGCCGATGTTTTGGTGTGTGCTAGCGACTTGCAATCTTCAGTTCACTAAACAGATCGGGTCGCGGACTATACTTTATCCGACGAACAGTTCTCCGCCGTATATACGGGGCGAAGCGTGGCTATCGTGAGCACCAGATACAGAGATAGCGATTGGGGACACATATAAATTCAAATACGTACGGGTAGCTCACAAATGTAGGTCCCCAGGGTGCGTCGTAACCACCAGCGCTAACCGCCCGGGAGTTAGAGAGTCCAGTGGTGTGTGATCAAAGACCCGTTTAGCCGATGCCTACCACACCCGAACGGCAAACAGCGGTGTTCAACTACCGTGGCCGCCGCGTGCTTCCAGTCTTATAGTCCCTGTACCTACGGAGTGATCTACATCGAATAGGTTGTGATTGAACCGCGGCTCTCGGCACCCTAAGGCCTCTTCATTAATACCTCAATTTGGCATGAGGAGCGCTTCGCCATTCTGCTTATACATGTACCGGCTTGGGTGAGGTTGGAGAAAAAGCGACCTGTGGCGCCACGTGATGTCCTCCTAAGAGGCAGAATCCCCTCGCTTGTGGTTTTGCCGTAATCCTGGTGTAAGGTTAGGTGTACAATATCGCTGGTACTCTGATCGCCGAGATCCAGTATCGGCCCTGTGCAAAATCACACCATATTGTATAGTCAGGCCGTACAGAAATGACACCATTCGAGAGAGCCTTTCCACAAGAAATATCGGTTCTACTGTCGAGATTCCCGCCGGACTCGATCTCACGCCCGGAGGTCGGGGAACGTTTCCTTTGTGATTAGCATATGGAGACTATTTATGACTGGCGATGCTGTGGAGTCACTTAGTGGAAAGACACCTAATCGTGAGGGTACTATCAACGTGGCTGAGCCAATACATTGGATGAGTGTCCCCCCTGTCCCCCTTTCTATGTTCGTCCCGGAGGTCCCGATGTGTTTGATAGCCGCGAGGGATGATCGATGAGTACTGCCGCTGTCTTTCTGCGAGGTGCCAGCTTCCAAAAATGTGTCGGAGTCGTATCTTTCTTACGAAGGTTAGAAGTCTGAGCGCTAGATTTCTTAAATTTGCCGAGATAAAGCGCCGTGACTTTAATATGAGGATGGGAGCAACTACCTTCGCGCTCAGCATCCGTACCTTCGTGCGTTACCACAACCCCGAAGGCGTACAGGTAACCGTTCGAATTGACTACCCAAGGGCCCGGAAGTTAAATAGTAGGTTAGTGCAATGTGCGACTACTGTGGGTGTAAGTATATAATCGCCGGGACGTACAACCCTGGCAGCTTGTAGTCCAATTTCGCACATGTCGGTATAATTCTCGCTTAATCAGCATCATGGAGATCCCTTCGAGGCCAAGGGCCTAGAGAAACTAACGCGTAAACTACGCACTCTAAGGTACAGGGGTGAATCCGTAGCGACTACATTATCGCTGAAACCTCGGATCGTCGCTTTTTTCCAATCCTCAGGCGGCGAAACTTCGTAAATTGTACCAACCTGTGGCCGTGGCTAGGGTCGGTAAGATAGCGGGGAAACATGGTAAGTTACGATCGGGATGTCTGTAAGAACCAACCACGGACGCGACCGAAACCCCTACGCCATTAAAATCGGTTCTAATCCAGATTTATTCTATAATGCGCCTGTTGATCGTCGGCGGAACGAGCACGGCTGATCGACGTAGTACTCGCTTAGGTGCCCTCGGCCGTCCCCAACTTGTTTTATAGTTGTCTAAATTCTCCGTCTAGGACGTGGCCATCCGAGAGTTTTTACAACGAGAATTAGGAAACTATCGTCGCCGATTCCTTACCCTTATTGGAATGATGGGGCCGGGCTATAGTATCAGGACAGACCTGTTGACAATTAATATCTACTAGGATTGAAGCGACAGAACTCGGGTTATGACTTAACTATGTCTTCTTTATAATGACGAGACCTCAATTTGGGCGTAATGTGAGGAGCATAAGGATGTTCGTCACAAAAACAGTATGTCCGTCACACATATTCCTTATGGGTGGGTAAGCGGCTAAAATGTCTCGATCACAAACAAAGAACTGGATATCGGGGTGTATTACGGGGGGTATGCAATGTAAGCGCTGAGTAATCGCAAGAGGCTTAAAATGACGAATCTAAGTTCATTGCCTACCCTTAACGAGTATGGCTAATCGGTAGCCCTTCGCTGATGACTAAAACCTAAGCGCCGCCACAGA
+EOF
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).read.should == <<EOF
+>scaffold1 scaffold seq1:seq2
+AACTTATCAACCCACAGGATGTGCGAAGCAGGATACGTTTGCGGAGCTGAAGCGGACTCCGCGCGGCCGGCAGATGTAGATGGCCTCGGCGCCCAAGTTTGGAATATGGTCAGTCCAACAAGAAAGTTTTTAAGCGCGAAGATTATGTCGCGAACTTCCTCCGCAGCGTCAGTGGTATAAGAAGACAGCGCGGGAGTTGAGGAGAACAGGAGATACCTACCGGGACACATCACCAGGCGCGTAGCTGGGCAGGTCAGCCGCTGGAGTGGGTTTATCATCTAAAACGAGGCTCCGGCATTTCGGTTAATCATAGCTCGGGGCTAGGTTGATTGTCGGAGGTCTTCTGTTCGGTCCGGCGTTAGTAATAAGCTGCCTCGGATATTGACTTCCTGGATTAGCCGATATATCTTACAGGCAGGACTTTATCAGCGGTTACCAACGCAAAATACTTTAAGAAATGGCTGACCCACGCCCTAACGCGTTACTTGGGTACACGTGTTGAAAAGCCGTCCAATCGCCCTCATATCGAATACTGGGTTCCTACATATGTGGGTGGCACGTGACCTCTCGAAGTCGCTATTGGTTAAGTACTACTATACTTCCAAATTGAACTCTCTCGAAGCTTAATCGCCATCTGCTATCGTGCCCCCCTGCTTGCGTGACCAAACGCCTAGGGATGAAATTAGAAATAAACGAATTCTCAGGGCCAAACTCTAACGACCAGCCGAGGCAGCACGCTGTGATCTTCGTGTGTTCACCATGACTAGGACACAAGGGCCGGAGCGGGACCGGCCATGCAATACTGGCCCGGCCTCTATCAAAGGTTTCTGGGCCATGGTGATACGGGTGTGTGTAGCCGATTCATTTGCTAGTCCTCAATGCCATGCGCGGAGCCTGAGTAAGGCCGTTCGTATCTGTCCACTAATCACGGGTGATTACCACCCGGGCACTAGCCGCGGTAATATCTACCTACAGCGAGAAGCCCCTCGAAGATTATCGCGACGACGTGCTGCCCCTGGGCATCCACTTGTCACTCCAGAACTGTGGTAGGTTATCCGGCAATATATAATTTTAGATACGACTAGACCGTACAGATCATGTTAATGTTACCGTCACGTCCTCTATTGGGAACATCGCACGACACCCAGCTGGACCCCGCCACCGTTACTGCGGAACTCCAGTCTTTTAGCTTGCCGCAGTGATGGACAGTACAAGTCGCAGGTGCGGGCCTGTCAGCCTCACCTTTTTCGCAACGGCAAGTTATGAGGGAATCTTGATCAAGAGGTTAAGATGAAATGCGAAGTGATTCGTGAATGTCTTCGCGTACAACCGCGCTGAGGATATAGATAGAATAACGCAATTCACTCGTCACCAGGATCCCTATAAGGGTTAAGACCTCTTACGGTTTAAAGTAATCTGTTGATGCTGCATTGTCATGACTGGGTGATTTTTAGATCCCTATAAGGACTCCTCGTATCTATAGACGGCGCCTATAAATACCACAGGCTACCCTTTGAGGTGTGACTCCCCGTATTTGAAGTGGTCCACTGCTGAATTATGGATTTTTCGAATCTACAGGATGACTACGGTCATCCACGGACCTGGCGAGTGGATTTATGCTTCTGTAAGCGATAAGGATTCGGTGGGTATTAGATGCGGCGCGCATGGTGTCCATCCTGGCCCGCCAAGCTAACGTGCCGGCGTTACGGAGTATGACGAGCATTTAGCGACGCTTCTGTCAAGGAGCCGGAAGTGGGAGTAGGCTGTTTGCCAGCGCGGGTCCCCATGCATCTCACCTGAGTACCCTTCGGACAACTGCCTCGTAGAGATTAATCTGGCAAACCTAGAGATATGCCAAGCTTTTTCACTGCCATTATAAATAAGGCTTGGGAGTTGAGTAACATATGAAAGCATCGTTCCTTCACCAGAGGTGAATTTACCACGCAAACTTGGTCTGCGTTACTTGCAAAACTGCAGGAACGGCTAAAAAGCACTGGGGCTGATCGAGTACGTTCTATGTCATGTGCCCCTTGTAAGTGCTGATATATATCCCTCTAATGGAAAGGCTACTAGGACTGCGCAAATCGCACGCTCCGTCGCACGGTAGATTCAGGCCTGATGAACGTTAATATAGGTTTTCACTCCATGTTGCGAATCTTCGGTCTCTAGACCGACTACCTTCATGACTCGGGGAAACGTAGGAAGCCGGAGCATGATGTTGTGCACTAACTCTCCCTAATCACCATGTCGAGATTAACAAGCAAAGTTCCCTGGGGGTTCCTAGCCGCACATCCCACACTTAGGTGTTGCCTCTACGTCTGAGGGACAAAAAACATAGGCCTGGTGCATGTACTAAGGATTACCTTTACTATGAGCTTGATAGGCACTTCGGCCGATCGAGGTTTAACCGGCGCGCTAGCAAAAGGTGGCGTAGTTGCGCAATTGGTCGACTTGGGCGTCTTACAACTGCCGGTTCCTCAGTAGTTCTTTCTCGTATAGGCATGTAATCACGCCACACCCCGCCACTAAGGGGTAGCCGGTCGCGATTGTAAGTGTACCGCATTTAGGTGTCAGGCGAATCGGACCTCTCCTTCGGCGTGTAAAACTATCGCTGACCCCAATAGTATTCCCGCCCCTAATTGGCTCCTCGCCCCGATCCAGGGGCGATTTGTTTGACTACACCGCTTCCACCAATACATGCACAAACTCGTAAGATTGTAGAAACATGCAGTATTTGTGCGACACCGAGCATTATTTAGGACACACCGGCCGGTGCATACCCCAACGGTGAGGCTCTCTATCGCGTATCCGACTTTGTAACTATGGCGTCCTATAACCACTAGTTGAAGTAATTCAGCCTATCTAAAGCCGGTTTGTGCGGTGTGTGACATGTTGCCATTAGACAGACTAACTCCGTTACTCAATGAAGAACTAGCGTCAAGCCAATGCGATAAGATGAACACTATGGAAGAGCAGGTCAAGTGGCTAGGCTGCGACGTG
+EOF
+      end
+    end
+  end
+
+  it 'should deal with insufficient overhang space with a too-small contig in the middle' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+        t.puts '>seq1'
+        t.puts answer2[0..1000]
+        t.puts 'N'*50
+        t.puts answer2[1100..1155]
+        t.puts 'N'*30
+        t.puts answer2[2000..-1]
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR}/tweak/2_second_genome/reads.fa.gz "+
+          "--genomes #{t.path} --output-directory #{tmpdir}"
+        Bio::Commandeer.run(command).should == ''
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).read.should == <<EOF
+>scaffold1 scaffold seq1
+AACTTATCAACCCACAGGATGTGCGAAGCAGGATACGTTTGCGGAGCTGAAGCGGACTCCGCGCGGCCGGCAGATGTAGATGGCCTCGGCGCCCAAGTTTGGAATATGGTCAGTCCAACAAGAAAGTTTTTAAGCGCGAAGATTATGTCGCGAACTTCCTCCGCAGCGTCAGTGGTATAAGAAGACAGCGCGGGAGTTGAGGAGAACAGGAGATACCTACCGGGACACATCACCAGGCGCGTAGCTGGGCAGGTCAGCCGCTGGAGTGGGTTTATCATCTAAAACGAGGCTCCGGCATTTCGGTTAATCATAGCTCGGGGCTAGGTTGATTGTCGGAGGTCTTCTGTTCGGTCCGGCGTTAGTAATAAGCTGCCTCGGATATTGACTTCCTGGATTAGCCGATATATCTTACAGGCAGGACTTTATCAGCGGTTACCAACGCAAAATACTTTAAGAAATGGCTGACCCACGCCCTAACGCGTTACTTGGGTACACGTGTTGAAAAGCCGTCCAATCGCCCTCATATCGAATACTGGGTTCCTACATATGTGGGTGGCACGTGACCTCTCGAAGTCGCTATTGGTTAAGTACTACTATACTTCCAAATTGAACTCTCTCGAAGCTTAATCGCCATCTGCTATCGTGCCCCCCTGCTTGCGTGACCAAACGCCTAGGGATGAAATTAGAAATAAACGAATTCTCAGGGCCAAACTCTAACGACCAGCCGAGGCAGCACGCTGTGATCTTCGTGTGTTCACCATGACTAGGACACAAGGGCCGGAGCGGGACCGGCCATGCAATACTGGCCCGGCCTCTATCAAAGGTTTCTGGGCCATGGTGATACGGGTGTGTGTAGCCGATTCATTTGCTAGTCCTCAATGCCATGCGCGGAGCCTGAGTAAGGCCGTTCGTATCTGTCCACTAATCACGGGTGATTACCACCCGGGCACTAGCCGCGGTAATATCTACCTACAGCGAGAAGCCCCTCGAAGATTATCGCGACGACGTGCTGCCCCTGGGCATCCACTTGTCACTCCAGAACTGTGGTAGGTTATCCGGCAATATATAATTTTAGATACGACTAGACCGTACAGATCATGTTAATGTTACCGTCACGTCCTCTATTGGGAACATCGCACGACACCCAGCTGGACCCCGCCACCGTTACTGCGGAACTCCAGTCTTTTAGCTTGCCGCAGTGATGGACAGTACAAGTCGCAGGTGCGGGCCTGTCAGCCTCACCTTTTTCGCAACGGCAAGTTATGAGGGAATCTTGATCAAGAGGTTAAGATGAAATGCGAAGTGATTCGTGAATGTCTTCGCGTACAACCGCGCTGAGGATATAGATAGAATAACGCAATTCACTCGTCACCAGGATCCCTATAAGGGTTAAGACCTCTTACGGTTTAAAGTAATCTGTTGATGCTGCATTGTCATGACTGGGTGATTTTTAGATCCCTATAAGGACTCCTCGTATCTATAGACGGCGCCTATAAATACCACAGGCTACCCTTTGAGGTGTGACTCCCCGTATTTGAAGTGGTCCACTGCTGAATTATGGATTTTTCGAATCTACAGGATGACTACGGTCATCCACGGACCTGGCGAGTGGATTTATGCTTCTGTAAGCGATAAGGATTCGGTGGGTATTAGATGCGGCGCGCATGGTGTCCATCCTGGCCCGCCAAGCTAACGTGCCGGCGTTACGGAGTATGACGAGCATTTAGCGACGCTTCTGTCAAGGAGCCGGAAGTGGGAGTAGGCTGTTTGCCAGCGCGGGTCCCCATGCATCTCACCTGAGTACCCTTCGGACAACTGCCTCGTAGAGATTAATCTGGCAAACCTAGAGATATGCCAAGCTTTTTCACTGCCATTATAAATAAGGCTTGGGAGTTGAGTAACATATGAAAGCATCGTTCCTTCACCAGAGGTGAATTTACCACGCAAACTTGGTCTGCGTTACTTGCAAAACTGCAGGAACGGCTAAAAAGCACTGGGGCTGATCGAGTACGTTCTATGTCATGTGCCCCTTGTAAGTGCTGATATATATCCCTCTAATGGAAAGGCTACTAGGACTGCGCAAATCGCACGCTCCGTCGCACGGTAGATTCAGGCCTGATGAACGTTAATATAGGTTTTCACTCCATGTTGCGAATCTTCGGTCTCTAGACCGACTACCTTCATGACTCGGGGAAACGTAGGAAGCCGGAGCATGATGTTGTGCACTAACTCTCCCTAATCACCATGTCGAGATTAACAAGCAAAGTTCCCTGGGGGTTCCTAGCCGCACATCCCACACTTAGGTGTTGCCTCTACGTCTGAGGGACAAAAAACATAGGCCTGGTGCATGTACTAAGGATTACCTTTACTATGAGCTTGATAGGCACTTCGGCCGATCGAGGTTTAACCGGCGCGCTAGCAAAAGGTGGCGTAGTTGCGCAATTGGTCGACTTGGGCGTCTTACAACTGCCGGTTCCTCAGTAGTTCTTTCTCGTATAGGCATGTAATCACGCCACACCCCGCCACTAAGGGGTAGCCGGTCGCGATTGTAAGTGTACCGCATTTAGGTGTCAGGCGAATCGGACCTCTCCTTCGGCGTGTAAAACTATCGCTGACCCCAATAGTATTCCCGCCCCTAATTGGCTCCTCGCCCCGATCCAGGGGCGATTTGTTTGACTACACCGCTTCCACCAATACATGCACAAACTCGTAAGATTGTAGAAACATGCAGTATTTGTGCGACACCGAGCATTATTTAGGACACACCGGCCGGTGCATACCCCAACGGTGAGGCTCTCTATCGCGTATCCGACTTTGTAACTATGGCGTCCTATAACCACTAGTTGAAGTAATTCAGCCTATCTAAAGCCGGTTTGTGCGGTGTGTGACATGTTGCCATTAGACAGACTAACTCCGTTACTCAATGAAGAACTAGCGTCAAGCCAATGCGATAAGATGAACACTATGGAAGAGCAGGTCAAGTGGCTAGGCTGCGACGTG
+EOF
+      end
+    end
+  end
+
+  it 'should deal with contigs that are too small to wander' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+        t.puts '>seq1'
+        t.puts answer2[0..1000]
+        t.puts '>too_small'
+        t.puts answer2[1100..1150]
+        t.puts '>seq2'
+        t.puts answer2[2000..-1]
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR}/tweak/2_second_genome/reads.fa.gz "+
+          "--genomes #{t.path} --output-directory #{tmpdir}"
+        Bio::Commandeer.run(command).should == ''
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).read.should == <<EOF
+>scaffold1 scaffold seq1:seq2
+AACTTATCAACCCACAGGATGTGCGAAGCAGGATACGTTTGCGGAGCTGAAGCGGACTCCGCGCGGCCGGCAGATGTAGATGGCCTCGGCGCCCAAGTTTGGAATATGGTCAGTCCAACAAGAAAGTTTTTAAGCGCGAAGATTATGTCGCGAACTTCCTCCGCAGCGTCAGTGGTATAAGAAGACAGCGCGGGAGTTGAGGAGAACAGGAGATACCTACCGGGACACATCACCAGGCGCGTAGCTGGGCAGGTCAGCCGCTGGAGTGGGTTTATCATCTAAAACGAGGCTCCGGCATTTCGGTTAATCATAGCTCGGGGCTAGGTTGATTGTCGGAGGTCTTCTGTTCGGTCCGGCGTTAGTAATAAGCTGCCTCGGATATTGACTTCCTGGATTAGCCGATATATCTTACAGGCAGGACTTTATCAGCGGTTACCAACGCAAAATACTTTAAGAAATGGCTGACCCACGCCCTAACGCGTTACTTGGGTACACGTGTTGAAAAGCCGTCCAATCGCCCTCATATCGAATACTGGGTTCCTACATATGTGGGTGGCACGTGACCTCTCGAAGTCGCTATTGGTTAAGTACTACTATACTTCCAAATTGAACTCTCTCGAAGCTTAATCGCCATCTGCTATCGTGCCCCCCTGCTTGCGTGACCAAACGCCTAGGGATGAAATTAGAAATAAACGAATTCTCAGGGCCAAACTCTAACGACCAGCCGAGGCAGCACGCTGTGATCTTCGTGTGTTCACCATGACTAGGACACAAGGGCCGGAGCGGGACCGGCCATGCAATACTGGCCCGGCCTCTATCAAAGGTTTCTGGGCCATGGTGATACGGGTGTGTGTAGCCGATTCATTTGCTAGTCCTCAATGCCATGCGCGGAGCCTGAGTAAGGCCGTTCGTATCTGTCCACTAATCACGGGTGATTACCACCCGGGCACTAGCCGCGGTAATATCTACCTACAGCGAGAAGCCCCTCGAAGATTATCGCGACGACGTGCTGCCCCTGGGCATCCACTTGTCACTCCAGAACTGTGGTAGGTTATCCGGCAATATATAATTTTAGATACGACTAGACCGTACAGATCATGTTAATGTTACCGTCACGTCCTCTATTGGGAACATCGCACGACACCCAGCTGGACCCCGCCACCGTTACTGCGGAACTCCAGTCTTTTAGCTTGCCGCAGTGATGGACAGTACAAGTCGCAGGTGCGGGCCTGTCAGCCTCACCTTTTTCGCAACGGCAAGTTATGAGGGAATCTTGATCAAGAGGTTAAGATGAAATGCGAAGTGATTCGTGAATGTCTTCGCGTACAACCGCGCTGAGGATATAGATAGAATAACGCAATTCACTCGTCACCAGGATCCCTATAAGGGTTAAGACCTCTTACGGTTTAAAGTAATCTGTTGATGCTGCATTGTCATGACTGGGTGATTTTTAGATCCCTATAAGGACTCCTCGTATCTATAGACGGCGCCTATAAATACCACAGGCTACCCTTTGAGGTGTGACTCCCCGTATTTGAAGTGGTCCACTGCTGAATTATGGATTTTTCGAATCTACAGGATGACTACGGTCATCCACGGACCTGGCGAGTGGATTTATGCTTCTGTAAGCGATAAGGATTCGGTGGGTATTAGATGCGGCGCGCATGGTGTCCATCCTGGCCCGCCAAGCTAACGTGCCGGCGTTACGGAGTATGACGAGCATTTAGCGACGCTTCTGTCAAGGAGCCGGAAGTGGGAGTAGGCTGTTTGCCAGCGCGGGTCCCCATGCATCTCACCTGAGTACCCTTCGGACAACTGCCTCGTAGAGATTAATCTGGCAAACCTAGAGATATGCCAAGCTTTTTCACTGCCATTATAAATAAGGCTTGGGAGTTGAGTAACATATGAAAGCATCGTTCCTTCACCAGAGGTGAATTTACCACGCAAACTTGGTCTGCGTTACTTGCAAAACTGCAGGAACGGCTAAAAAGCACTGGGGCTGATCGAGTACGTTCTATGTCATGTGCCCCTTGTAAGTGCTGATATATATCCCTCTAATGGAAAGGCTACTAGGACTGCGCAAATCGCACGCTCCGTCGCACGGTAGATTCAGGCCTGATGAACGTTAATATAGGTTTTCACTCCATGTTGCGAATCTTCGGTCTCTAGACCGACTACCTTCATGACTCGGGGAAACGTAGGAAGCCGGAGCATGATGTTGTGCACTAACTCTCCCTAATCACCATGTCGAGATTAACAAGCAAAGTTCCCTGGGGGTTCCTAGCCGCACATCCCACACTTAGGTGTTGCCTCTACGTCTGAGGGACAAAAAACATAGGCCTGGTGCATGTACTAAGGATTACCTTTACTATGAGCTTGATAGGCACTTCGGCCGATCGAGGTTTAACCGGCGCGCTAGCAAAAGGTGGCGTAGTTGCGCAATTGGTCGACTTGGGCGTCTTACAACTGCCGGTTCCTCAGTAGTTCTTTCTCGTATAGGCATGTAATCACGCCACACCCCGCCACTAAGGGGTAGCCGGTCGCGATTGTAAGTGTACCGCATTTAGGTGTCAGGCGAATCGGACCTCTCCTTCGGCGTGTAAAACTATCGCTGACCCCAATAGTATTCCCGCCCCTAATTGGCTCCTCGCCCCGATCCAGGGGCGATTTGTTTGACTACACCGCTTCCACCAATACATGCACAAACTCGTAAGATTGTAGAAACATGCAGTATTTGTGCGACACCGAGCATTATTTAGGACACACCGGCCGGTGCATACCCCAACGGTGAGGCTCTCTATCGCGTATCCGACTTTGTAACTATGGCGTCCTATAACCACTAGTTGAAGTAATTCAGCCTATCTAAAGCCGGTTTGTGCGGTGTGTGACATGTTGCCATTAGACAGACTAACTCCGTTACTCAATGAAGAACTAGCGTCAAGCCAATGCGATAAGATGAACACTATGGAAGAGCAGGTCAAGTGGCTAGGCTGCGACGTG
+EOF
+      end
+    end
+  end
+
+  it 'should handle gaps that are too close to the end of the scaffold' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+        t.puts '>seq1'
+        t.puts answer2[0..50]
+        t.puts '>seq2'
+        t.puts answer2[700..1155]
+        t.puts '>seq3'
+        t.puts answer2[2000..-1]
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR}/tweak/2_second_genome/reads.fa.gz "+
+          "--genomes #{t.path} --output-directory #{tmpdir}"
+        Bio::Commandeer.run(command).should == ''
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).readlines.should == [
+          '>scaffold1 scaffold seq2:seq3'+"\n",
+          answer2[700..-1]+"\n"
+          ]
+      end
+    end
+  end
+
+  it 'should handle unbridgeable gaps in one scaffold' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+        input_sequence = [
+          answer2[0..500],
+          'N'*20,
+          answer2[1000..1500],
+          'N'*5,
+          answer2[2000..-1],
+          ].join('')
+
+        t.puts '>seq1'
+        t.puts input_sequence
+        t.close
+
+        Tempfile.open('reads_dummy') do |reads|
+          100.times do
+            reads.puts '>seq1'
+            reads.puts answer2[0..500]
+            reads.puts '>s2'
+            reads.puts answer2[1000..1500]
+            reads.puts '>s3'
+            reads.puts answer2[2000..-1]
+          end
+          reads.close
+
+          command = "#{path_to_script} --quiet --fasta #{reads.path} "+
