Mercurial > repos > iuc > mummer_nucmer

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,69 @@
+<macros>
+    <xml name="citation">
+        <citations>
+            <citation type="bibtex">
+                @misc{githubmummer,
+                author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg},
+                year = {2012},
+                title = {mummer4},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://github.com/mummer4/mummer},
+            }</citation>
+        </citations>
+    </xml>
+    <token name="@MUMMER_VERSION@">4.0.0beta2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="mumplot_input" >
+        <yield />
+        <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length"
+            help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
+        <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
+            <option value="">Color</option>
+            <option value="-color">No color (-color)</option>
+        </param>
+        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
+            <option value="">Dotplot</option>
+            <option value="-c">Coverage Plot (-c)</option>
+        </param>
+        <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
+            help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
+        <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
+        <conditional name="labels" >
+            <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
+                <option value="no">NO</option>
+                <option value="yes">YES</option>
+            </param>
+            <when value="yes" >
+                <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" />
+                <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" />
+            </when>
+            <when value="no" />
+        </conditional>
+        <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" >
+            <option value="small">Small</option>
+            <option value="medium">Medium</option>
+            <option value="large">Large</option>
+        </param>
+        <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
+        <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
+        <conditional name="range" >
+            <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
+                <option value="no">NO</option>
+                <option value="yes">YES</option>
+            </param>
+            <when value="yes" >
+                <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" />
+                <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" />
+                <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" />
+                <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" />
+            </when>
+            <when value="no" />
+        </conditional>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucmer.xml	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,235 @@
+<tool id="mummer_nucmer" name="Nucmer" version="@MUMMER_VERSION@">
+    <description>Align two or more sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="5.2.3">gnuplot</requirement>
+    </expand>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        ln -s $reference_sequence reference.fa &&
+        ln -s $query_sequence query.fa &&
+        nucmer
+            $anchoring
+            -b '$breaklen'
+            -c '$mincluster'
+            -D '$diagdiff'
+            -d '$diagfactor'
+            $noextend
+            $direction
+            -g '$maxgap'
+            -l '$minmatch'
+            -L '$minalign'
+            $nooptimize
+            $nosimplify
+            --threads "\${GALAXY_SLOTS:-1}"
+            #if $options.advanced == 'enable':
+                $options.banded
+                $options.large
+                $options.genome
+                -M '$options.max_chunk'
+            #end if
+            'reference.fa' 'query.fa'
+            #if $mumplot.plot == 'yes':
+                && mummerplot
+                    #if $mumplot.sequences.seq_input == 'yes':
+                        -R '$reference_sequence'
+                        -Q '$query_sequence'
+                        $mumplot.sequences.layout
+                    #end if
+                    -b '$mumplot.breaklen'
+                    $mumplot.color
+                    $mumplot.coverage
+                    $mumplot.filter
+                    $mumplot.fat
+                    #if $mumplot.labels.IDs == 'yes':
+                        -IdR '$mumplot.labels.ref_id'
+                        -IdQ '$mumplot.labels.query_id'
+                    #end if
+                    -s '$mumplot.size'
+                    -terminal png
+                    -title '$mumplot.title'
+                    $mumplot.snp
+                    #if $mumplot.range.custom == 'yes':
+                        -x [$mumplot.range.min_x:$mumplot.range.max_x]
+                        -y [$mumplot.range.min_y:$mumplot.range.max_y]
+                    #end if
+                    'out.delta'
+            #end if
+        ]]>
+    </command>
+    <inputs>
+        <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
+        <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
+        <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
+            <option value="">Use default</option>
+            <option value="--mum">Unique matches only (--mum)</option>
+            <option value="--maxmatch">All matches (--maxmatch)</option>
+        </param>
+        <param name="breaklen" type="integer" argument="-b" value="200" label="Break Length"
+            help="Set the distance an alignment extension will attempt to extend poor scoring regions before giving up. (-b)" />
