Mercurial > repos > iuc > quast

--- a/quast.xml	Fri Sep 29 05:51:26 2017 -0400
+++ b/quast.xml	Mon Feb 12 09:05:20 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="quast" name="Quast" version="4.5" >
+<tool id="quast" name="Quast" version="4.6.3" >
     <description>Genome assembly Quality</description>
     <requirements>
-        <requirement type="package" version="4.5">quast</requirement>
+        <requirement type="package" version="4.6.3">quast</requirement>
     </requirements>
     <stdio>
         <regex match="ERROR! exception caught!"
@@ -34,104 +34,194 @@
         #end if
         --min-contig $min_contig
         -l
-        #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ])
+        #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.element_identifier))+'"' for $x in $input ])

         $names
         --contig-thresholds $threshold_contig
-        #for $k in $files:
-            #if $k.type_file == "scaffold":
-                -s
-            #end if
-        $k.input
+        #for $k in $input:
+            $k
         #end for
         &&
-        mv outputdir/report.txt '$quast_out' &&
         mv outputdir/report.tsv '$quast_tsv' &&
-        mv outputdir/report.tex '$quast_tex' &&
-        mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' &&
-        mv outputdir/report.html '$report_html'
+        ## The sed string below removes non-functional "Main menu" button from the viewer
+        sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/contig_size_viewer.html > '$contig_size_viewer' &&
+        #if $input_ref:
+            ## The sed string below removes non-functional "Main menu" button from the viewer
+            sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/alignment_viewer.html > '$alignment_viewer' &&
+        #end if
+        ## The sed string below removes non-functional link from the report page
+        sed "\:<div id='icarus-json'>:,\:</div>:d" outputdir/report.html > '$report_html' &&
+        mv outputdir/report.pdf '$report_pdf' &&
+        mv outputdir/contigs_reports/misassemblies_report.tsv '$mis_ass_tsv' &&
+        mv outputdir/contigs_reports/unaligned_report.tsv '$unalign_tsv' &&
+        mv outputdir/quast.log '$log_txt'
     ]]>
     </command>
     <inputs>
-        <repeat name="files" title="Input assembly files" min="1">
-            <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/>
-            <param name="type_file" type="select" label="Type of data">
-                <option value="contig">Contig</option>
-                <option value="scaffold">Scaffold</option>
-            </param>
-        </repeat>
+        <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/>
+        <param name="type_file" type="select" label="Type of data">
+            <option value="contig">Contig</option>
+            <option value="scaffold">Scaffold</option>
+        </param>
         <param name="input_size" type="integer" label="Size of reference genome" optional="True"  argument="--est-ref-size"
             help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
-        <param name="input_ref" type="data" format="fasta"  label="Reference File" optional="True"  argument="-R"
+        <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True"  argument="-R"
             help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>
-        <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G"
-            help="File with gene positions in the reference genome. "/>
-        <param name="input_operon" type="data" format="txt" label="Operon Annotations"  optional="True" argument="-O"
-            help="File with operon positions in the reference genome"/>
+        <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G"
+            help="Gene coordinates for the reference genome (only relevant if the reference genome is used). "/>
+        <param name="input_operon" type="data" format="gff, gff3, bed" label="Operon Annotations"  optional="True" argument="-O" help="Operon coordinates for the reference genome (only relevant if the reference genome is used)."/>
         <param name="gene_selection" type="select" label="Type of organism">
             <option value="prokaryotes">Prokaryotes</option>
             <option value="eukaryote">Eukaryote</option>
-            <option value="metagenes">Metagenomes</option>
         </param>
         <param name="min_contig" type="integer" value="500" label="Lower Threshold"  argument="--min-contig"
-            help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account (default is 500)"/>
+            help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account [default is 500]"/>
         <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
-            help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.(default is 0,1000)"/>
+            help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/>
     </inputs>
     <outputs>
-        <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
-        <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/>
-        <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/>
-        <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/>
-        <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/>
+        <data format="txt" name="log_txt" label="Quast: Log" />
+        <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies">
+            <filter>input_ref is not None</filter>
+        </data>
+        <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs">
+            <filter>input_ref is not None</filter>
+        </data>
+        <data format="html" name="contig_size_viewer" label="Quast: Contig view"/>
+        <data format="html" name="alignment_viewer" label="Quast: Alignment view">
+            <filter>input_ref is not None</filter>
+        </data>
+        <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)"/>
+        <data format="html" name="report_html" label="Quast: Report (HTML)"/>
+        <data format="pdf" name="report_pdf" label="Quast: Report (PDF)"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="contigs_1.fasta"/>
-            <param name="input.type_file" value="contig"/>
+            <!-- Test with reference and genes annotations -->
+            <param name="input" value="contigs2.fna,contigs1.fna"/>
+            <param name="input_ref" value="reference.fna"/>
+            <param name="type_file" value="contig"/>
+            <param name="annot" value="genes.gff"/>
             <param name="gene_selection" value="prokaryotes"/>
-            <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/>
+            <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/>
         </test>
         <test>
-            <param name="input" value="contigs_1.fasta"/>
-            <param name="input.type_file" value="contig"/>
-            <param name="input_ref" value="NC000913.3_1-6650.fasta"/>
-            <param name="gene_selection" value="prokaryotes"/>
-            <output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/>
-        </test>
-        <test>
-            <param name="input" value="contigs_1.fasta"/>
-            <param name="input.type_file" value="contig"/>
-            <param name="input_ref" value="NC000913.3_1-6650.fasta"/>
-            <param name="annot" value="NC000913.3_1-6650.gff"/>
-            <param name="gene_selection" value="prokaryotes"/>
-            <output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/>
+            <!-- Test without reference -->
+            <param name="input" value="contigs2.fna,contigs1.fna"/>
+            <param name="type_file" value="contig"/>
+            <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/>
         </test>
     </tests>
     <help>
 <![CDATA[
-**Description**
+**What it does**
+
+QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
+
+If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.bioinf.spbau.ru/manual.html>`_.