+            "--genomes #{t.path} --output-directory #{tmpdir}"
+          Bio::Commandeer.run(command).should == ''
+          output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+          File.exist?(output_file2).should == true
+          File.open(output_file2).readlines.should == [
+            '>scaffold1 scaffold seq1'+"\n",
+            input_sequence+"\n"
+            ]
+        end
+      end
+    end
+  end
+
+  it 'should handle unbridgeable gaps in the second scaffold' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+      #File.open('/tmp/testing_scaffolds2','w') do |t|
+        input_sequence = [
+          answer2[0..500],
+          'N'*20,
+          answer2[600..1000]
+          ].join('')
+        input_sequence2 = [
+          answer2[1300..1900],
+          'N'*5,
+          answer2[2000..-1],
+          ].join('')
+
+        t.puts '>seq1'
+        t.puts input_sequence
+        t.puts '>seq2'
+        t.puts input_sequence2
+        t.close
+
+        Tempfile.open('reads_dummy') do |reads|
+        #File.open('/tmp/reads_dummy','w') do |reads|
+          100.times do
+            reads.puts '>s2' #bridge the gap between the first and second sequence
+            reads.puts answer2[700..1500]
+          end
+          reads.close
+
+          command = "#{path_to_script} --quiet --fasta #{reads.path} "+
+            "--genomes #{t.path} --output-directory #{tmpdir}"
+          Bio::Commandeer.run(command).should == ''
+          output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+          File.exist?(output_file2).should == true
+          File.open(output_file2).readlines.should == [
+            '>scaffold1 scaffold seq1:seq2'+"\n",
+            [
+              answer2[0..500],
+              'N'*20,
+              answer2[600..1900],
+              'N'*5,
+              answer2[2000..-1],
+              ].join('')+"\n"
+            ]
+        end
+      end
+    end
+  end
+
+  it 'should handle circular contigs that are only 1 scaffold' do
+    Dir.mktmpdir do |tmpdir|
+      answer2 = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/2_second_genome/answer2.fa").entries[0].to_biosequence.to_s
+      Tempfile.open('testing_scaffolds2') do |t|
+      #File.open('/tmp/testing_scaffolds2','w') do |t|
+        t.puts '>seq1'
+        t.puts answer2[-100..-1]+answer2[0..400]
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR}/tweak/2_second_genome/reads.fa.gz "+
+          "--genomes #{t.path} --output-directory #{tmpdir}"
+        Bio::Commandeer.run(command).should == ''
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).readlines.should == [
+          '>scaffold1 circular seq1'+"\n",
+          answer2[-100..-1]+answer2[0...-100]+"\n"
+          ]#known bug
+      end
+    end
+  end
+
+  it 'should not wander when --gapfill-only is specified' do
+    Dir.mktmpdir do |tmpdir|
+      command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/1_gap_then_unscaffolded/reads.fa.gz "+
+        "--genomes #{TEST_DATA_DIR}/tweak/1_gap_then_unscaffolded/scaffolds.fa --output-directory #{tmpdir} --gapfill-only"
+      Bio::Commandeer.run(command).should == ''
+      output_file = File.join(tmpdir,'scaffolds.fa.scaffolds.fasta')
+      File.exist?(output_file).should == true
+      File.open(output_file).read.should == <<EOF
+>scaffold1 scaffold random_sequence_length_5000_chopped_1-600_then_N_then_chopped_700-2000
