| Next changeset 1:abe34706eddf (2020-01-24) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107 |
|
added:
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 |
| b |
| diff -r 000000000000 -r 502018997bae delta-filter.xml --- /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> |
| b |
| diff -r 000000000000 -r 502018997bae macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 05 02:37:10 2018 -0500 |
| b |
| @@ -0,0 +1,69 @@ +<macros> + <xml name="citation"> + <citations> + <citation type="bibtex"> + @misc{githubmummer, + author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg}, + year = {2012}, + title = {mummer4}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/mummer4/mummer}, + }</citation> + </citations> + </xml> + <token name="@MUMMER_VERSION@">4.0.0beta2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement> + <yield /> + </requirements> + </xml> + <xml name="mumplot_input" > + <yield /> + <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length" + help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" /> + <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." > + <option value="">Color</option> + <option value="-color">No color (-color)</option> + </param> + <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." > + <option value="">Dotplot</option> + <option value="-c">Coverage Plot (-c)</option> + </param> + <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter" + help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" /> + <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" /> + <conditional name="labels" > + <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." > + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + <when value="yes" > + <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" /> + <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" /> + </when> + <when value="no" /> + </conditional> + <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" > + <option value="small">Small</option> + <option value="medium">Medium</option> + <option value="large">Large</option> + </param> + <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" /> + <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" /> + <conditional name="range" > + <param name="custom" type="select" label="Choose custom X and Y axis ranges?" > + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + <when value="yes" > + <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" /> + <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" /> + <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" /> + <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" /> + </when> + <when value="no" /> + </conditional> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 502018997bae test-data/1coords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1coords.txt Wed Dec 05 02:37:10 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 502018997bae test-data/1delta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1delta.txt Wed Dec 05 02:37:10 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 502018997bae test-data/delta-filter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta-filter.txt Wed Dec 05 02:37:10 2018 -0500 |
| b |
| @@ -0,0 +1,20 @@ +/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0 |
| b |
| diff -r 000000000000 -r 502018997bae test-data/delta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta.txt Wed Dec 05 02:37:10 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 502018997bae test-data/fplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fplot.txt Wed Dec 05 02:37:10 2018 -0500 |