+
+**Using Quast without reference**

-Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics.
+Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
+
+ * Quast report in HTML format
+ * `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
+ * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format
+ * Quast log (a file technical information about Quast tool execution)
+
+The **tab delimited Quast report** will contain the following information::

------
+ Assembly                  pit_fna cef_fna car_fna
+ # contigs (>= 0 bp)           100      91      94
+ # contigs (>= 1000 bp)         62      58      61
+ Total length (>= 0 bp)    6480635 6481216 6480271
+ Total length (>= 1000 bp) 6466917 6468946 6467103
+ # contigs                      71      66      70
+ Largest contig             848753  848766  662053
+ Total length              6473173 6474698 6473810
+ GC (%)                      66.33   66.33   66.33
+ N50                        270269  289027  254671
+ N75                        136321  136321  146521
+ L50                             7       7       8
+ L75                            15      15      16
+ # N's per 100 kbp            0.00    0.00    0.00
+
+where values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_

-**Inputs and Outputs**
+**Quast report in HTML format** contains graphs in addition to the above metrics, while **Contig viewer** draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel:
+
+.. image:: $PATH_TO_IMAGES/contig_view_noR.png
+   :width: 558
+   :height: 412
+
+Also see `Plot description <http://quast.bioinf.spbau.ru/manual.html#sec3.2>`_ section of the manual.
+
+**Using Quast with reference**
+
+Car, pit, and cef are in fact assemblies of *Pseudomonas aeruginosa* UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing *P. aeruginosa* pa14 genome to **Reference genome** input box). The following outputs will be produced (note the alignment viewer):
+
+ * Quast report in HTML format
+ * `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
+ * `Alignment viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
+ * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format
+ * Summary of `misassemblies <http://quast.bioinf.spbau.ru/manual.html#sec3.1.2>`_
+ * Summary of `unaligned contigs <http://quast.bioinf.spbau.ru/manual.html#sec3.1.3>`_
+ * Quast log (a file technical information about Quast tool execution)

-- Input:
-    + The tool accepts assemblies and references in FASTA format.
