# HG changeset patch
# User iuc
# Date 1543995528 18000
# Node ID 26f2cc1cc1e913827c957f66ac131af69e0cce51

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107

diff -r 000000000000 -r 26f2cc1cc1e9 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 05 02:38:48 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>
diff -r 000000000000 -r 26f2cc1cc1e9 mummer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mummer.xml	Wed Dec 05 02:38:48 2018 -0500
@@ -0,0 +1,194 @@
+<tool id="mummer_mummer" name="Mummer" 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[
+        mummer 
+            $anchoring
+            -l '$min'
+            $direction
+            $force
+            $chars
+            $print_length
+            $substring
+            $position
+            #if $options.advanced == 'enable'
+                -k '$options.suffix'
+                -threads '$options.threads'
+                -qthreads '$options.qthreads'
+                -suflink '$'options.suflink'
+                -child '$options.child'
+                -skip '$options.skip'
+                -kmer '$options.kmer'
+            #end if
+            '$reference_sequence' '$query_sequence' > '$output'
+            #if $mumplot.plot == 'yes':
+                && mummerplot
+                    -b '$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:$mumplot.range.max_y]
+                    #end if
+                    '$output'
+            #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="">Maximal matches unique in only reference sequence (-mumreference) (Default)</option>
+            <option value="-mum">Maximal matches unique in both sequences (-mum)</option>
+            <option value="-maxmatch">All matches reguardless of uniqueness (-maxmatch)</option>
+        </param>
+        <param name="min" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Minimum length of a match. (-l)" />
+        <param name="direction" type="select" label="Direction" help="Direction of complement sequence to use">
+            <option value="-b">Compute forward and reverse complement matches (-b)</option>
+            <option value="-r">Compute only reverse complement matches (-r)</option>
+        </param>
+        <param name="force" type="boolean" argument="-F" truevalue="-F" falsevalue="" label="Force 4 column output"
+            help="force 4 column output format regardless of the number of reference sequence inputs. (-F)" />
+        <param name="chars" type="boolean" argument="-n" truevalue="-n" falsevalue="" label="Match only the characters a, c, g, or t" help="(-n)" />
+        <param name="print_length" type="boolean" argument="-L" truevalue="-L" falsevalue="" label="Print length of query sequence in header of matches" help="(-L)" />
+        <param name="substring" type="boolean" argument="-s" truevalue="-s" falsevalue="" label= "Print first 53 characters of the matching substring" help="(-s)" />
+        <param name="position" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Position"
+            help="Report the query position of a reverse complement match relative to the forward strand of the query sequence. (-c)" />
+        <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="suffix" type="integer" argument="-k" value="1" label="Suffix" help="Sampled suffix positions. (-k)" />
+                <param name="threads" type="integer" argument="-threads" value="3" label="Threads"
+                    help="Number of threads to use for -maxmatch; only valid if above parameter is greater than one. (-threads)" />
+                <param name="qthreads" type="integer" argument="-qthreads" value="3" label="Qthreads" help="Number of threads to use for queries. (-qthreads)" />
+                <param name="suflink" type="select" label="Suflink" help="Use suffix links in the index and during search? (-suflink)" >
+                    <option value="0">No</option>
+                    <option value="1">Yes</option>
+                </param>
+                <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" >
+                    <option value="0">No</option>
+                    <option value="1">Yes</option>
+                </param>
+                <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
+                    help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
+                <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
+                    help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
+            </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?" >
+                <option value="yes">YES</option>
+                <option value="no">NO</option>
+            </param>
+            <when value="yes" >
+                <expand macro="mumplot_input" />
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="mummer.txt" 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="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
+            <param name="options" value="defaults" />
+            <param name="plot" value="yes" />
+            <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />
+            <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
+        </test>
+    </tests>
+   <help><![CDATA[
+        This is the core program of the MUMmer package. It is the suffix-tree based match finding routine, and the main part of every MUMmer script. By default, mummer now finds maximal matches regardless of their uniqueness. Limiting the output to only unique matches can be specified by choosing alternative Anchoring strategies.
+
+**Options:**::
+
+    mummer
+
+    -mumreference    Compute maximal matches that are unique in the reference- sequence but not 
+                     necessarily in the query-sequence (default)
+
+    -maxmatch        Compute all maximal matches regardless of their uniqueness
+
+    -l               Set the minimum length of a match
+
+    -b               Compute forward and reverse complement matches
+
+    -r               Compute only reverse complement matches
+
+    -mum             Compute maximal matches that are unique in both sequences
+
+    -F               Force 4 column output format regardless of the number of reference sequence inputs
+
+    -n               Match only the characters a, c, g, or t
+
+    -L               Print length of query sequence in header of matches
+
+    -s               Print first 53 characters of the matching substring
+
+    -c               Report the query position of a reverse complement match
+                     relative to the forward strand of the query sequence
+
+    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>
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/1coords.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1coords.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/1delta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1delta.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/delta-filter.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta-filter.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/delta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/fplot.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fplot.txt	Wed Dec 05 02:38:48 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
+
+
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/gnuplot.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gnuplot.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/hplot.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hplot.txt	Wed Dec 05 02:38:48 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
+
+
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/human_aqp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_aqp3.fasta	Wed Dec 05 02:38:48 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
+
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/mcoords.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mcoords.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/mdelta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mdelta.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/mouse_aqp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mouse_aqp3.fasta	Wed Dec 05 02:38:48 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
+
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/mummer.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mummer.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/nucmer.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucmer.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/plot.png
Binary file test-data/plot.png has changed
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/qdiff.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/qdiff.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/rdiff.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rdiff.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.txt	Wed Dec 05 02:38:48 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]
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/rplot.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rplot.txt	Wed Dec 05 02:38:48 2018 -0500
@@ -0,0 +1,5 @@
+#-- reverse hits sorted by %sim
+0 0 0
+0 0 0
+
+
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/show-coords.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/show-coords.txt	Wed Dec 05 02:38:48 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
diff -r 000000000000 -r 26f2cc1cc1e9 test-data/snps.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snps.txt	Wed Dec 05 02:38:48 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
+133	C	T	104	3	104	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+136	C	T	107	3	107	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+148	C	T	119	12	119	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
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