| Next changeset 1:5b0b49b5421c (2020-01-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107 |
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added:
macros.xml nucmer.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 |
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| diff -r 000000000000 -r a18fb4f826fc macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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> |
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| diff -r 000000000000 -r a18fb4f826fc nucmer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucmer.xml Wed Dec 05 02:37:36 2018 -0500 |
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| b'@@ -0,0 +1,235 @@\n+<tool id="mummer_nucmer" name="Nucmer" version="@MUMMER_VERSION@">\n+ <description>Align two or more sequences</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="5.2.3">gnuplot</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ ln -s $reference_sequence reference.fa &&\n+ ln -s $query_sequence query.fa &&\n+ nucmer \n+ $anchoring\n+ -b \'$breaklen\'\n+ -c \'$mincluster\'\n+ -D \'$diagdiff\'\n+ -d \'$diagfactor\'\n+ $noextend\n+ $direction\n+ -g \'$maxgap\'\n+ -l \'$minmatch\'\n+ -L \'$minalign\'\n+ $nooptimize\n+ $nosimplify\n+ --threads "\\${GALAXY_SLOTS:-1}"\n+ #if $options.advanced == \'enable\':\n+ $options.banded\n+ $options.large\n+ $options.genome\n+ -M \'$options.max_chunk\'\n+ #end if\n+ \'reference.fa\' \'query.fa\' \n+ #if $mumplot.plot == \'yes\':\n+ && mummerplot\n+ #if $mumplot.sequences.seq_input == \'yes\':\n+ -R \'$reference_sequence\'\n+ -Q \'$query_sequence\'\n+ $mumplot.sequences.layout\n+ #end if\n+ -b \'$mumplot.breaklen\'\n+ $mumplot.color\n+ $mumplot.coverage\n+ $mumplot.filter\n+ $mumplot.fat\n+ #if $mumplot.labels.IDs == \'yes\':\n+ -IdR \'$mumplot.labels.ref_id\'\n+ -IdQ \'$mumplot.labels.query_id\'\n+ #end if\n+ -s \'$mumplot.size\'\n+ -terminal png\n+ -title \'$mumplot.title\'\n+ $mumplot.snp\n+ #if $mumplot.range.custom == \'yes\':\n+ -x [$mumplot.range.min_x:$mumplot.range.max_x]\n+ -y [$mumplot.range.min_y:$mumplot.range.max_y]\n+ #end if\n+ \'out.delta\'\n+ #end if\n+ ]]> \t\n+ </command> \n+ <inputs>\n+ <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />\n+ <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />\n+ <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">\n+ <option value="">Use default</option>\n+ <option value="--mum">Unique matches only (--mum)</option>\n+ <option value="--maxmatch">All matches (--maxmatch)</option>\n+ </param>\n+ <param name="breaklen" type="integer" argument="-b" value="200" label="Break Length"\n+ help="Set the distance an alignment extension will attempt to extend poor scoring regions before giving up. (-b)" />\n+ <param name="mincluster" type="integer" argument="-c" value="65" label="Minumum Cluster Length" help="Sets the minimum length of a cluster of matches. (-c)" />\n+ <param name="diagdiff" type="integer" argument="-D" value="5" label="Maximum Diagonal Difference"\n+ help="Set the maximum diagonal difference between two adjacent anchors in a cluster. (-D)" />\n+ <param name="diagfactor" type="float" argument="-d" value="0.12" label="Maximum Diagonal Difference"\n+ help="Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length. (-d)" />\n+ <param name="noextend" type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step. (--noextend)" />\n+ <param name="direction" type="select" label="Direction" help="C'..b'utput coordinates reference the forward strand of the involved sequence, regardless of the match direction. Also, nucmer now uses only matches that are unique in the reference sequence by default, use different Anchoring options to change this behavior.\n+\n+**Options:**::\n+\n+ Defaults in parentheses\n+\n+ nucmer\n+\n+ --mum Use anchor matches that are unique in both the reference and query (false)\n+\n+ --maxmatch Use all anchor matches regardless of their uniqueness (false)\n+\n+ -b Set the distance an alignment extension will attempt to extend poor scoring regions \n+ before giving up (200)\n+\n+ -c Sets the minimum length of a cluster of matches (65)\n+\n+ -D Set the maximum diagonal difference between two adjacent anchors in a cluster (5)\n+\n+ -d Set the maximum diagonal difference between two adjacent anchors in a cluster as a \n+ differential fraction of the gap length (0.12)\n+\n+ --noextend Do not perform cluster extension step (false)\n+\n+ -f Use only the forward strand of the Query sequences (false)\n+\n+ -r Use only the reverse complement of the Query sequences (false)\n+\n+ -g Set the maximum gap between two adjacent matches in a cluster (90)\n+\n+ -l Set the minimum length of a single exact match (20)\n+\n+ -L Minimum length of an alignment, after clustering and extension (0)\n+\n+ --nooptimize No alignment score optimization, i.e. if an alignment extension reaches the end of a \n+ sequence, it will not backtrack to optimize the alignment score and instead terminate\n+ the alignment at the end of the sequence (false)\n+\n+ --nosimplify Don\'t simplify alignments by removing shadowed clusters. Use this option when aligning\n+ a sequence to itself to look for repeats (false)\n+\n+ --banded Enforce absolute banding of dynamic programming matrix based on diagdiff parameter (false)\n+\n+ --large Force the use of large offsets (false)\n+\n+ -G Map genome to genome (long query sequences) (false)\n+\n+ -M Max chunk. Stop adding sequence for a thread if more than MAX already. (50000)\n+\n+ mummerplot\n+\n+ -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest \n+ sequence end\n+\n+ -color Color plot lines with a percent similarity gradient or turn off all plot color (default \n+ color by match dir) If the plot is very sparse, edit the .gp script to plot with \n+ \'linespoints\' instead of \'lines\'\n+\n+ -c Generate a reference coverage plot (default for .tiling)\n+\n+ --filter Only display .delta alignments which represent the "best" hit to any particular spot on \n+ either sequence, i.e. a one-to-one mapping of reference and query subsequences\n+\n+ --fat Layout sequences using fattest alignment only\n+\n+ -IdR Plot a particular reference sequence ID on the X-axis\n+\n+ -IdQ Plot a particular query sequence ID on the Y-axis\n+\n+ -s Set the output size to small, medium or large (--small) (--medium) (--large) (default \'small\')\n+\n+ --SNP Highlight SNP locations in each alignment\n+\n+ -title Specify the gnuplot plot title (default none)\n+\n+ -x Set the xrange for the plot \'[min:max]\'\n+\n+ -y Set the yrange for the plot \'[min:max]\'\n+\n+ -R Plot an ordered set of reference sequences from Rfile\n+\n+ -Q Plot an ordered set of query sequences from Qfile\n+\n+ --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options\n+\n+ ]]></help>\n+ <expand macro="citation" />\n+</tool>\n' |
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| diff -r 000000000000 -r a18fb4f826fc test-data/1coords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1coords.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r a18fb4f826fc test-data/1delta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1delta.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r a18fb4f826fc test-data/delta-filter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta-filter.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r a18fb4f826fc test-data/delta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r a18fb4f826fc test-data/fplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fplot.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 + + |
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| diff -r 000000000000 -r a18fb4f826fc test-data/gnuplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gnuplot.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r a18fb4f826fc test-data/hplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hplot.txt Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 + + |