+TTCCGGGTGTTATGGTGTCGCCGTGTTAACTAATAACTTTGTCCGTGTCAATTGATAACGTAAACTGCCTATCTCACGTACGATCCACTACGCGCACCCGAACTTCGGAGAATTAGCAAAGGAAAGTGTATCAAGCATTTGGTAAAACAGATGGTATTCCTCAATACTGGGCTGACGCGGAAATAGCGCGAACTTATTTATCGGTACGTTAGGTGTATCTACTAAGTAAGATTTCTGATAGTTATCAGGGCGTTCTAAATTTAGTCTCACAGACCCCTGCGTATGCAGCCGCACAGCCAATGCCGATCCTTTCTAAGATAACTCCCGCAGGAAACGTGTAGATCCAAGCTTGTTCCTCGGAGTAGCAAGCTAACTTCAAGCTTACTCAAAGCAGACAAGTTTTAATAGTGCACGCCGTAACGTTCCCCGCAACGAGTATGTGATCCGGATGCGATAAACAAGCTGAGTCACCGTGACGGGGTACTAAGTAATGACATATTGCGAGCATATGCTCCACAAGAAATGTCATACAATAGCACCAATGAGCAAGTTCATATCTGTTATTATTCAGTTACTAAAAATATACTAGTAACTCGACCTGTTAGGTTATCTGCAAATCACTAGCTACTGTATCTCATAAGATTGTCAATCGCGTCATGTCCGCAACCAGGTGCGAACGTCTTGTCCCGGTATCTTGGAATTGAAAGGGACTTGCCAGTCATTAGGACACTAAACCGGATAAACCAGAAAAAAGGAATGCGCGCCGCGGAGGTGCACGATGCCAGCGCAGACAATAACGCCGGACCTTCCAGGGTTCATGGTCAAGTTAAGCGTGCGGCTGCAGCGCAAAATCGTTATCCCACCTCTTATATGCAACACCGTCGACGAAGCGAAGGATTATGAGGGTAGCTCGATAGAATGAAAGCACGTCTTGGGCGGAGGTTCGTTATGATGAAGGCGGTCTGGAGGTACGAGCCGAAAGAGGAGCCGCGTGCGACTCCGACTCGCGTAGTTGAAATCAGGGGGTTTAAACTCTACTTGCCAATTCACCTGATGTGTAACCTGAGGCTATGAGTTGCCAGAGGTCCAATATTTGCTAGTCTGGCTGAGGTTAAGCTAGTAGTTCTAACTACAGGCGGCAGGCCAATTGTGAGCCAACGCACTAGATCACGTGCATACAACCACAACACATAAACTCGCTTTAAAGTGCGGGGTGCCCCCGGTCGAACTAAGCTCTCGTCCACGTTTTGGGGGAAAAGTCCTATGGATCCTGAGACAGCGCGCCTCCACGGAGCAAAAGTTGTTGACCAATAGTCTGACCATAACAACATGTGACTGGGTAGCCCCTGGTCATCCCCCCACATTGCCGATTTGTCAACAGTTGCACTGCCTGGAGGATCATGCGTCAGGATCAAGTCTATCGCCCACGACATATGAATTTCCACTGTCCGTGCGTCGAACCACGACAGTATGTGAGACGTGTCGAAGTCCCCCCCTTAGTGAAACGGCACTTTCTTAACCAAAGATTAAGCGGCGCCTTGGAATGGTTATCCTACGAGGAGTATGTCATACTCACTCTGTTTCTAGAACAAGTCCGTGAGAATTAGGCTGTCGGAGTAGTTTAGATAAGTGTATTTTATCTTCCGAGGCTATGGCTGGTGTGAACAATTCCCCAGACTTCCGAATTTGACTTCCTCAGTTCCGGGGCTCCCCATGACCAAACTAGATGGAATAACCTACATGACCAAACTGTCGCTTCCTGTATTGTGCTCTCAAGACTATATGAGTCGAATTCCAAGGCGCTATATCGCCTATTAAGGCAAGGCAGCCTCTAGCGCTATGCATTTCGTAACGGAATTAACGCCCACACCATCCTCAATTAACGTTAGGTACTCATATCCCCCTCATATTGGGGCCAATACCCCAAGGAGTTCGGACACGATCAACCAGCGGCGTCACCGCCCCCAGTGTGCAACGTTGTGGGGGAACACGAAATATAT
+>scaffold2 scaffold random_sequence_length_5000_chopped_3000-5000$
+TAACCACCAGCGCTAACCGCCCGGGAGTTAGAGAGTCCAGTGGTGTGTGATCAAAGACCCGTTTAGCCGATGCCTACCACACCCGAACGGCAAACAGCGGTGTTCAACTACCGTGGCCGCCGCGTGCTTCCAGTCTTATAGTCCCTGTACCTACGGAGTGATCTACATCGAATAGGTTGTGATTGAACCGCGGCTCTCGGCACCCTAAGGCCTCTTCATTAATACCTCAATTTGGCATGAGGAGCGCTTCGCCATTCTGCTTATACATGTACCGGCTTGGGTGAGGTTGGAGAAAAAGCGACCTGTGGCGCCACGTGATGTCCTCCTAAGAGGCAGAATCCCCTCGCTTGTGGTTTTGCCGTAATCCTGGTGTAAGGTTAGGTGTACAATATCGCTGGTACTCTGATCGCCGAGATCCAGTATCGGCCCTGTGCAAAATCACACCATATTGTATAGTCAGGCCGTACAGAAATGACACCATTCGAGAGAGCCTTTCCACAAGAAATATCGGTTCTACTGTCGAGATTCCCGCCGGACTCGATCTCACGCCCGGAGGTCGGGGAACGTTTCCTTTGTGATTAGCATATGGAGACTATTTATGACTGGCGATGCTGTGGAGTCACTTAGTGGAAAGACACCTAATCGTGAGGGTACTATCAACGTGGCTGAGCCAATACATTGGATGAGTGTCCCCCCTGTCCCCCTTTCTATGTTCGTCCCGGAGGTCCCGATGTGTTTGATAGCCGCGAGGGATGATCGATGAGTACTGCCGCTGTCTTTCTGCGAGGTGCCAGCTTCCAAAAATGTGTCGGAGTCGTATCTTTCTTACGAAGGTTAGAAGTCTGAGCGCTAGATTTCTTAAATTTGCCGAGATAAAGCGCCGTGACTTTAATATGAGGATGGGAGCAACTACCTTCGCGCTCAGCATCCGTACCTTCGTGCGTTACCACAACCCCGAAGGCGTACAGGTAACCGTTCGAATTGACTACCCAAGGGCCCGGAAGTTAAATAGTAGGTTAGTGCAATGTGCGACTACTGTGGGTGTAAGTATATAATCGCCGGGACGTACAACCCTGGCAGCTTGTAGTCCAATTTCGCACATGTCGGTATAATTCTCGCTTAATCAGCATCATGGAGATCCCTTCGAGGCCAAGGGCCTAGAGAAACTAACGCGTAAACTACGCACTCTAAGGTACAGGGGTGAATCCGTAGCGACTACATTATCGCTGAAACCTCGGATCGTCGCTTTTTTCCAATCCTCAGGCGGCGAAACTTCGTAAATTGTACCAACCTGTGGCCGTGGCTAGGGTCGGTAAGATAGCGGGGAAACATGGTAAGTTACGATCGGGATGTCTGTAAGAACCAACCACGGACGCGACCGAAACCCCTACGCCATTAAAATCGGTTCTAATCCAGATTTATTCTATAATGCGCCTGTTGATCGTCGGCGGAACGAGCACGGCTGATCGACGTAGTACTCGCTTAGGTGCCCTCGGCCGTCCCCAACTTGTTTTATAGTTGTCTAAATTCTCCGTCTAGGACGTGGCCATCCGAGAGTTTTTACAACGAGAATTAGGAAACTATCGTCGCCGATTCCTTACCCTTATTGGAATGATGGGGCCGGGCTATAGTATCAGGACAGACCTGTTGACAATTAATATCTACTAGGATTGAAGCGACAGAACTCGGGTTATGACTTAACTATGTCTTCTTTATAATGACGAGACCTCAATTTGGGCGTAATGTGAGGAGCATAAGGATGTTCGTCACAAAAACAGTATGTCCGTCACACATATTCCTTATGGGTGGGTAAGCGGCTAAAATGTCTCGATCACAAACAAAGAACTGGATATCGGGGTGTATTACGGGGGGTATGCAATGTAAGCGCTGAGTAATCGCAAGAGGCTTAAAATGACGAATCTAAGTTCATTGCCTACCCTTAACGAGTATGGCTAATCGGTAGCCCTTCGCTGATGACTAAAACCTAAGCGCCGCCACAGA