| b |
| @@ -0,0 +1,13 @@ +#-- forward hits sorted by %sim +0 0 0 +0 0 0 + + +5080 4148 86.1804222648752 +5599 4658 86.1804222648752 + + +74 43 87.5 +223 194 87.5 + + |
| b |
| diff -r 000000000000 -r 502018997bae test-data/gnuplot.txt --- /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 |
| b |
| diff -r 000000000000 -r 502018997bae test-data/hplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hplot.txt Wed Dec 05 02:37:10 2018 -0500 |
| b |
| @@ -0,0 +1,13 @@ +#-- highlighted hits sorted by %sim +0 0 0 +0 0 0 + + +5080 4148 86.1804222648752 +5599 4658 86.1804222648752 + + +74 43 87.5 +223 194 87.5 + + |
| b |
| diff -r 000000000000 -r 502018997bae test-data/human_aqp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_aqp3.fasta Wed Dec 05 02:37:10 2018 -0500 |
| b |
| @@ -0,0 +1,95 @@ +>NG_007476.1:4960-11439 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), RefSeqGene on chromosome 9 +AGCGCTCCTATAAAGGGAGCCACCAGCGCTGGAGGCCGCTGCTCGCTGCGCCACCGCCTCCCGCCACCCC +TGCCCGCCCGACAGCGCCGCCGCCTGCCCCGCCATGGGTCGACAGAAGGAGCTGGTGTCCCGCTGCGGGG +AGATGCTCCACATCCGCTACCGGCTGCTCCGACAGGCGCTGGCCGAGTGCCTGGGGACCCTCATCCTGGT +GGTGAGTGGAGGGAGCCGGGGAAGCCCTTCTCTCTCCAGCCCTTGCACTCCCCAAACTCTCACTTCCCCG +AAGGGGCTGTGTTTTCCAAGGTAGCCTGGACCCACCTCCCCAGCTGTGACCCCCACGCTTAACCGCGGAG +GATCAAGCTGACTTCCAAAGTCCTCTTCCCCACGGTTCTAACCCCCTCTCTGACAGCTCCGACTCTTGCC +AGAATGACAGCTGTTACTCCCCAGTGATAGTGCCGATCGTTTACCCTCCCACAAGTGACTCAGCCAACAG +GCTGGGGGCAGCGGTCACGCTTGCAGTCTGGGACAGCCAGCCACTTCCCCTGCCTCCCACACCCCTCCAG +ATTCCCAGAATCCCAGCCCCCAGATGTAGGGGAGGGGGCGGAGGCAAATGAGCCATTATTAGGTTATTTG +GGTCCTGGGTGTCTGGCCTCTAATGAATAATTAAGCCTCAAAAAGTCCAAAGGTTGAAGTGAGTGAGGAC +AGTTTGCACGAGTGGGGGCAGAGGGTGCAGGCCACATGGGCTGCGAACAGCGAAGTGGGAAGGGAGGCAG +ATTCTGACGGTAGAAGGGTGGGAGGAAGCTAGGCCCAGGCACAGAGGACGCGTGTCTAAAGTTGCTCACC +TGGTGCTCAGCGACTCCCAGGCCCTGTCTGTTATCCAGACAGATGCTGTCAGCGTCTGTGCAGAAGACGA +CAAGCATTCTGGTTACTCCCTGGCCTCTTGGTTACTCTGTGGGTTCTCTGAGTGAGCATTTCCCTGCCTG +AGTTACTCCTCAGTCCTAGTTACTCCTTGGTCACACCAGTTTCACCCTGGTTTTGTTCTGAGTGACTCTG +TTTGCACTTCTTAGGTCTGGCAGACCCACCAGTTATGTTCTATTTCCTGTCCCAGTTACTCTGATTTTTC +AGCCGCTCATGTGGTTACACCTGTTTTCCTCTGTGTTCAGTTGCTACATTGCAGTGAGTGGGTTACTCCG +TTCCTGCCCCAGCCCTGGGTAGTACAGACCAGCTGGCCCACTGTGGACTAGGAAGCCTAACTAAGGGCAA +GTAGGGATCCCCAAATGGTTGAGGATCAGGATCTATGGGCAGAGGAGGGCTGAAACCCACTTCTGGCTTC +CAAGAATAGGAAGTGGGGAAGCCACAGGGGGCATTTTATCCACAGCCTCCCATAAGATTAGTCGTCCTAT +CAGCCAGCCCTAGCCCCTCTCTCCTGTGCCAAGAAGGCAATAGGAGGTGGCCTTTATCACTCTCCTGCCT +CGGAGCCCTCACTCCTATCGGAGTCCTGAGTCCAGCCACCTGTTTTAGAGCAGCCAGGCTAGGGGAGGAT +GATGTCTTCTATTTTCCTAGAGGGGCCTCCTCATTCCCTCCCAAGTCTCAGTTCACTCTCTCACAAAGGA +GCCGTTAGTCCTCCCACTGAGCCCCAGGATCATCAGGCTTATCCCAGACCACAAAAGAAGAGTGTTAAAT +TTTAGGGGAAGGGTTGCAGACTCAGATGGATGTGAGGTATTGGATATCAGTGAGAAGCAGAACTTCAAGG +ACTGCATGAACTGGAGGGGCAGGCCTGGGGATCCCTTTGTAGTGGGTGAGTGCCTGCCTGCCTACCTGCG +TGTTGGGAGCCTAGGCCTGCAGTGGCAGAATCAGGGTTGGCTTTGGGGTGAGGAAAGCCCCTTTCTCTGA +GATACCTGGTGTGAGGGCAGGGGGCGGTGCTGGCCGAGAACTCAGGGCAGGGGTTGGGGGAGGAAGAGGA +AGATTAGCCCCAAGGTGGTGGAACTGGCTCTGACAGCTCCTCCCTCCAAGGCGTCCTGGGATGGAGCCAG +GTCTGAGCCTTTGGCAGGCAAGGAGCTGCTGCCAGGGCCTCCCAAGCAGGGCAGGGCGCCTCAGACCCTC +ACGTGCCTGTCTCCCACCACCCCTCCTCACACATACACCTGCAATCTCTGATCTTTGCTCTCACCTGCCT +GCACACCTTTGCCCCATGTCATTGCCGCTGGCTTCTCCGTTATCTCTTGGTCTTTCTGGGATGATAATCA +AAATGCTTAACTATCCAGTACAACAGGCACTGACCCGTCAGAATAAACAAGGTCTGTAGCACAGGTCCTG +GAAACTGCCTGCTCTGTGGGCATAAAACCTTTAGTTATGGGCAGGTGGGAGAGGAGACCAGGGCAAGGCA +TTGGAGCAGCTTTGAGGGACACTCAGGGGGCTCAGGGCAACAATGCTTTACAGCTGCTGCAGAAGTATTT +TCAGGCTTGAACAAGGGGAACAGACATAGTACGTTCTTTTTCTTTTTTAAATAGAGACAAAGTCTCACTA +TGTTGCCCAGGCTGTTCTCAAACTCCTGGGTTCAAGATCCTCCCATCTCAGCCTCCAAAGTGCTGGGATT +ACAGGTGTGAGCCACCACAGCTGGCTCCAGTATGTTCTATATTTGTAGAACACCAGGGCTCTTAGTCTCT +TTTAGTTCCCCCATTTTTGGCAGAAAGTTTAGAACCGATCTCCCCATTTCTACAGCCCTGGGTCCCGGGC +TGGGGATAGTGAGAGGAGCCACACAGATCCCTGTCTGTAGGACCTCCAAATCTGAGTGGGGAATCTGGAC +CCCTGAGAGCAGAGAGGTCATGGGTGGAGAGAGGAGACGCTGGGACAGGGACAGGTAAAGGAAGGGGAGG +TTGTTGAGGGGGACATGGTGAAGGCTGGGGCTCTGGCATCCTGGACTCAGGAGAAGTGGATTCAACCTCA +CTTCTGGTCTCCTCCCTATTTATTTATGCCGCCCATTGCCACCACTACCACCACCACATGAGCTTTTCTT +TTCAACTCTTTTTTTTTTTTTTTTGAGATGGAGTCCCGCTCTGTCGCCCAGGCTGAAGTGCAGTGGCGCA +ATCTTGGCTCACTGCAACATCTGCCTCCCATTTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG +GGATTACAGGCACCTGCCACCACGCCTGGCTAATTTTTGTACTTTTAGTAGAGATGGGGTTTCACTATGT +TGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTACCAAAGTGCTGGGATT +ACAGTGTGAGCCACTGCACCGGGCCTACATGAGCTTTTCTTTGGGGCAGCTGGGGGATGAGTGAGAGGCT +TCCCACCTTTATGGTCCAGGCCTGAAGGGCTGTGGAGAAACTTGTGCTAAGGTGAAAGCTGTTCCCCTAC +ACCTACGCCTGCTGAAATTCAAGGAAAATCAGTGAAGATGGTTCAGTCATCTTCTAGGATCCCAGTCGCA +GACCCTGCTTCCAGCCCTTTCCATAGGGCCCTCTCATATTAGAGTTGGGACAGTGGGGTGGGAAGGCATG +TGTCCTTTTTCTGGAAAGTGCAATTACAGCAGAAGGGGTTTGGGCTGGGTTCCAGGAAGCGCCTCTAGTC +CTCCCAGTGGTGGCGAGTGGGCATGTTGCTGGCTTCACCCCTTCCTTCTGGAGTGAGAGTTGCTGGTCCT +CACCCTCCCTGCCTGTTCTTCTTCCTGACAGATGTTTGGCTGTGGCTCCGTGGCCCAGGTTGTGCTCAGC +CGGGGCACCCACGGTGGTTTCCTCACCATCAACCTGGCCTTTGGCTTTGCTGTCACTCTGGGCATCCTCA +TCGCTGGCCAGGTCTCTGGTAAGGCCTTAACCCTGCCCCCAGCCCTTGGCCCTCAATAGCATTCCCACTA +GGTGTCCTGGCATTCCTAAGGGCAGGTCACAGCTGTGGCCTCTGCTTTGGCCCCTTGGGAAAGGAGGGTG +GAGAAGAAACTTGACACTTAGAACTTTCGACTCTCACCTTGGAATCAGAGATTATCAGCTGACCTGTTAC +ATAGACCAACCGCCATCCTGTGCAAGAAACCCCTCTCTGCACCCCTTCTCAGGGGACCCTAGCCTGCCGA +CTGTGGCAGGCTGCAGCTAATAGGTCCCTTGTCCCCTCTGCCCAGGGGCCCACCTGAACCCTGCCGTGAC +CTTTGCCATGTGCTTCCTGGCTCGTGAGCCCTGGATCAAGCTGCCCATCTACACCCTGGCACAGACGCTG +GGAGCCTTCTTGGGTGCTGGAATAGTTTTTGGGCTGTATTATGGTAAGCATTCCCCACCCTGTCCTCCTC +CACTACCCCCGTCCCTCTGTTCAGGACCTGCTGGCACCAGGCCTTTTGATGACAGACGGCTAGGACCTGC +CCAGGCCCCGGGCTCATGACTCACTCATTCACGCACAGGGTCAAGGTAGGGGGCACGAAGGGAAAGAAAC +AAGTTGGGCAATAACAGAGTCTCAGGCCCTCCACCCCACCCCACGCCACCCCCTCTGCCTGCTGCAATAC +AGCAGTATTGCTACTTACCCATAACTCATGGGAGGGTGGGGAGGGCACACCTGAGAGGGAAGTCTGGGCT +CAGGCCTCTCCCCCGACTCACTGTGTGTCTAATCTGTCACCAGATGCAATCTGGCACTTCGCCGACAACC +AGCTTTTTGTTTCGGGCCCCAATGGCACAGCCGGCATCTTTGCTACCTACCCCTCTGGACACTTGGATAT +GATCAATGGCTTCTTTGACCAGGTATGGGCTGGGGACGTGTGAGGGGAACGCAGGGAGGGGACCGAGTTG +CCTTGGTAGCTCATGGGCTGGTTGGGGGACAGGACTCCTCGACTGTAGCAGGGTTTCTCCAATCTGTGGG +GTAACCCGCATCAGAACATGGTGGCAAGTACTTACAAAACATGCGGCTCTCCAGCGGGTTCTTGTCACGC +AGACATTCTAGCACCATTGCTTTCAGGAGAAGAGCATGGGCGGGCGCTGACAAGAGTTTAAGAGCTAGAG +GGAAGACGGGGGATGGAAGGAGGGGTCAGAGAAAGGGAGGGAGCTGCAGCTCACCCTGTTCTCCCCACTC +CCCAGTTCATAGGCACAGCCTCCCTTATCGTGTGTGTGCTGGCCATTGTTGACCCCTACAACAACCCCGT +CCCCCGAGGCCTGGAGGCCTTCACCGTGGGCCTGGTGGTCCTGGTCATTGGCACCTCCATGGGCTTCAAC +TCCGGCTATGCCGTCAACCCTGCCCGGGACTTTGGCCCCCGCCTTTTTACAGCCCTTGCGGGCTGGGGCT +CTGCAGTCTTCACGTGAGTACAGCCCCCACCCAGCTCACCCCAGCCTGCCTCTCCTCTGCCCTGCCCCCC +ATGTCCCTGACTATGAGTGTCTGTCCCCCCAGGACCGGCCAGCATTGGTGGTGGGTGCCCATCGTGTCCC +CACTCCTGGGCTCCATTGCGGGTGTCTTCGTGTACCAGCTGATGATCGGCTGCCACCTGGAGCAGCCCCC +ACCCTCCAACGAGGAAGAGAATGTGAAGCTGGCCCATGTGAAGCACAAGGAGCAGATCTGAGTGGGCAGG +GGCCATCTCCCCACTCCGCTGCCCTGGCCTTGAGCATCCACTGACTGTCCAAGGGCCACTCCCAAGAAGC +CCCCTTCACGATCCACCCTTTCAGGCTAAGGAGCTCCCTATCTACCCTCACCCCACGAGACAGCCCCTTC +AGGATTTCCACTGGACCTTGCCCAAATAGCACCTTAGGCCACTGCCCCTAAGCTGGGGTGGAACCGGAAT +TTGGGTCAATACATCCTTTTGTCTCCCAAGGGAAGAGAATGGGCAGCAGGTATGTGTGTGTGTGCATGTG +TGTGCATGTGTGTGCATGTGTGTGCAGGGGTGTGTGTGTGTGGGGGGGGTTCCCAGATATTCAGGGCAAG +GGACCAGTCGGAAGGGATTCTGGCTATTGGGGGAGCCCAGAGACAGGGGAAGGCAGCCTGTCCATCTGTG +CATAAGGAGAGGAAAGTTCCAGGGTGTGTATGTTTCAGGGGCTTCACATGGAGGAGCTGCAGATAGATAT +GTGTTTCTGTGTATGTGTATGTCTGCCTTTTTTTCTAAGTGGGGGCTTCTACAGGCTTTTGGGAAGTAGG +GTGGATGTGGGTAGGGCTGGGAGGAGGGGGCCACAGCTTAGGTTTGGAGCTCTGGATGTACATACATAAG +TAGGAGCAGTGGGACGTGTTTCTGTCATAATGCAGGCATGAAGGGTGGAGTGAAGTCAGGTCATAAGTTT +CATGTTTGCTTTTGTTTTGTTTTGTTTTTAATGTATGTAGCAGATGTTACAGTCTTAGGGATCCGGGATG +GGAGACCCCACTTTAGAAAGGGTCGTCACTCCTTTAATCCTCTACTCAACAATGTACTCTTTTACTTTTA +TATTAAAAAAAATAAAATAAATATGTGCCTAAAACCTCCA + |