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| diff -r 000000000000 -r a18fb4f826fc test-data/human_aqp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_aqp3.fasta Wed Dec 05 02:37:36 2018 -0500 |
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| @@ -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 a18fb4f826fc test-data/mcoords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcoords.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/mdelta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mdelta.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/mouse_aqp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_aqp3.fasta Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/mummer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mummer.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/nucmer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nucmer.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/plot.png |
| b |
| Binary file test-data/plot.png has changed |
| b |
| diff -r 000000000000 -r a18fb4f826fc test-data/qdiff.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qdiff.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/rdiff.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdiff.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.txt Wed Dec 05 02:37:36 2018 -0500 |
| [ |
| @@ -0,0 +1,87 @@ + + + + + + + + + + + + [REF] [QRY] +.A 0(0.00%) 0(0.00%) +.A 0(0.00%) 3(23.08%) +.C 0(0.00%) 0(0.00%) +.C 0(0.00%) 5(38.46%) +.G 0(0.00%) 0(0.00%) +.G 1(7.69%) 2(15.38%) +.T 0(0.00%) 0(0.00%) +.T 2(15.38%) 0(0.00%) +/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta +1-to-1 2 2 +A. 0(0.00%) 0(0.00%) +A. 3(23.08%) 0(0.00%) +AC 6(7.69%) 5(6.41%) +AC 1(100.00%) 0(0.00%) +AG 0(0.00%) 0(0.00%) +AG 2(2.56%) 5(6.41%) +AT 0(0.00%) 0(0.00%) +AT 2(2.56%) 2(2.56%) +AlignedBases 670(10.34%) 663(12.14%) +AlignedSeqs 1(100.00%) 1(100.00%) +AvgIdentity 86.48 86.48 +AvgIdentity 86.48 86.48 +AvgLength 335.00 331.50 +AvgLength 335.00 331.50 +Breakpoints 4 4 +C. 0(0.00%) 0(0.00%) +C. 5(38.46%) 0(0.00%) +CA 0(0.00%) 1(100.00%) +CA 5(6.41%) 6(7.69%) +CG 0(0.00%) 0(0.00%) +CG 6(7.69%) 6(7.69%) +CT 0(0.00%) 0(0.00%) +CT 28(35.90%) 9(11.54%) +G. 0(0.00%) 0(0.00%) +G. 2(15.38%) 1(7.69%) +GA 0(0.00%) 0(0.00%) +GA 5(6.41%) 2(2.56%) +GC 0(0.00%) 0(0.00%) +GC 6(7.69%) 6(7.69%) +GT 0(0.00%) 0(0.00%) +GT 5(6.41%) 2(2.56%) +InsertionAvg 1936.67 1599.00 +InsertionSum 5810 4797 +Insertions 3 3 +Inversions 0 0 +M-to-M 2 2 +NUCMER +Relocations 0 0 +T. 0(0.00%) 0(0.00%) +T. 0(0.00%) 2(15.38%) +TA 0(0.00%) 0(0.00%) +TA 2(2.56%) 2(2.56%) +TC 0(0.00%) 0(0.00%) +TC 9(11.54%) 28(35.90%) +TG 0(0.00%) 0(0.00%) +TG 2(2.56%) 5(6.41%) +TandemIns 0 0 +TandemInsAvg 0.00 0.00 +TandemInsSum 0 0 +TotalBases 6480 5460 +TotalGIndels 0 0 +TotalGSNPs 1 1 +TotalIndels 13 13 +TotalLength 670 663 +TotalLength 670 663 +TotalSNPs 78 78 +TotalSeqs 1 1 +Translocations 0 0 +UnalignedBases 5810(89.66%) 4797(87.86%) +UnalignedSeqs 0(0.00%) 0(0.00%) +[Alignments] +[Bases] +[Feature Estimates] +[SNPs] +[Sequences] |
| b |
| diff -r 000000000000 -r a18fb4f826fc test-data/rplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rplot.txt Wed Dec 05 02:37:36 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +#-- reverse hits sorted by %sim +0 0 0 +0 0 0 + + |
| b |
| diff -r 000000000000 -r a18fb4f826fc test-data/show-coords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/show-coords.txt Wed Dec 05 02:37:36 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 a18fb4f826fc test-data/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snps.txt Wed Dec 05 02:37:36 2018 -0500 |
| b |
| b'@@ -0,0 +1,91 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