+EOF
+    #not the right answer
+    end
+  end
+
+  it 'should handle a simple variant in the gap' do
+    Dir.mktmpdir do |tmpdir|
+      command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/3_variant/reads.fa.gz "+
+        "--genomes #{TEST_DATA_DIR}/tweak/3_variant/with_gaps.fa --output-directory #{tmpdir}"
+      Bio::Commandeer.run(command).should == ''
+      output_file = File.join(tmpdir,'with_gaps.fa.scaffolds.fasta')
+      File.exist?(output_file).should == true
+      File.open(output_file).read.should == <<EOF
+>scaffold1 scaffold random_sequence_length_with_gaps
+AATGCACATCGACTATATTTAGGCGTCAGGCCTCGCGTCTGAGGGGATAGCACCATTATAGATGGAAAGTGACTGCTGATACGGAGTGCTGAGTTGTAGTGCGAGAGGCAGCCAAGTGTCGAGAATGTCGGAACGTTGTGACATAGTCGATGTACGTTCATCGAAGCAAGAGCCTAAAGACCGTCCGCTATGACTATTGGGCGAGGACCGGCCGAATGTTAAACATCCGATACAGCACGTACAAGGTCGCTCACCGAAGGCGCAAGATATTTTCCGCGATTGAAAAGTAACCACTTCCACGCAATTGAGGCGAAACCAACTAGCAGCTGCTCCCACTGTCGTCCATTGCCGTCAGGGGGATAAGCTCCATGCTACGTGGAACTATTGGGACCAGGTCGGTACACTCGTACCATGCATACTGGCGCGGGTGACGTTGGCCCGACGCGGACGACGTTTGTTCAGATACCGTGCAGTTACAATCCCATGTAAGCGATTCCCGGGGTTGAAATGCTTCCCGGCATACTCTGACGAAGATGCTCGAGTTCCAAGGTCAATCCGTAGCATTCGGGGATATGCGTCTGCTTCAGACAGGTCCTCCTCTCATTCACCGCTAGCGGGTCGTAAGGGGGAGTAAAGTTCGTGTCCCCAGGATGGGAGGAGCACACTCATCCCTGAGGGAAGCTAGGCCCAATCTGGACTTCCGAGCATCATACAATTTGAAAGGCCTGCAGGTCCCCAAGTCCGCCTCTGCCTGTGTTATAAAGTGGCCTACTATGCAGGACAGGGTCAAAAGGGCCCAGTCCGGGAACCAGAACCTTGAGGCCCCCGTGGCGTACGCCCCAAGCCCGCCTCCAGGGCGGCGCTGTTTTATTCTGACGGCTTTGATCGGCGAACACTGCCTGGTTAGGCACTGAATATAAAAATTCAGACACTGCCCTCCACTGAGTGACCAATCGAACATTCGTTGAGCATTGGCGCTTGTTTTCCCTTAGATTCTACC
+EOF
+      File.open(File.join(tmpdir,'with_gaps.fa.vcf')).readlines.should == [#known bug - the filename has been changed to at_least_half_completely_wrong since there are known issues there
+        %w(#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO).join("\t")+"\n",
+        %w(scaffold1	485	.	.	GGGGG	20	PASS	finishm).join("\t")+"\n"
+        ]
+    end
+  end
+
+  it 'should handle variants on the reverse strand' do
+    answer = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/3_variant/answer.fa").entries[0].to_biosequence.to_s
+    Dir.mktmpdir do |tmpdir|
+      Tempfile.open('testing_scaffolds2') do |t|
+        #File.open('/tmp/ta2','w') do |t|
+        t.puts '>seq1'
+        t.puts answer[0..200]
+        t.puts '>seq2'
+        t.puts Bio::Sequence::NA.new(answer[250..400]+'N'*50+answer[600..-1]).reverse_complement.to_s.upcase
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/3_variant/reads.fa.gz "+
+            "--genomes #{t.path} --output-directory #{tmpdir} --overhang 60"
+        Bio::Commandeer.run(command).should == ''
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).read.should == <<EOF
+>scaffold1 scaffold seq1:seq2