| b |
| diff -r 000000000000 -r 502018997bae test-data/mcoords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcoords.txt Wed Dec 05 02:37:10 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 502018997bae test-data/mdelta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mdelta.txt Wed Dec 05 02:37:10 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 502018997bae test-data/mouse_aqp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_aqp3.fasta Wed Dec 05 02:37:10 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 502018997bae test-data/mummer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mummer.txt Wed Dec 05 02:37:10 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 502018997bae test-data/nucmer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nucmer.txt Wed Dec 05 02:37:10 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 502018997bae test-data/plot.png |
| b |
| Binary file test-data/plot.png has changed |
| b |
| diff -r 000000000000 -r 502018997bae test-data/qdiff.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qdiff.txt Wed Dec 05 02:37:10 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 502018997bae test-data/rdiff.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdiff.txt Wed Dec 05 02:37:10 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 502018997bae test-data/report.txt --- /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] |
| b |
| diff -r 000000000000 -r 502018997bae test-data/rplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rplot.txt Wed Dec 05 02:37:10 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +#-- reverse hits sorted by %sim +0 0 0 +0 0 0 + + |
| b |
| diff -r 000000000000 -r 502018997bae test-data/show-coords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/show-coords.txt Wed Dec 05 02:37:10 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 502018997bae test-data/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snps.txt Wed Dec 05 02:37:10 2018 -0500 |
| b |
| b'@@ -0,0 +1,91 @@\n+79\tC\tG\t48\t4\t48\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+83\tA\tC\t52\t1\t52\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+84\tG\tT\t53\t1\t53\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+91\tC\tT\t60\t7\t60\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+98\t.\tT\t68\t1\t68\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+99\t.\tG\t70\t1\t70\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+122\tC\tT\t93\t3\t93\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+125\tG\tA\t96\t3\t96\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+128\tT\tA\t99\t1\t99\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+129\tC\tA\t100\t1\t100\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+130\tC\tT\t101\t1\t101\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+133\tC\tT\t104\t3\t104\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+136\tC\tT\t107\t3\t107\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+148\tC\tT\t119\t12\t119\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+169\tC\tT\t140\t3\t140\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+172\tA\tC\t143\t3\t143\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+184\tC\tG\t155