+        <param name="mincluster" type="integer" argument="-c" value="65" label="Minumum Cluster Length" help="Sets the minimum length of a cluster of matches. (-c)" />
+        <param name="diagdiff" type="integer" argument="-D" value="5" label="Maximum Diagonal Difference"
+            help="Set the maximum diagonal difference between two adjacent anchors in a cluster. (-D)" />
+        <param name="diagfactor" type="float" argument="-d" value="0.12" label="Maximum Diagonal Difference"
+            help="Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length. (-d)" />
+        <param name="noextend" type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step. (--noextend)" />
+        <param name="direction" type="select" label="Direction" help="Choose a direction of Query Sequence to Use">
+            <option value="">Use foward and reverse sequences</option>
+            <option value="-f">Use only forward sequence of query (-f)</option>
+            <option value="-r">Use only reverese sequence of query (-r)</option>
+        </param>
+        <param name="maxgap" type="integer" argument="-g" value="90" label="Maximum Gap Distance" help="Set the maximum gap between two adjacent matches in a cluster. (-g)" />
+        <param name="minmatch" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Set the minimum length of a single exact match. (-l)" />
+        <param name="minalign" type="integer" argument="-L" value="0" label="Minumum Alignment Length" help="Minimum length of an alignment, after clustering and extension. (-L)" />
+        <param name="nooptimize" type="boolean" argument="--nooptimize" truevalue="--nooptimize" falsevalue="" label="No Alignment Score Optimization"
+            help="No alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will not backtrack to optimize the alignment score and instead terminate the alignment at the end of the sequence. (--nooptimize)" />
+        <param name="nosimplify" type="boolean" argument="--nosimplify" truevalue="--nosimplify" falsevalue="" label="Don't Simplify Alignments"
+            help="Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats. (--nosimplify)" />
+        <conditional name="options">
+            <param name="advanced" type="select" label="Additional options">
+                <option value="defaults">Use defaults</option>
+                <option value="enable">Select additional options</option>
+            </param>
+            <when value="enable">
+                <param name="banded" type="boolean" argument="--banded" truevalue="--banded" falsevalue="" label="Banding"
+                    help="Enforce absolute banding of dynamic programming matrix based on diagdiff parameter. (--banded)" />
+                <param name="large" type="boolean" argument="--large" truevalue="--large" falsevalue="" label="Offsets" help="Force the use of large offsets. (--large)" />
+                <param name="genome" type="boolean" argument="-G" truevalue="-G" falsevalue="" label="Map genome to genome" help="For long query sequences. (-G)" />
+                <param name="max_chunk" type="integer" argument="-M" value="50000" label="Max Chunk" help="Stop adding sequence for a thread if more than MAX already. (-M)" />
+            </when>
+            <when value="defaults" />
+        </conditional>
+        <conditional name="mumplot" >
+            <param name="plot" type="select" label="Do you want to output a 2-D dotplot of the input sequences? (mummerplot)" >
+                <option value="yes">YES</option>
+                <option value="no">NO</option>
+            </param>
+            <when value="yes" >
+                <expand macro="mumplot_input" >
+                    <conditional name="sequences" >
+                        <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
+                            <option value="no">NO</option>
+                            <option value="yes">YES</option>
+                        </param>
+                        <when value="yes">
+                            <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="(-R)" />
+                            <param name="query_sequence" type="data" format="fasta" multiple="True" label="Query Sequence(s)" help="(-Q)" />
+                            <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                        </when>
+                        <when value="no" />
+                    </conditional>
+                </expand>
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="delta_output" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: alignment" />
+        <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
+            <filter>mumplot['plot'] == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="advanced" value="defaults" />
+            <param name="plot" value="yes" />
+            <param name="seq_input" value="yes" />
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
+            <output name="delta_output" ftype="tabular" compare="diff" lines_diff="2" value="nucmer.txt"/>
+            <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may have large rearrangements. Common use cases are: comparing two unfinished shotgun sequencing assemblies, mapping an unfinished sequencing assembly to a finished genome, and comparing two fairly similar genomes that may have large rearrangements and duplications.
+
+        All output coordinates reference the forward strand of the involved sequence, regardless of the match direction. Also, nucmer now uses only matches that are unique in the reference sequence by default, use different Anchoring options to change this behavior.