-    + The tool accepts annotation and operon files in:
-        + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon")
-        + the format used by NCBI for genes ("Summary (text)");
-        + four tab-separated columns: sequence name, gene/operon id, start position, end position
+With the reference Quast produces a much more comprehensive set of results::

-- Output:
-    + An assessment summary in plain text format
-    + An assessment summary in tabulation separated values format
-    + An assessment summary in LateX format
-    + An assessment summary in HTML format
-    + An HTML view of contig sizes wit Icarus
+ Assembly                  pit_fna cef_fna car_fna
+ # contigs (>= 0 bp)           100      91      94
+ # contigs (>= 1000 bp)         62      58      61
+ Total length (>= 0 bp)    6480635 6481216 6480271
+ Total length (>= 1000 bp) 6466917 6468946 6467103
+ # contigs                      71      66      70
+ Largest contig             848753  848766  662053
+ Total length              6473173 6474698 6473810
+ Reference length          6537648 6537648 6537648
+ GC (%)                      66.33   66.33   66.33
+ Reference GC (%)            66.29   66.29   66.29
+ N50                        270269  289027  254671
+ NG50                       270269  289027  254671
+ N75                        136321  136321  146521
+ NG75                       136321  136321  136321
+ L50                             7       7       8
+ LG50                            7       7       8
+ L75                            15      15      16
+ LG75                           15      15      17
+ # misassemblies                 0       0       0
+ # misassembled contigs          0       0       0
+ Misassembled contigs length     0       0       0
+ # local misassemblies           1       1       2
+ # unaligned mis. contigs        0       0       0
+ # unaligned contigs         0 + 0   0 + 0   0 + 0
+                              part    part    part
+ Unaligned length                0       0       0
+ Genome fraction (%)        99.015  99.038  99.025
+ Duplication ratio           1.000   1.000   1.000
+ # N's per 100 kbp            0.00    0.00    0.00
+ # mismatches per 100 kbp     3.82    3.63    3.49
+ # indels per 100 kbp         1.19    1.13    1.13
+ Largest alignment          848753  848766  662053
+ Total aligned length      6473163 6474660 6473792
+ NA50                       270269  289027  254671
+ NGA50                      270269  289027  254671
+ NA75                       136321  136321  146521
+ NGA75                      136321  136321  136321
+ LA50                            7       7       8
+ LGA50                           7       7       8
+ LA75                           15      15      16
+ LGA75                          15      15      17

+where, again, values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly.
+
+ Using reference also produces an **Alignment viewer**:
+
+.. image:: $PATH_TO_IMAGES/Align_view.png
+   :width: 515
+   :height: 395
+
+Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_).

     ]]>
     </help>
Binary file static/images/Align_view.png has changed
Binary file static/images/contig_view_noR.png has changed
--- a/test-data/NC000913.3_1-6650.fasta	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,112 +0,0 @@
->NC_000913.3:1-6650
-AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
-TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
-TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
-ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
-AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
-CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
-ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
-AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
-GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
-CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
-CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
-AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
-ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
-GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
-GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
-GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
-TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
-GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
-ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
-ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
-CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
-ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
-GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
-ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
-CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
-CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
-TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
-GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
-ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
-TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
-AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
-CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
-AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
-CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
-CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
-TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
-GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
-TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
-GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
-GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
-GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
-TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
-TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
-ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
-TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
-CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
-GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
-GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
-TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
-CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
-GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA
-AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
-GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT
-GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT
-TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
-GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
-CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT
-GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
-AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA
-GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
-CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA
-CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT
-ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
-GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
-GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC
-GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT
-GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT
-GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
-AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA
-TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
-CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA
-TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
-GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT
-CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA
-GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG
-TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
-CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
-GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT
-CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC
-GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
-AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC
-CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT
-GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA
-TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
-CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG
-ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA
-ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA
-AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
-CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT
-AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG
-GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
-GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
-TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG
-GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG
-CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG
-TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
-AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG
-ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
-GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC
-ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
-GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG
-GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA
-GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC
-GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
-CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
-GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA
-CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG
-GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT
-TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
-AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
-AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
--- a/test-data/NC000913.3_1-6650.gff	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-##gff-version 3
-#!gff-spec-version 1.21
-#!processor NCBI annotwriter
-#!genome-build ASM584v2
-#!genome-build-accession NCBI_Assembly:GCF_000005845.2
-##sequence-region NC_000913.3 1 4641652
-##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
-NC_000913.3	RefSeq	region	1	4641652	.	+	.	ID=id0;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
-NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene0;Dbxref=EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001,JW4367;locus_tag=b0001
-NC_000913.3	RefSeq	CDS	190	255	.	+	0	ID=cds0;Parent=gene0;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;Ontology_term=GO:0009088;gbkey=CDS;gene=thrL;go_process=threonine biosynthetic process|0009088||;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
-NC_000913.3	RefSeq	gene	337	2799	.	+	.	ID=gene1;Dbxref=EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,JW0001,thrA1,thrA2,thrD;locus_tag=b0002
-NC_000913.3	RefSeq	CDS	337	2799	.	+	0	ID=cds1;Parent=gene1;Dbxref=ASAP:ABE-0000008,UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;Note=bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal);Ontology_term=GO:0005737,GO:0009088,GO:0009086,GO:0009090;experiment=N-terminus verified by Edman degradation: PMID 354697%2C4562989;gbkey=CDS;gene=thrA;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||,methionine biosynthetic process|0009086||,homoserine biosynthetic process|0009090||;product=Bifunctional aspartokinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
-NC_000913.3	RefSeq	gene	2801	3733	.	+	.	ID=gene2;Dbxref=EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003,JW0002;locus_tag=b0003
-NC_000913.3	RefSeq	CDS	2801	3733	.	+	0	ID=cds2;Parent=gene2;Dbxref=ASAP:ABE-0000010,UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;Ontology_term=GO:0005737,GO:0009088;gbkey=CDS;gene=thrB;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
-NC_000913.3	RefSeq	gene	3734	5020	.	+	.	ID=gene3;Dbxref=EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004,JW0003;locus_tag=b0004
-NC_000913.3	RefSeq	CDS	3734	5020	.	+	0	ID=cds3;Parent=gene3;Dbxref=ASAP:ABE-0000012,UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;Ontology_term=GO:0005737,GO:0009088;experiment=N-terminus verified by Edman degradation: PMID 9298646%2C9600841%2C9740056;gbkey=CDS;gene=thrC;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=L-threonine synthase;protein_id=NP_414545.1;transl_table=11
-NC_000913.3	RefSeq	gene	5234	5530	.	+	.	ID=gene4;Dbxref=EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005,JW0004;locus_tag=b0005
-NC_000913.3	RefSeq	CDS	5234	5530	.	+	0	ID=cds4;Parent=gene4;Dbxref=ASAP:ABE-0000015,UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;product=DUF2502 family putative periplasmic protein;protein_id=NP_414546.1;transl_table=11
-NC_000913.3	RefSeq	repeat_region	5565	5669	.	+	.	ID=id1;Note=RIP1 (repetitive extragenic palindromic) element%3B contains 2 REP sequences and 1 IHF site;gbkey=repeat_region
-NC_000913.3	RefSeq	gene	5683	6459	.	-	.	ID=gene5;Dbxref=EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006,JW0005;locus_tag=b0006
-NC_000913.3	RefSeq	CDS	5683	6459	.	-	0	ID=cds5;Parent=gene5;Dbxref=ASAP:ABE-0000018,UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;product=peroxide resistance protein%2C lowers intracellular iron;protein_id=NP_414547.1;transl_table=11
-###
--- a/test-data/Quast_report.tex	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-\documentclass[12pt,a4paper]{article}
-\begin{document}
