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changeset 0:502018997bae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
author iuc
date Wed, 05 Dec 2018 02:37:10 -0500
parents
children abe34706eddf
files delta-filter.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
diffstat 22 files changed, 688 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/delta-filter.xml	Wed Dec 05 02:37:10 2018 -0500
@@ -0,0 +1,81 @@
+<tool id="mummer_delta_filter" name="Delta-Filter" version="@MUMMER_VERSION@">
+    <description>Filters alignment (delta) file from nucmer</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+        delta-filter
+            $alignment
+            -i '$min_identity'
+            -l '$min_length'
+            $overlap
+            -u '$min_uniqueness'
+            -o '$max_overlap'
+            '$delta' > '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="delta" type="data" format="tabular" label="Match file from nucmer" />
+        <param name="alignment" type="select" label="Alignment Strategy" >
+            <option value="-m">Use default [Many-to-many alignment allowing for rearrangements] (-m)</option>
+            <option value="-1">1-to-1 alignment allowing for rearrangements (-1)</option>
+            <option value="-g">1-to-1 global alignment not allowing rearrangements (-g)</option>
+        </param>
+        <param name="min_identity" type="float" argument="-i" value="0" min="0" max="100" label="Minimum Identity" help="Set the minimum alignment identity. (-i)" />
+        <param name="min_length" type="integer" argument="-l" value="0" label="Minumum Legnth" help="Set the minimum alignment length. (-l)" />
+        <param name="overlap" type="select" label="Overlaps"
+            help=" Maps each position of each query/reference to its best hit in the reference/query, allowing for reference/query overlaps." >
+            <option value="-q">Reference overlaps (-q)</option>
+            <option value="-r">Query overlaps (-r)</option>
+        </param>
+        <param name="min_uniqueness" type="float" argument="-u" value="0" min="0" max="100" label="Minimum Alignment Uniqueness"
+            help="Set the minimum alignment uniqueness, i.e. percent of the alignment matching to unique reference AND query sequence. (-u)" />
+        <param name="max_overlap" type="float" argument="-o" value="100" min="0" max="100" label="Maximum Alignment Overlap"
+            help="Set the maximum alignment overlap for overlap options as a percent of the alignment length. (-o)" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="delta-filter.txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="delta" ftype="tabular" value="nucmer.txt" />
+            <output name="output" ftype="tabular" compare="diff" lines_diff="2" value="delta-filter.txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        This program filters the alignment file produced by nucmer, leaving only the desired alignments. Its primary function is the LIS algorithm which calculates the longest increasing subset of alignments. This allows for the calculation of a global set of alignments (i.e. 1-to-1 and mutually consistent order) with the 1-1 global option or locally consistent with 1-1 with rearrangements or many-to-many alignment. Reference sequences can be mapped to query sequences with the reference option of the Overlaps parameter, or queries to references with the Query option. This allows the user to exclude chance and repeat induced alignments, leaving only the "best" alignments between the two data sets. Filtering can also be performed on length, identity, and uniqueness.
+
+        An important distinction between the alignment options is that 1-1 global requires the alignments to be mutually consistent in their order, while the other options are not required to be mutually consistent and therefore tolerate translocations, inversions, etc.
+
+        In general cases, the many-to-many option is the best choice, however 1-1 alignment allowing for rearrangements can be handy for applications such as SNP finding which require a 1-to-1 mapping. 
+
+        Finally, for mapping query contigs, or sequencing reads, to a reference genome, use the query option for the Overlaps parameter.
+
+**Options**::
+
+    -m      Many-to-many alignment allowing for rearrangements
+
+    -1      1-to-1 alignment allowing for rearrangements
+
+    -g      1-to-1 global alignment not allowing rearrangements
+
+    -i      Set the minimum alignment identity [0, 100], default 0
+
+    -l      Set the minimum alignment length, default 0
+
+    -q      Maps each position of each query to its best hit in the reference, allowing for reference 
+            overlaps
+
+    -r      Maps each position of each reference to its best hit in the query, allowing for query overlaps
+
+    -u      Set the minimum alignment uniqueness, i.e. percent of the alignment matching to unique reference 
+            AND query sequence [0,100], default 0
+
+    -o      Set the maximum alignment overlap for -r and -q options as a percent of the alignment length 
+            [0, 100], default 100
+
+    ]]></help>
+    <expand macro="citation" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 05 02:37:10 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/test-data/1coords.txt	Wed Dec 05 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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 02:37:10 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
+169	C	T	140	3	140	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+172	A	C	143	3	143	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+184	C	G	155	12	155	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+208	G	T	179	11	179	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+219	G	C	190	5	190	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5087	C	G	4155	1	1306	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5088	A	C	4156	1	1305	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5089	G	C	4157	1	1304	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5096	C	G	4164	3	1297	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5099	T	C	4167	3	1294	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5104	C	T	4172	3	1289	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5107	A	C	4175	3	1286	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5110	.	T	4179	3	1282	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5131	T	G	4200	8	1261	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5139	C	T	4208	8	1253	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5148	G	A	4217	9	1244	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5157	T	C	4226	9	1235	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5166	C	T	4235	3	1226	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5169	C	T	4238	3	1223	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5178	C	T	4247	3	1214	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5181	C	G	4250	3	1211	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5187	A	T	4256	6	1205	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5199	C	T	4268	6	1193	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5205	C	T	4274	6	1187	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5232	C	A	4301	18	1160	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5250	C	T	4319	3	1142	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5253	C	T	4322	3	1139	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5277	G	T	4346	9	1115	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5286	C	A	4355	3	1106	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5289	C	T	4358	3	1103	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5295	T	C	4364	3	1097	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5298	T	C	4367	3	1094	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5301	A	C	4370	3	1091	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
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