+
+**Options:**::
+
+    Defaults in parentheses
+
+    nucmer
+
+    --mum             Use anchor matches that are unique in both the reference and query (false)
+
+    --maxmatch        Use all anchor matches regardless of their uniqueness (false)
+
+    -b                Set the distance an alignment extension will attempt to extend poor scoring regions
+                      before giving up (200)
+
+    -c                Sets the minimum length of a cluster of matches (65)
+
+    -D                Set the maximum diagonal difference between two adjacent anchors in a cluster (5)
+
+    -d                Set the maximum diagonal difference between two adjacent anchors in a cluster as a
+                      differential fraction of the gap length (0.12)
+
+    --noextend        Do not perform cluster extension step (false)
+
+    -f                Use only the forward strand of the Query sequences (false)
+
+    -r                Use only the reverse complement of the Query sequences (false)
+
+    -g                Set the maximum gap between two adjacent matches in a cluster (90)
+
+    -l                Set the minimum length of a single exact match (20)
+
+    -L                Minimum length of an alignment, after clustering and extension (0)
+
+    --nooptimize      No alignment score optimization, i.e. if an alignment extension reaches the end of a
+                      sequence, it will not backtrack to optimize the alignment score and instead terminate
+                      the alignment at the end of the sequence (false)
+
+    --nosimplify      Don't simplify alignments by removing shadowed clusters. Use this option when aligning
+                      a sequence to itself to look for repeats (false)
+
+    --banded          Enforce absolute banding of dynamic programming matrix based on diagdiff parameter (false)
+
+    --large           Force the use of large offsets (false)
+
+    -G                Map genome to genome (long query sequences) (false)
+
+    -M                Max chunk. Stop adding sequence for a thread if more than MAX already. (50000)
+
+    mummerplot
+
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
+                   sequence end
+
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
+                   'linespoints' instead of 'lines'
+
+    -c             Generate a reference coverage plot (default for .tiling)
+
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
+                   either sequence, i.e. a one-to-one mapping of reference and query subsequences
+
+    --fat          Layout sequences using fattest alignment only
+
+    -IdR           Plot a particular reference sequence ID on the X-axis
+
+    -IdQ           Plot a particular query sequence ID on the Y-axis
+
+    -s             Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')
+
+    --SNP          Highlight SNP locations in each alignment
+
+    -title         Specify the gnuplot plot title (default none)
+
+    -x             Set the xrange for the plot '[min:max]'
+
+    -y             Set the yrange for the plot '[min:max]'
+
+    -R             Plot an ordered set of reference sequences from Rfile
+
+    -Q             Plot an ordered set of query sequences from Qfile
+
+    --layout       Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options
+
+    ]]></help>
+        <expand macro="citation" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1coords.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,2 @@
+74	223	43	194	150	152	87.50	6480	5460	2.31	2.78	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5080	5599	4148	4658	520	511	86.18	6480	5460	8.02	9.36	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1delta.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,20 @@
+reference.fa query.fa
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta-filter.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,20 @@
+/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,20 @@
+reference.fa query.fa
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fplot.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,13 @@