-\begin{table}[ht]
-\begin{center}
-\caption{All statistics are based on contigs of size $\geq$ 500 bp, unless otherwise noted (e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}
-\begin{tabular}{|l*{1}{|r}|}
-\hline
-Assembly & contigs\_1\_fasta \\ \hline
-\# contigs ($\geq$ 0 bp) & 3 \\ \hline
-\# contigs ($\geq$ 1000 bp) & 3 \\ \hline
-Total length ($\geq$ 0 bp) & 6710 \\ \hline
-Total length ($\geq$ 1000 bp) & 6710 \\ \hline
-\# contigs & 3 \\ \hline
-Largest contig & 3980 \\ \hline
-Total length & 6710 \\ \hline
-GC (\%) & 51.28 \\ \hline
-N50 & 3980 \\ \hline
-N75 & 1610 \\ \hline
-L50 & 1 \\ \hline
-L75 & 2 \\ \hline
-\# N's per 100 kbp & 0.00 \\ \hline
-\end{tabular}
-\end{center}
-\end{table}
-\end{document}
--- a/test-data/Quast_report.tsv	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-Assembly	contigs_1_fasta
-# contigs (>= 0 bp)	3
-# contigs (>= 1000 bp)	3
-Total length (>= 0 bp)	6710
-Total length (>= 1000 bp)	6710
-# contigs	3
-Largest contig	3980
-Total length	6710
-GC (%)	51.28
-N50	3980
-N75	1610
-L50	1
-L75	2
-# N's per 100 kbp	0.00
--- a/test-data/Quast_report.txt	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
-
-Assembly                   contigs_1_fasta
-# contigs (>= 0 bp)        3
-# contigs (>= 1000 bp)     3
-Total length (>= 0 bp)     6710
-Total length (>= 1000 bp)  6710
-# contigs                  3
-Largest contig             3980
-Total length               6710
-GC (%)                     51.28
-N50                        3980
-N75                        1610
-L50                        1
-L75                        2
-# N's per 100 kbp          0.00
--- a/test-data/Quast_report_withref.tsv	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-Assembly	contigs_1_fasta
-# contigs (>= 0 bp)	3
-# contigs (>= 1000 bp)	3
-Total length (>= 0 bp)	6710
-Total length (>= 1000 bp)	6710
-# contigs	3
-Largest contig	3980
-Total length	6710
-Reference length	6650
-GC (%)	51.28
-Reference GC (%)	52.00
-N50	3980
-NG50	3980
-N75	1610
-NG75	1610
-L50	1
-LG50	1
-L75	2
-LG75	2
-# misassemblies	0
-# misassembled contigs	0
-Misassembled contigs length	0
-# local misassemblies	0
-# unaligned mis. contigs	0
-# unaligned contigs	0 + 1 part
-Unaligned length	1950
-Genome fraction (%)	71.579
-Duplication ratio	1.000
-# N's per 100 kbp	0.00
-# mismatches per 100 kbp	0.00
-# indels per 100 kbp	0.00
-Largest alignment	2030
-Total aligned length	4760
-NA50	1610
-NGA50	1610
-LA50	2
-LGA50	2
--- a/test-data/Quast_report_withref_withgenes.tsv	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-Assembly	contigs_1_fasta
-# contigs (>= 0 bp)	3
-# contigs (>= 1000 bp)	3
-Total length (>= 0 bp)	6710
-Total length (>= 1000 bp)	6710
-# contigs	3
-Largest contig	3980
-Total length	6710
-Reference length	6650
-GC (%)	51.28
-Reference GC (%)	52.00
-N50	3980
-NG50	3980
-N75	1610
-NG75	1610
-L50	1
-LG50	1
-L75	2
-LG75	2
-# misassemblies	0
-# misassembled contigs	0
-Misassembled contigs length	0
-# local misassemblies	0
-# unaligned mis. contigs	0
-# unaligned contigs	0 + 1 part
-Unaligned length	1950
-Genome fraction (%)	71.579
-Duplication ratio	1.000
-# N's per 100 kbp	0.00
-# mismatches per 100 kbp	0.00
-# indels per 100 kbp	0.00
-# genes	3 + 3 part
-Largest alignment	2030
-Total aligned length	4760
-NA50	1610
-NGA50	1610
-LA50	2
-LGA50	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs1.fna	Mon Feb 12 09:05:20 2018 -0500
@@ -0,0 +1,99 @@
+>contig1
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT
+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
+>contig2
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG
+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA
+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA
+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC
+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG
+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG
+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA
+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT
+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG
+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA
+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC
+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG
+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG
+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT
+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC
+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC
+>contig3
+GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA
+ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT
+TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA
+TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT
+CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC
+TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA
+AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT
+CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC
+TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC
+CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG
+ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
+GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA
+ATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
+GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCA
+TTGACTGCAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCA
+AAGAAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAAC
+GACTCATCAGACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
+GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCC
+AGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCC
+AGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATAAGGCTGCAT
+TAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
+TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGC
+GGGCATTCGCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
+GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAACTGCTGGGAA
+TTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAG
+GTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAATGAGAATGA
+GTTGATCGATAGTTGTGATTACTCCTGCGAAACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATA
+TCCGGATAACGCAATGGATCAAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
+CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAATGGCGGGCGATATCAACGCAGTGTCAGAAATCCGA
+AACAGTCTCGCCTGGCGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGTCGTGATATCATCAGGGC
+AGACCGGTTACATCCCCCTAACAAGCTGTTTAAAGAGAAATACTATCATGACGGACAAATTGACCTCCCT
+TCGTCAGTACACCACCGTAGTGGCCGACACTGGGGACATCGCGGCAATGAAGCTGTATCAACCGCAGGAT
+GCCACAACCAACCCTTCTCTCATTCTTAACGCAGCGCAGATTCCGGAATACCGTAAGTTGATTGATGATG