+AATGCACATCGACTATATTTAGGCGTCAGGCCTCGCGTCTGAGGGGATAGCACCATTATAGATGGAAAGTGACTGCTGATACGGAGTGCTGAGTTGTAGTGCGAGAGGCAGCCAAGTGTCGAGAATGTCGGAACGTTGTGACATAGTCGATGTACGTTCATCGAAGCAAGAGCCTAAAGACCGTCCGCTATGACTATTGGGCGAGGACCGGCCGAATGTTAAACATCCGATACAGCACGTACAAGGTCGCTCACCGAAGGCGCAAGATATTTTCCGCGATTGAAAAGTAACCACTTCCACGCAATTGAGGCGAAACCAACTAGCAGCTGCTCCCACTGTCGTCCATTGCCGTCAGGGGGATAAGCTCCATGCTACGTGGAACTATTGGGACCAGGTCGGTACACTCGTACCATGCATACTGGCGCGGGTGACGTTGGCCCGACGCGGACGACGTTTGTTCAGATACCGTGCAGTTACAATCCCATGTAAGCGATTCCCGGGGTTGAAATGCTTCCCGGCATACTCTGACGAAGATGCTCGAGTTCCAAGGTCAATCCGTAGCATTCGGGGATATGCGTCTGCTTCAGACAGGTCCTCCTCTCATTCACCGCTAGCGGGTCGTAAGGGGGAGTAAAGTTCGTGTCCCCAGGATGGGAGGAGCACACTCATCCCTGAGGGAAGCTAGGCCCAATCTGGACTTCCGAGCATCATACAATTTGAAAGGCCTGCAGGTCCCCAAGTCCGCCTCTGCCTGTGTTATAAAGTGGCCTACTATGCAGGACAGGGTCAAAAGGGCCCAGTCCGGGAACCAGAACCTTGAGGCCCCCGTGGCGTACGCCCCAAGCCCGCCTCCAGGGCGGCGCTGTTTTATTCTGACGGCTTTGATCGGCGAACACTGCCTGGTTAGGCACTGAATATAAAAATTCAGACACTGCCCTCCACTGAGTGACCAATCGAACATTCGTTGAGCATTGGCGCTTGTTTTCCCTTAGATTCTACC
+EOF
+        File.open(File.join(tmpdir, File.basename(t.path)+'.at_least_half_completely_wrong.vcf')).readlines.should == [
+          %w(#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO).join("\t")+"\n",
+          %w(scaffold1	485	.	.	GGGGG	20	PASS	finishm).join("\t")+"\n"
+          ]# need contig_printer to give an offset that can be added to each variant
+      end
+    end
+  end
+
+  it 'should respect --max-gapfill-paths' do
+    answer = Bio::FlatFile.open("#{TEST_DATA_DIR}/tweak/3_variant/answer.fa").entries[0].to_biosequence.to_s
+    #Dir.mktmpdir do |tmpdir|
+    begin tmpdir = '/tmp/testfi'
+      #Tempfile.open('testing_scaffolds2') do |t|
+        File.open('/tmp/ta2','w') do |t|
+        t.puts '>seq1'
+        t.puts answer[0..200]
+        t.puts '>seq2'
+        t.puts Bio::Sequence::NA.new(answer[250..400]+'N'*50+answer[600..-1]).reverse_complement.to_s.upcase
+        t.close
+
+        command = "#{path_to_script} --quiet --fasta-gz #{TEST_DATA_DIR }/tweak/3_variant/reads.fa.gz "+
+            "--genomes #{t.path} --output-directory #{tmpdir} --overhang 60 --max-gapfill-paths 1"
+        Bio::Commandeer.run(command).should == ''
+        output_file2 = File.join(tmpdir, File.basename(t.path)+'.scaffolds.fasta')
+        File.exist?(output_file2).should == true
+        File.open(output_file2).read.should == <<EOF
+>scaffold1 scaffold seq1:seq2
+AATGCACATCGACTATATTTAGGCGTCAGGCCTCGCGTCTGAGGGGATAGCACCATTATAGATGGAAAGTGACTGCTGATACGGAGTGCTGAGTTGTAGTGCGAGAGGCAGCCAAGTGTCGAGAATGTCGGAACGTTGTGACATAGTCGATGTACGTTCATCGAAGCAAGAGCCTAAAGACCGTCCGCTATGACTATTGGGCGAGGACCGGCCGAATGTTAAACATCCGATACAGCACGTACAAGGTCGCTCACCGAAGGCGCAAGATATTTTCCGCGATTGAAAAGTAACCACTTCCACGCAATTGAGGCGAAACCAACTAGCAGCTGCTCCCACTGTCGTCCATTGCCGTCAGGGGGATAAGCTCCATGCTACGTGGAACTATTGGGACCAGGTCGGTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCATTCACCGCTAGCGGGTCGTAAGGGGGAGTAAAGTTCGTGTCCCCAGGATGGGAGGAGCACACTCATCCCTGAGGGAAGCTAGGCCCAATCTGGACTTCCGAGCATCATACAATTTGAAAGGCCTGCAGGTCCCCAAGTCCGCCTCTGCCTGTGTTATAAAGTGGCCTACTATGCAGGACAGGGTCAAAAGGGCCCAGTCCGGGAACCAGAACCTTGAGGCCCCCGTGGCGTACGCCCCAAGCCCGCCTCCAGGGCGGCGCTGTTTTATTCTGACGGCTTTGATCGGCGAACACTGCCTGGTTAGGCACTGAATATAAAAATTCAGACACTGCCCTCCACTGAGTGACCAATCGAACATTCGTTGAGCATTGGCGCTTGTTTTCCCTTAGATTCTACC
+EOF
+        File.open(File.join(tmpdir, File.basename(t.path)+'.at_least_half_completely_wrong.vcf')).readlines.should == [
+          %w(#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO).join("\t")+"\n",
+          ]
+      end
+    end
+
+  end
+
+  it 'should handle circular scaffolds made up of multiple input scaffolds and are on different nodes' do
+    fail
+  end
+
+  it 'should handle circular scaffolds made up of multiple input scaffolds and are on the same velvet node' do
+    fail #known bug
+  end
+
+  it 'should print variants correctly after two contigs have been joined together' do
+    fail 'unlikely to work'
+  end
+end