+#-- forward hits sorted by %sim
+0 0 0
+0 0 0
+
+
+5080 4148 86.1804222648752
+5599 4658 86.1804222648752
+
+
+74 43 87.5
+223 194 87.5
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gnuplot.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,23 @@
+set terminal png tiny size 800,800
+set output "out.png"
+set title "Title"
+set size 1,1
+set grid
+unset key
+set border 15
+set tics scale 0
+set xlabel "NG_007476.1:4960-11439"
+set ylabel "NC_000070.6:c41098183-41092724"
+set format "%.0f"
+set mouse format "%.0f"
+set mouse mouseformat "[%.0f, %.0f]"
+if(GPVAL_VERSION < 5) { set mouse clipboardformat "[%.0f, %.0f]" }
+set xrange [1:6480]
+set yrange [1:5460]
+set style line 1  lt 2 lw 3 pt 6 ps 1
+set style line 2  lt 2 lw 3 pt 6 ps 1
+set style line 3  lt 1 lw 3 pt 6 ps 1
+plot \
+ "out.fplot" title "FWD" w lp ls 1, \
+ "out.rplot" title "REV" w lp ls 2, \
+ "out.hplot" title "HLT" w lp ls 3
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hplot.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,13 @@
+#-- highlighted hits sorted by %sim
+0 0 0
+0 0 0
+
+
+5080 4148 86.1804222648752
+5599 4658 86.1804222648752
+
+
+74 43 87.5
+223 194 87.5
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_aqp3.fasta	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,95 @@
+>NG_007476.1:4960-11439 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), RefSeqGene on chromosome 9
+AGCGCTCCTATAAAGGGAGCCACCAGCGCTGGAGGCCGCTGCTCGCTGCGCCACCGCCTCCCGCCACCCC
+TGCCCGCCCGACAGCGCCGCCGCCTGCCCCGCCATGGGTCGACAGAAGGAGCTGGTGTCCCGCTGCGGGG
+AGATGCTCCACATCCGCTACCGGCTGCTCCGACAGGCGCTGGCCGAGTGCCTGGGGACCCTCATCCTGGT
+GGTGAGTGGAGGGAGCCGGGGAAGCCCTTCTCTCTCCAGCCCTTGCACTCCCCAAACTCTCACTTCCCCG
+AAGGGGCTGTGTTTTCCAAGGTAGCCTGGACCCACCTCCCCAGCTGTGACCCCCACGCTTAACCGCGGAG
+GATCAAGCTGACTTCCAAAGTCCTCTTCCCCACGGTTCTAACCCCCTCTCTGACAGCTCCGACTCTTGCC
+AGAATGACAGCTGTTACTCCCCAGTGATAGTGCCGATCGTTTACCCTCCCACAAGTGACTCAGCCAACAG
+GCTGGGGGCAGCGGTCACGCTTGCAGTCTGGGACAGCCAGCCACTTCCCCTGCCTCCCACACCCCTCCAG
+ATTCCCAGAATCCCAGCCCCCAGATGTAGGGGAGGGGGCGGAGGCAAATGAGCCATTATTAGGTTATTTG
+GGTCCTGGGTGTCTGGCCTCTAATGAATAATTAAGCCTCAAAAAGTCCAAAGGTTGAAGTGAGTGAGGAC
+AGTTTGCACGAGTGGGGGCAGAGGGTGCAGGCCACATGGGCTGCGAACAGCGAAGTGGGAAGGGAGGCAG
+ATTCTGACGGTAGAAGGGTGGGAGGAAGCTAGGCCCAGGCACAGAGGACGCGTGTCTAAAGTTGCTCACC
+TGGTGCTCAGCGACTCCCAGGCCCTGTCTGTTATCCAGACAGATGCTGTCAGCGTCTGTGCAGAAGACGA
+CAAGCATTCTGGTTACTCCCTGGCCTCTTGGTTACTCTGTGGGTTCTCTGAGTGAGCATTTCCCTGCCTG
+AGTTACTCCTCAGTCCTAGTTACTCCTTGGTCACACCAGTTTCACCCTGGTTTTGTTCTGAGTGACTCTG
+TTTGCACTTCTTAGGTCTGGCAGACCCACCAGTTATGTTCTATTTCCTGTCCCAGTTACTCTGATTTTTC
+AGCCGCTCATGTGGTTACACCTGTTTTCCTCTGTGTTCAGTTGCTACATTGCAGTGAGTGGGTTACTCCG
+TTCCTGCCCCAGCCCTGGGTAGTACAGACCAGCTGGCCCACTGTGGACTAGGAAGCCTAACTAAGGGCAA
+GTAGGGATCCCCAAATGGTTGAGGATCAGGATCTATGGGCAGAGGAGGGCTGAAACCCACTTCTGGCTTC
+CAAGAATAGGAAGTGGGGAAGCCACAGGGGGCATTTTATCCACAGCCTCCCATAAGATTAGTCGTCCTAT
+CAGCCAGCCCTAGCCCCTCTCTCCTGTGCCAAGAAGGCAATAGGAGGTGGCCTTTATCACTCTCCTGCCT
+CGGAGCCCTCACTCCTATCGGAGTCCTGAGTCCAGCCACCTGTTTTAGAGCAGCCAGGCTAGGGGAGGAT
+GATGTCTTCTATTTTCCTAGAGGGGCCTCCTCATTCCCTCCCAAGTCTCAGTTCACTCTCTCACAAAGGA
+GCCGTTAGTCCTCCCACTGAGCCCCAGGATCATCAGGCTTATCCCAGACCACAAAAGAAGAGTGTTAAAT
+TTTAGGGGAAGGGTTGCAGACTCAGATGGATGTGAGGTATTGGATATCAGTGAGAAGCAGAACTTCAAGG
+ACTGCATGAACTGGAGGGGCAGGCCTGGGGATCCCTTTGTAGTGGGTGAGTGCCTGCCTGCCTACCTGCG
+TGTTGGGAGCCTAGGCCTGCAGTGGCAGAATCAGGGTTGGCTTTGGGGTGAGGAAAGCCCCTTTCTCTGA
+GATACCTGGTGTGAGGGCAGGGGGCGGTGCTGGCCGAGAACTCAGGGCAGGGGTTGGGGGAGGAAGAGGA
+AGATTAGCCCCAAGGTGGTGGAACTGGCTCTGACAGCTCCTCCCTCCAAGGCGTCCTGGGATGGAGCCAG
+GTCTGAGCCTTTGGCAGGCAAGGAGCTGCTGCCAGGGCCTCCCAAGCAGGGCAGGGCGCCTCAGACCCTC
+ACGTGCCTGTCTCCCACCACCCCTCCTCACACATACACCTGCAATCTCTGATCTTTGCTCTCACCTGCCT
+GCACACCTTTGCCCCATGTCATTGCCGCTGGCTTCTCCGTTATCTCTTGGTCTTTCTGGGATGATAATCA
+AAATGCTTAACTATCCAGTACAACAGGCACTGACCCGTCAGAATAAACAAGGTCTGTAGCACAGGTCCTG
+GAAACTGCCTGCTCTGTGGGCATAAAACCTTTAGTTATGGGCAGGTGGGAGAGGAGACCAGGGCAAGGCA
+TTGGAGCAGCTTTGAGGGACACTCAGGGGGCTCAGGGCAACAATGCTTTACAGCTGCTGCAGAAGTATTT
+TCAGGCTTGAACAAGGGGAACAGACATAGTACGTTCTTTTTCTTTTTTAAATAGAGACAAAGTCTCACTA
+TGTTGCCCAGGCTGTTCTCAAACTCCTGGGTTCAAGATCCTCCCATCTCAGCCTCCAAAGTGCTGGGATT