+CTGTCGCCTGGGCGAAACAGCAGAGCAACGATCGCGCGCAGCAGATCGTGGACGCGACCGACAAACTGGC
+AGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTT
+TCCTATGACACCGAAGCGTCAATTGCGAAAGCAAAACGCCTGATCAAACTCTACAACGATGCTGGTATTA
+GCAACGATCGTATTCTGATCAAACTGGCTTCTACCTGGCAGGGTATCCGTGCTGCAGAACAGCTGGAAAA
+AGAAGGCATCAACTGTAACCTGACCCTGCTGTTCTCCTTCGCTCAGGCTCGTGCTTGTGCGGAAGCGGGC
+GTGTTCCTGATCTCGCCGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGAATACCGATAAGAAAGAGT
+ACGCTCCGGCAGAAGATCCGGGCGTGGTTTCTGTATCTGAAATCTACCAGTACTACAAAGAGCACGGTTA
+TGAAACCGTGGTTATGGGCGCAAGCTTCCGTAACATCGGCGAAATTCTGGAACTGGCAGGCTGCGACCGT
+CTGACCATCGCACCGGCACTGCTGAAAGAGCTGGCGGAGAGCGAAGGGGCTATCGAACGTAAACTGTCTT
+ACACCGGCGAAGTGAAAGCGCGTCCGGCGCGTATCACTGAGTCCGAGTTCCTGTGGCAGCACAACCAGGA
+TCCAATGGCAGTAGATAAACTGGCGGAAGGTATCCGTAAGTTTGCTATTGACCAGGAAAAACTGGAAAAA
+ATGATCGGCGATCTGCTGTAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGCC
+TGTCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACGAGACTGTTTAAACGGAAAAATCTTGATGAA
+TACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAGGCATC
+CCTGCGCTGGAAGAATGGCTGACATCGGCGCTAACCACGCCGTTTGAACTGGAAACCCGCTTAATCCCCG
+ATGAGCAGGCGATCATCGAGCAAACGTTGTGTGAGCTGGTGGATGAAATGAGTTGCCATCTGGTGCTCAC
+CACGGGCGGAACTGGCCCGGCGCGTCGTGACGTAACGCCCGATGCGACGCTGGCAGTAGCGGACCGCGAG
+ATGCCTGGCTTTGGTGAACAGATGCGCCAGATCAGCCTGCATTTTGTACCAACTGCGATCCTTTCGCGTC
+AGGTGGGCGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCGGTCAGCCGAAGTCTATTAAAGAGAC
+GCTGGAAGGTGTGAAGGACGCTGAGGGTAACGTTGTGGTACACGGTATTTTTGCCAGCGTACCGTACTGC
+ATTCAGTTGCTGGAAGGGCCATACGTTGAAACGGCACCGGAAGTGGTTGCAGCATTCAGACCGAAGAGTG
+CAAGACGCGACGTTAGCGAATAAAAAAATCCCCCCGAGCGGGGGGATCTCAAAACAATTAGTGGGATTCA
+CCAATCGGCAGAACGGTGCGACCAAACTGCTCGTTCAGTACTTCACCCATCGCCAGATAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs2.fna	Mon Feb 12 09:05:20 2018 -0500
@@ -0,0 +1,112 @@
+>NC_000913.3:1-6650
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
+GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA
+AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
+GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT
+GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT
+TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
+GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT
+GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
+AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA
+GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
+CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA
+CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT
+ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
+GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
+GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC
+GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT
+GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT
+GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
+AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA
+TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
+CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA
+TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
+GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT
+CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA
+GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG
+TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
+CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
+GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT
+CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC
+GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
+AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC
+CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT
+GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA
+TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG
+ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA
+ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA
+AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
+CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT
+AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG
+GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
+GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
+TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG
+GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG
+CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG
+TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
+AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG
+ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
+GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC
+ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
+GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG
+GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA
+GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC
+GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
+CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
+GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA
+CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG
+GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT
+TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
+AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
+AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
--- a/test-data/contigs_1.fasta	Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
->contig1
-AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
-TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
-TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
-ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
-CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
-GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
-AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
-AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
-GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
-GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
-TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
-TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
-GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
-CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
-TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT
-CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
->contig2
-ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG
-GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA
-TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
-GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA
-AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC
-CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
-TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG
-GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
-TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG
-CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA
-AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT
-GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
-TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG
-ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA
-AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC
-AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
-ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG
-TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
-CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG
-CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT
-CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
-GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC
-GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC
->contig3
-GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA
-ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT
-TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA
-TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT
-CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC
-TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
-CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA
-AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT
-CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC
-TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC
-CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG
-ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
-GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA
-ATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
-GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCA
-TTGACTGCAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCA
-AAGAAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAAC
-GACTCATCAGACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
-GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCC
-AGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCC
-AGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATAAGGCTGCAT
-TAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
-TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGC
-GGGCATTCGCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
-GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAACTGCTGGGAA
-TTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAG
-GTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAATGAGAATGA
-GTTGATCGATAGTTGTGATTACTCCTGCGAAACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATA
-TCCGGATAACGCAATGGATCAAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
-CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAATGGCGGGCGATATCAACGCAGTGTCAGAAATCCGA
-AACAGTCTCGCCTGGCGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGTCGTGATATCATCAGGGC
-AGACCGGTTACATCCCCCTAACAAGCTGTTTAAAGAGAAATACTATCATGACGGACAAATTGACCTCCCT
-TCGTCAGTACACCACCGTAGTGGCCGACACTGGGGACATCGCGGCAATGAAGCTGTATCAACCGCAGGAT
-GCCACAACCAACCCTTCTCTCATTCTTAACGCAGCGCAGATTCCGGAATACCGTAAGTTGATTGATGATG
-CTGTCGCCTGGGCGAAACAGCAGAGCAACGATCGCGCGCAGCAGATCGTGGACGCGACCGACAAACTGGC
-AGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTT
-TCCTATGACACCGAAGCGTCAATTGCGAAAGCAAAACGCCTGATCAAACTCTACAACGATGCTGGTATTA
-GCAACGATCGTATTCTGATCAAACTGGCTTCTACCTGGCAGGGTATCCGTGCTGCAGAACAGCTGGAAAA
-AGAAGGCATCAACTGTAACCTGACCCTGCTGTTCTCCTTCGCTCAGGCTCGTGCTTGTGCGGAAGCGGGC
-GTGTTCCTGATCTCGCCGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGAATACCGATAAGAAAGAGT
-ACGCTCCGGCAGAAGATCCGGGCGTGGTTTCTGTATCTGAAATCTACCAGTACTACAAAGAGCACGGTTA
-TGAAACCGTGGTTATGGGCGCAAGCTTCCGTAACATCGGCGAAATTCTGGAACTGGCAGGCTGCGACCGT
-CTGACCATCGCACCGGCACTGCTGAAAGAGCTGGCGGAGAGCGAAGGGGCTATCGAACGTAAACTGTCTT
-ACACCGGCGAAGTGAAAGCGCGTCCGGCGCGTATCACTGAGTCCGAGTTCCTGTGGCAGCACAACCAGGA
-TCCAATGGCAGTAGATAAACTGGCGGAAGGTATCCGTAAGTTTGCTATTGACCAGGAAAAACTGGAAAAA
-ATGATCGGCGATCTGCTGTAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGCC
-TGTCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACGAGACTGTTTAAACGGAAAAATCTTGATGAA
-TACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAGGCATC
-CCTGCGCTGGAAGAATGGCTGACATCGGCGCTAACCACGCCGTTTGAACTGGAAACCCGCTTAATCCCCG
-ATGAGCAGGCGATCATCGAGCAAACGTTGTGTGAGCTGGTGGATGAAATGAGTTGCCATCTGGTGCTCAC
-CACGGGCGGAACTGGCCCGGCGCGTCGTGACGTAACGCCCGATGCGACGCTGGCAGTAGCGGACCGCGAG
-ATGCCTGGCTTTGGTGAACAGATGCGCCAGATCAGCCTGCATTTTGTACCAACTGCGATCCTTTCGCGTC
-AGGTGGGCGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCGGTCAGCCGAAGTCTATTAAAGAGAC
-GCTGGAAGGTGTGAAGGACGCTGAGGGTAACGTTGTGGTACACGGTATTTTTGCCAGCGTACCGTACTGC
-ATTCAGTTGCTGGAAGGGCCATACGTTGAAACGGCACCGGAAGTGGTTGCAGCATTCAGACCGAAGAGTG
-CAAGACGCGACGTTAGCGAATAAAAAAATCCCCCCGAGCGGGGGGATCTCAAAACAATTAGTGGGATTCA
-CCAATCGGCAGAACGGTGCGACCAAACTGCTCGTTCAGTACTTCACCCATCGCCAGATAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.gff	Mon Feb 12 09:05:20 2018 -0500
@@ -0,0 +1,22 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM584v2
+#!genome-build-accession NCBI_Assembly:GCF_000005845.2
+##sequence-region NC_000913.3 1 4641652
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
+NC_000913.3	RefSeq	region	1	4641652	.	+	.	ID=id0;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
+NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene0;Dbxref=EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001,JW4367;locus_tag=b0001
+NC_000913.3	RefSeq	CDS	190	255	.	+	0	ID=cds0;Parent=gene0;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;Ontology_term=GO:0009088;gbkey=CDS;gene=thrL;go_process=threonine biosynthetic process|0009088||;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
+NC_000913.3	RefSeq	gene	337	2799	.	+	.	ID=gene1;Dbxref=EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,JW0001,thrA1,thrA2,thrD;locus_tag=b0002
+NC_000913.3	RefSeq	CDS	337	2799	.	+	0	ID=cds1;Parent=gene1;Dbxref=ASAP:ABE-0000008,UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;Note=bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal);Ontology_term=GO:0005737,GO:0009088,GO:0009086,GO:0009090;experiment=N-terminus verified by Edman degradation: PMID 354697%2C4562989;gbkey=CDS;gene=thrA;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||,methionine biosynthetic process|0009086||,homoserine biosynthetic process|0009090||;product=Bifunctional aspartokinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
+NC_000913.3	RefSeq	gene	2801	3733	.	+	.	ID=gene2;Dbxref=EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003,JW0002;locus_tag=b0003
