Mercurial > repos > iuc > mummer_mummer
changeset 0:26f2cc1cc1e9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
| author | iuc |
|---|---|
| date | Wed, 05 Dec 2018 02:38:48 -0500 |
| parents | |
| children | 48badcd29c5d |
| files | macros.xml mummer.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, 801 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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>
--- /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
--- /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
--- /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
--- /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
--- /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 + +
--- /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
--- /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 + +
--- /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 +
--- /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
--- /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
--- /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 +
--- /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
--- /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
--- /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
--- /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
--- /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]
--- /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 + +
--- /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
--- /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 +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 +5307 T G 4376 3 1085 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5310 G T 4379 3 1082 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5322 T A 4391 2 1070 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5324 C A 4393 2 1068 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5344 C T 4413 6 1048 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5350 C . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5351 C . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5352 C . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5353 A . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5354 G . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5357 C . 4420 1 1041 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5358 A . 4420 1 1041 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5366 C T 4428 7 1033 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5373 T C 4435 6 1026 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5379 G . 4440 1 1021 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5380 C T 4441 1 1020 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5387 C G 4448 1 1013 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5388 C A 4449 1 1012 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5391 A . 4451 3 1010 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5396 C T 4456 5 1005 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5401 C T 4461 2 1000 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5403 A T 4463 1 998 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5404 T C 4464 1 997 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5405 G C 4465 1 996 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5406 A G 4466 1 995 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5411 C . 4470 2 991 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5413 G C 4472 2 989 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5418 C T 4477 5 984 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5426 C T 4485 5 976 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5431 A G 4490 4 971 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5435 T C 4494 4 967 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5447 G A 4506 6 955 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5453 C T 4512 3 949 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5456 G C 4515 3 946 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5471 C T 4530 6 931 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5477 T C 4536 3 925 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5480 G T 4539 3 922 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5501 G C 4560 6 901 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5507 C T 4566 3 895 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5510 C T 4569 3 892 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5539 A C 4598 28 863 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5567 T C 4626 1 835 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5568 G A 4627 1 834 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5573 G A 4632 5 829 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724