+ACAGGTGTGAGCCACCACAGCTGGCTCCAGTATGTTCTATATTTGTAGAACACCAGGGCTCTTAGTCTCT
+TTTAGTTCCCCCATTTTTGGCAGAAAGTTTAGAACCGATCTCCCCATTTCTACAGCCCTGGGTCCCGGGC
+TGGGGATAGTGAGAGGAGCCACACAGATCCCTGTCTGTAGGACCTCCAAATCTGAGTGGGGAATCTGGAC
+CCCTGAGAGCAGAGAGGTCATGGGTGGAGAGAGGAGACGCTGGGACAGGGACAGGTAAAGGAAGGGGAGG
+TTGTTGAGGGGGACATGGTGAAGGCTGGGGCTCTGGCATCCTGGACTCAGGAGAAGTGGATTCAACCTCA
+CTTCTGGTCTCCTCCCTATTTATTTATGCCGCCCATTGCCACCACTACCACCACCACATGAGCTTTTCTT
+TTCAACTCTTTTTTTTTTTTTTTTGAGATGGAGTCCCGCTCTGTCGCCCAGGCTGAAGTGCAGTGGCGCA
+ATCTTGGCTCACTGCAACATCTGCCTCCCATTTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG
+GGATTACAGGCACCTGCCACCACGCCTGGCTAATTTTTGTACTTTTAGTAGAGATGGGGTTTCACTATGT
+TGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTACCAAAGTGCTGGGATT
+ACAGTGTGAGCCACTGCACCGGGCCTACATGAGCTTTTCTTTGGGGCAGCTGGGGGATGAGTGAGAGGCT
+TCCCACCTTTATGGTCCAGGCCTGAAGGGCTGTGGAGAAACTTGTGCTAAGGTGAAAGCTGTTCCCCTAC
+ACCTACGCCTGCTGAAATTCAAGGAAAATCAGTGAAGATGGTTCAGTCATCTTCTAGGATCCCAGTCGCA
+GACCCTGCTTCCAGCCCTTTCCATAGGGCCCTCTCATATTAGAGTTGGGACAGTGGGGTGGGAAGGCATG
+TGTCCTTTTTCTGGAAAGTGCAATTACAGCAGAAGGGGTTTGGGCTGGGTTCCAGGAAGCGCCTCTAGTC
+CTCCCAGTGGTGGCGAGTGGGCATGTTGCTGGCTTCACCCCTTCCTTCTGGAGTGAGAGTTGCTGGTCCT
+CACCCTCCCTGCCTGTTCTTCTTCCTGACAGATGTTTGGCTGTGGCTCCGTGGCCCAGGTTGTGCTCAGC
+CGGGGCACCCACGGTGGTTTCCTCACCATCAACCTGGCCTTTGGCTTTGCTGTCACTCTGGGCATCCTCA
+TCGCTGGCCAGGTCTCTGGTAAGGCCTTAACCCTGCCCCCAGCCCTTGGCCCTCAATAGCATTCCCACTA
+GGTGTCCTGGCATTCCTAAGGGCAGGTCACAGCTGTGGCCTCTGCTTTGGCCCCTTGGGAAAGGAGGGTG
+GAGAAGAAACTTGACACTTAGAACTTTCGACTCTCACCTTGGAATCAGAGATTATCAGCTGACCTGTTAC
+ATAGACCAACCGCCATCCTGTGCAAGAAACCCCTCTCTGCACCCCTTCTCAGGGGACCCTAGCCTGCCGA
+CTGTGGCAGGCTGCAGCTAATAGGTCCCTTGTCCCCTCTGCCCAGGGGCCCACCTGAACCCTGCCGTGAC
+CTTTGCCATGTGCTTCCTGGCTCGTGAGCCCTGGATCAAGCTGCCCATCTACACCCTGGCACAGACGCTG
+GGAGCCTTCTTGGGTGCTGGAATAGTTTTTGGGCTGTATTATGGTAAGCATTCCCCACCCTGTCCTCCTC
+CACTACCCCCGTCCCTCTGTTCAGGACCTGCTGGCACCAGGCCTTTTGATGACAGACGGCTAGGACCTGC
+CCAGGCCCCGGGCTCATGACTCACTCATTCACGCACAGGGTCAAGGTAGGGGGCACGAAGGGAAAGAAAC
+AAGTTGGGCAATAACAGAGTCTCAGGCCCTCCACCCCACCCCACGCCACCCCCTCTGCCTGCTGCAATAC
+AGCAGTATTGCTACTTACCCATAACTCATGGGAGGGTGGGGAGGGCACACCTGAGAGGGAAGTCTGGGCT
+CAGGCCTCTCCCCCGACTCACTGTGTGTCTAATCTGTCACCAGATGCAATCTGGCACTTCGCCGACAACC
+AGCTTTTTGTTTCGGGCCCCAATGGCACAGCCGGCATCTTTGCTACCTACCCCTCTGGACACTTGGATAT
+GATCAATGGCTTCTTTGACCAGGTATGGGCTGGGGACGTGTGAGGGGAACGCAGGGAGGGGACCGAGTTG
+CCTTGGTAGCTCATGGGCTGGTTGGGGGACAGGACTCCTCGACTGTAGCAGGGTTTCTCCAATCTGTGGG
+GTAACCCGCATCAGAACATGGTGGCAAGTACTTACAAAACATGCGGCTCTCCAGCGGGTTCTTGTCACGC
+AGACATTCTAGCACCATTGCTTTCAGGAGAAGAGCATGGGCGGGCGCTGACAAGAGTTTAAGAGCTAGAG
+GGAAGACGGGGGATGGAAGGAGGGGTCAGAGAAAGGGAGGGAGCTGCAGCTCACCCTGTTCTCCCCACTC
+CCCAGTTCATAGGCACAGCCTCCCTTATCGTGTGTGTGCTGGCCATTGTTGACCCCTACAACAACCCCGT
+CCCCCGAGGCCTGGAGGCCTTCACCGTGGGCCTGGTGGTCCTGGTCATTGGCACCTCCATGGGCTTCAAC
+TCCGGCTATGCCGTCAACCCTGCCCGGGACTTTGGCCCCCGCCTTTTTACAGCCCTTGCGGGCTGGGGCT
+CTGCAGTCTTCACGTGAGTACAGCCCCCACCCAGCTCACCCCAGCCTGCCTCTCCTCTGCCCTGCCCCCC
+ATGTCCCTGACTATGAGTGTCTGTCCCCCCAGGACCGGCCAGCATTGGTGGTGGGTGCCCATCGTGTCCC
+CACTCCTGGGCTCCATTGCGGGTGTCTTCGTGTACCAGCTGATGATCGGCTGCCACCTGGAGCAGCCCCC
+ACCCTCCAACGAGGAAGAGAATGTGAAGCTGGCCCATGTGAAGCACAAGGAGCAGATCTGAGTGGGCAGG
+GGCCATCTCCCCACTCCGCTGCCCTGGCCTTGAGCATCCACTGACTGTCCAAGGGCCACTCCCAAGAAGC
+CCCCTTCACGATCCACCCTTTCAGGCTAAGGAGCTCCCTATCTACCCTCACCCCACGAGACAGCCCCTTC
+AGGATTTCCACTGGACCTTGCCCAAATAGCACCTTAGGCCACTGCCCCTAAGCTGGGGTGGAACCGGAAT
+TTGGGTCAATACATCCTTTTGTCTCCCAAGGGAAGAGAATGGGCAGCAGGTATGTGTGTGTGTGCATGTG
+TGTGCATGTGTGTGCATGTGTGTGCAGGGGTGTGTGTGTGTGGGGGGGGTTCCCAGATATTCAGGGCAAG
+GGACCAGTCGGAAGGGATTCTGGCTATTGGGGGAGCCCAGAGACAGGGGAAGGCAGCCTGTCCATCTGTG
+CATAAGGAGAGGAAAGTTCCAGGGTGTGTATGTTTCAGGGGCTTCACATGGAGGAGCTGCAGATAGATAT
+GTGTTTCTGTGTATGTGTATGTCTGCCTTTTTTTCTAAGTGGGGGCTTCTACAGGCTTTTGGGAAGTAGG
+GTGGATGTGGGTAGGGCTGGGAGGAGGGGGCCACAGCTTAGGTTTGGAGCTCTGGATGTACATACATAAG
+TAGGAGCAGTGGGACGTGTTTCTGTCATAATGCAGGCATGAAGGGTGGAGTGAAGTCAGGTCATAAGTTT
+CATGTTTGCTTTTGTTTTGTTTTGTTTTTAATGTATGTAGCAGATGTTACAGTCTTAGGGATCCGGGATG
+GGAGACCCCACTTTAGAAAGGGTCGTCACTCCTTTAATCCTCTACTCAACAATGTACTCTTTTACTTTTA
+TATTAAAAAAAATAAAATAAATATGTGCCTAAAACCTCCA