+NC_000913.3	RefSeq	CDS	2801	3733	.	+	0	ID=cds2;Parent=gene2;Dbxref=ASAP:ABE-0000010,UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;Ontology_term=GO:0005737,GO:0009088;gbkey=CDS;gene=thrB;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
+NC_000913.3	RefSeq	gene	3734	5020	.	+	.	ID=gene3;Dbxref=EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004,JW0003;locus_tag=b0004
+NC_000913.3	RefSeq	CDS	3734	5020	.	+	0	ID=cds3;Parent=gene3;Dbxref=ASAP:ABE-0000012,UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;Ontology_term=GO:0005737,GO:0009088;experiment=N-terminus verified by Edman degradation: PMID 9298646%2C9600841%2C9740056;gbkey=CDS;gene=thrC;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=L-threonine synthase;protein_id=NP_414545.1;transl_table=11
+NC_000913.3	RefSeq	gene	5234	5530	.	+	.	ID=gene4;Dbxref=EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005,JW0004;locus_tag=b0005
+NC_000913.3	RefSeq	CDS	5234	5530	.	+	0	ID=cds4;Parent=gene4;Dbxref=ASAP:ABE-0000015,UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;product=DUF2502 family putative periplasmic protein;protein_id=NP_414546.1;transl_table=11
+NC_000913.3	RefSeq	repeat_region	5565	5669	.	+	.	ID=id1;Note=RIP1 (repetitive extragenic palindromic) element%3B contains 2 REP sequences and 1 IHF site;gbkey=repeat_region
+NC_000913.3	RefSeq	gene	5683	6459	.	-	.	ID=gene5;Dbxref=EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006,JW0005;locus_tag=b0006
+NC_000913.3	RefSeq	CDS	5683	6459	.	-	0	ID=cds5;Parent=gene5;Dbxref=ASAP:ABE-0000018,UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;product=peroxide resistance protein%2C lowers intracellular iron;protein_id=NP_414547.1;transl_table=11
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fna	Mon Feb 12 09:05:20 2018 -0500
@@ -0,0 +1,112 @@
+>NC_000913.3:1-6650
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
+GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA
+AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
+GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT
+GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT
+TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
+GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT
+GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
+AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA
+GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
+CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA
+CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT
+ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
+GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
+GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC
+GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT
+GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT
+GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
+AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA
+TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
+CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA
+TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
+GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT
+CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA
+GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG
+TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
+CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
+GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT
+CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC
+GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
+AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC
+CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT
+GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA
+TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG
+ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA
+ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA
+AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
+CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT
+AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG
+GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
+GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
+TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG
+GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG
+CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG
+TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
+AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG
+ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
+GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC
+ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
+GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG
+GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA
+GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC
+GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
+CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
+GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA
+CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG
+GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT
+TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
+AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
+AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_output.tsv	Mon Feb 12 09:05:20 2018 -0500
@@ -0,0 +1,42 @@
+Assembly	contigs2_fna	contigs1_fna
+# contigs (>= 0 bp)	1	3
+# contigs (>= 1000 bp)	1	3
+Total length (>= 0 bp)	6650	6710
+Total length (>= 1000 bp)	6650	6710
+# contigs	1	3
+Largest contig	6650	3980
+Total length	6650	6710
+Reference length	6650	6650
+GC (%)	52.00	51.28
+Reference GC (%)	52.00	52.00
+N50	6650	3980
+NG50	6650	3980
+N75	6650	1610
+NG75	6650	1610
+L50	1	1
+LG50	1	1
+L75	1	2
+LG75	1	2
+# misassemblies	0	0
+# misassembled contigs	0	0
+Misassembled contigs length	0	0
+# local misassemblies	0	0
+# unaligned mis. contigs	0	0
+# unaligned contigs	0 + 0 part	0 + 1 part
+Unaligned length	0	1950
+Genome fraction (%)	100.000	71.579
+Duplication ratio	1.000	1.000
+# N's per 100 kbp	0.00	0.00
+# mismatches per 100 kbp	0.00	0.00
+# indels per 100 kbp	0.00	0.00
+# genes	6 + 0 part	3 + 3 part
+Largest alignment	6650	2030
+Total aligned length	6650	4760
+NA50	6650	1610
+NGA50	6650	1610
+NA75	6650	-
+NGA75	6650	-
+LA50	1	2
+LGA50	1	2
+LA75	1	-
+LGA75	1	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_output.tsv	Mon Feb 12 09:05:20 2018 -0500
@@ -0,0 +1,14 @@
+Assembly	contigs2_fna	contigs1_fna
+# contigs (>= 0 bp)	1	3
+# contigs (>= 1000 bp)	1	3
+Total length (>= 0 bp)	6650	6710
+Total length (>= 1000 bp)	6650	6710
+# contigs	1	3
+Largest contig	6650	3980
+Total length	6650	6710
+GC (%)	52.00	51.28
+N50	6650	3980
+N75	6650	1610
+L50	1	1
+L75	1	2
+# N's per 100 kbp	0.00	0.00