Repository 'mummer_dnadiff'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff

Changeset 0:deacc6b40cc0 (2018-12-05)
Next changeset 1:315c678562d2 (2020-01-24)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
added:
dnadiff.xml
macros.xml
test-data/1coords.txt
test-data/1delta.txt
test-data/delta-filter.txt
test-data/delta.txt
test-data/fplot.txt
test-data/gnuplot.txt
test-data/hplot.txt
test-data/human_aqp3.fasta
test-data/mcoords.txt
test-data/mdelta.txt
test-data/mouse_aqp3.fasta
test-data/mummer.txt
test-data/nucmer.txt
test-data/plot.png
test-data/qdiff.txt
test-data/rdiff.txt
test-data/report.txt
test-data/rplot.txt
test-data/show-coords.txt
test-data/snps.txt
b
diff -r 000000000000 -r deacc6b40cc0 dnadiff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dnadiff.xml Wed Dec 05 02:38:01 2018 -0500
[
@@ -0,0 +1,98 @@
+<tool id="mummer_dnadiff" name="DNAdiff" version="@MUMMER_VERSION@">
+    <description>Evaluate similarities/differences between two sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+        ln -s $reference_sequence reference.fa &&
+        ln -s $query_sequence query.fa &&
+        dnadiff
+            'reference.fa' 'query.fa'
+
+        ]]>  
+    </command>
+    <inputs>
+        <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
+        <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA" />
+        <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files">
+            <option value="yes">YES</option>
+            <option value="no">NO</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report" />
+        <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta">
+            <filter> report_only == 'no'</filter>
+        </data>
+        <data name="1delta" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" >
+            <filter> report_only == 'no' </filter>
+        </data>
+        <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" >
+            <filter> report_only == 'no' </filter>
+        </data>
+        <data name="1coords" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                    <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
+            </actions>
+        </data>
+        <data name="mcoords" format="tabular" from_work_dir="out.mcoords" label="${tool.name} on ${on_string}: mcoords" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                    <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
+            </actions>
+        </data>
+        <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+             <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
+            </actions>
+        </data>
+        <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
+            </actions>
+        </data>
+        <data name="qdiff" format="tabular" from_work_dir="out.qdiff" label="${tool.name} on ${on_string}: qdiff" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
+            </actions>
+        </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="input_type" value="sequence" />
+            <param name="report_only" value="no" />
+            <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
+            <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>
+            <output name="1delta" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
+            <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
+            <output name="1coords" ftype="tabular" compare="diff" value="1coords.txt"/>
+            <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
+            <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
+            <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
+            <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
+        </test>
+    </tests>
+     <help><![CDATA[
+This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species.
+
+**Output files:**
+    * report: Summary of alignments, differences and SNPs
+    * delta: Standard nucmer alignment output
+    * 1delta: 1-to-1 alignment from delta-filter -1
+    * mdelta: M-to-M alignment from delta-filter -m
+    * 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
+    * mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
+    * snps: SNPs from show-snps -rlTHC .1delta
+    * rdiff: Classified ref breakpoints from show-diff -rH .mdelta
+    * qdiff: Classified qry breakpoints from show-diff -qH .mdelta
+    ]]></help>
+    <expand macro="citation" />
+</tool>
b
diff -r 000000000000 -r deacc6b40cc0 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Dec 05 02:38:01 2018 -0500
b
@@ -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>
b
diff -r 000000000000 -r deacc6b40cc0 test-data/1coords.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1coords.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/1delta.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1delta.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/delta-filter.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta-filter.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/delta.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/fplot.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fplot.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
+
+
b
diff -r 000000000000 -r deacc6b40cc0 test-data/gnuplot.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gnuplot.txt Wed Dec 05 02:38:01 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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/hplot.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hplot.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
+
+
b
diff -r 000000000000 -r deacc6b40cc0 test-data/human_aqp3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_aqp3.fasta Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
+
b
diff -r 000000000000 -r deacc6b40cc0 test-data/mcoords.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mcoords.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/mdelta.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mdelta.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/mouse_aqp3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mouse_aqp3.fasta Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
+
b
diff -r 000000000000 -r deacc6b40cc0 test-data/mummer.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mummer.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/nucmer.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucmer.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/plot.png
b
Binary file test-data/plot.png has changed
b
diff -r 000000000000 -r deacc6b40cc0 test-data/qdiff.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/qdiff.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/rdiff.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rdiff.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -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
b
diff -r 000000000000 -r deacc6b40cc0 test-data/report.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.txt Wed Dec 05 02:38:01 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]
b
diff -r 000000000000 -r deacc6b40cc0 test-data/rplot.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rplot.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -0,0 +1,5 @@
+#-- reverse hits sorted by %sim
+0 0 0
+0 0 0
+
+
b
diff -r 000000000000 -r deacc6b40cc0 test-data/show-coords.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/show-coords.txt Wed Dec 05 02:38:01 2018 -0500
b
@@ -0,0 +1,2 @@
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b
diff -r 000000000000 -r deacc6b40cc0 test-data/snps.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snps.txt Wed Dec 05 02:38:01 2018 -0500
b
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