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mcoords.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,2 @@
+74	223	43	194	150	152	87.50	6480	5460	2.31	2.78	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5080	5599	4148	4658	520	511	86.18	6480	5460	8.02	9.36	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mdelta.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,20 @@
+reference.fa query.fa
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mouse_aqp3.fasta	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,80 @@
+>NC_000070.6:c41098183-41092724 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J
+ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCG
+CGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTT
+CGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTAT
+CTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAG
+TTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGA
+CAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGG
+AGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAA
+CTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGG
+TCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCG
+GATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGA
+TTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGT
+CCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCT
+CTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGG
+CGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTG
+ACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCA
+GCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACA
+TGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTC
+CTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAA
+GAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTA
+TTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAA
+AAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAA
+AGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGT
+TGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAG
+GTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATA
+AGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTG
+GCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGAC
+GGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGAC
+CTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGC
+ACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTT
+GTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTC
+TCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGA
+AAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAG
+TTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCC
+CTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGG
+ACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGA
+GGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACA
+TTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATG
+ACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGG
+CAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATT
+TAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGT
+CTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCAT
+GTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGG
+TGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCT
+TGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAG
+CATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACA
+GCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTG
+GAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAA
+AGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACC
+CCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGC
+ACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCC
+CGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGG
+CCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGA
+AACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATAT
+GCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAAT
+GGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACG
+GCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGT
+ATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTG
+TAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAA
+GCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGG
+ACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCG
+CCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTT
+CACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCT
+GCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTAC
+AGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCA
+GGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGT
+GTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTG
+GCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGA
+GTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTC
+CCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTC
+CCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
+GAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACC
+AAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAA
+TGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTAT
+GCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAG
+AAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGAT
+AGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATAC
+ATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTT
+AATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mummer.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,19 @@
+> NC_000070.6:c41098183-41092724
+     100        71        22
+     149       120        20
+     185       156        23
+     650       578        21
+    1092       945        27
+    1861      1578        21
+    1960      1691        30
+    3737      2908        28
+    4226      3396        26
+    4648      3784        27
+    5111      4180        20
+    5206      4275        26
+    5254      4323        23
+    5481      4540        20
+    5511      4570        28
+    5540      4599        27
+    5574      4633        26
+> NC_000070.6:c41098183-41092724 Reverse
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucmer.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,20 @@
+reference.fa query.fa
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
Binary file test-data/plot.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/qdiff.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,3 @@
+NC_000070.6:c41098183-41092724	BRK	1	42	42
+NC_000070.6:c41098183-41092724	GAP	195	4147	3953	4856	-903
+NC_000070.6:c41098183-41092724	BRK	4659	5460	802
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rdiff.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,3 @@
+NG_007476.1:4960-11439	BRK	1	73	73
+NG_007476.1:4960-11439	GAP	224	5079	4856	3953	903
+NG_007476.1:4960-11439	BRK	5600	6480	881
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,87 @@
+
+
+
+
+
+
+
+
+
+
+
+                               [REF]                [QRY]
+.A                          0(0.00%)             0(0.00%)
+.A                          0(0.00%)            3(23.08%)
+.C                          0(0.00%)             0(0.00%)
+.C                          0(0.00%)            5(38.46%)
+.G                          0(0.00%)             0(0.00%)
+.G                          1(7.69%)            2(15.38%)
+.T                          0(0.00%)             0(0.00%)
+.T                         2(15.38%)             0(0.00%)
+/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta
+1-to-1                             2                    2
+A.                          0(0.00%)             0(0.00%)
+A.                         3(23.08%)             0(0.00%)
+AC                          6(7.69%)             5(6.41%)
+AC                        1(100.00%)             0(0.00%)
+AG                          0(0.00%)             0(0.00%)
+AG                          2(2.56%)             5(6.41%)
+AT                          0(0.00%)             0(0.00%)
+AT                          2(2.56%)             2(2.56%)
+AlignedBases             670(10.34%)          663(12.14%)
+AlignedSeqs               1(100.00%)           1(100.00%)
+AvgIdentity                    86.48                86.48
+AvgIdentity                    86.48                86.48
+AvgLength                     335.00               331.50
+AvgLength                     335.00               331.50
+Breakpoints                        4                    4
+C.                          0(0.00%)             0(0.00%)
+C.                         5(38.46%)             0(0.00%)
+CA                          0(0.00%)           1(100.00%)
+CA                          5(6.41%)             6(7.69%)
+CG                          0(0.00%)             0(0.00%)
+CG                          6(7.69%)             6(7.69%)
+CT                          0(0.00%)             0(0.00%)
+CT                        28(35.90%)            9(11.54%)
+G.                          0(0.00%)             0(0.00%)
+G.                         2(15.38%)             1(7.69%)
+GA                          0(0.00%)             0(0.00%)
+GA                          5(6.41%)             2(2.56%)
+GC                          0(0.00%)             0(0.00%)
+GC                          6(7.69%)             6(7.69%)
+GT                          0(0.00%)             0(0.00%)
+GT                          5(6.41%)             2(2.56%)
+InsertionAvg                 1936.67              1599.00
+InsertionSum                    5810                 4797
+Insertions                         3                    3
+Inversions                         0                    0
+M-to-M                             2                    2
+NUCMER
+Relocations                        0                    0
+T.                          0(0.00%)             0(0.00%)
+T.                          0(0.00%)            2(15.38%)
+TA                          0(0.00%)             0(0.00%)
+TA                          2(2.56%)             2(2.56%)
+TC                          0(0.00%)             0(0.00%)
+TC                         9(11.54%)           28(35.90%)
+TG                          0(0.00%)             0(0.00%)
+TG                          2(2.56%)             5(6.41%)
+TandemIns                          0                    0
+TandemInsAvg                    0.00                 0.00
+TandemInsSum                       0                    0
+TotalBases                      6480                 5460
+TotalGIndels                       0                    0
+TotalGSNPs                         1                    1
+TotalIndels                       13                   13
+TotalLength                      670                  663
+TotalLength                      670                  663
+TotalSNPs                         78                   78
+TotalSeqs                          1                    1
+Translocations                     0                    0
+UnalignedBases          5810(89.66%)         4797(87.86%)
+UnalignedSeqs               0(0.00%)             0(0.00%)
+[Alignments]
+[Bases]
+[Feature Estimates]
+[SNPs]
+[Sequences]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rplot.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,5 @@
+#-- reverse hits sorted by %sim
+0 0 0
+0 0 0
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/show-coords.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,2 @@
+74	223	43	194	150	152	87.50	6480	5460	2.31	2.78	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5080	5599	4148	4658	520	511	86.18	6480	5460	8.02	9.36	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snps.txt	Wed Dec 05 02:37:36 2018 -0500
@@ -0,0 +1,91 @@
+79	C	G	48	4	48	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+83	A	C	52	1	52	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+84	G	T	53	1	53	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+91	C	T	60	7	60	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+98	.	T	68	1	68	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+99	.	G	70	1	70	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+122	C	T	93	3	93	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+125	G	A	96	3	96	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+128	T	A	99	1	99	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+129	C	A	100	1	100	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+130	C	T	101	1	101	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
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