\t12\t155\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+208\tG\tT\t179\t11\t179\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+219\tG\tC\t190\t5\t190\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5087\tC\tG\t4155\t1\t1306\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5088\tA\tC\t4156\t1\t1305\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5089\tG\tC\t4157\t1\t1304\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5096\tC\tG\t4164\t3\t1297\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5099\tT\tC\t4167\t3\t1294\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5104\tC\tT\t4172\t3\t1289\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5107\tA\tC\t4175\t3\t1286\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5110\t.\tT\t4179\t3\t1282\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5131\tT\tG\t4200\t8\t1261\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5139\tC\tT\t4208\t8\t1253\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5148\tG\tA\t4217\t9\t1244\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5157\tT\tC\t4226\t9\t1235\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5166\tC\tT\t4235\t3\t1226\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5169\tC\tT\t4238\t3\t1223\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5178\tC\tT\t4247\t3\t1214\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5181\tC\tG\t4250\t3\t1211\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5187\tA\tT\t4256\t6\t1205\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5199\tC\tT\t4268\t6\t1193\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5205\tC\tT\t4274\t6\t1187\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5232\tC\tA\t4301\t18\t1160\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5250\tC\tT\t4319\t3\t1142\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5253\tC\tT\t4322\t3\t1139\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5277\tG\tT\t4346\t9\t1115\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5286\tC\tA\t4355\t3\t1106\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5289\tC\tT\t4358\t3\t1103\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5295\tT\tC\t4364\t3\t1097\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5298\tT\tC'..b'60\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5307\tT\tG\t4376\t3\t1085\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5310\tG\tT\t4379\t3\t1082\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5322\tT\tA\t4391\t2\t1070\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5324\tC\tA\t4393\t2\t1068\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5344\tC\tT\t4413\t6\t1048\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5350\tC\t.\t4418\t1\t1043\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5351\tC\t.\t4418\t1\t1043\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5352\tC\t.\t4418\t1\t1043\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5353\tA\t.\t4418\t1\t1043\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5354\tG\t.\t4418\t1\t1043\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5357\tC\t.\t4420\t1\t1041\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5358\tA\t.\t4420\t1\t1041\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5366\tC\tT\t4428\t7\t1033\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5373\tT\tC\t4435\t6\t1026\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5379\tG\t.\t4440\t1\t1021\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5380\tC\tT\t4441\t1\t1020\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5387\tC\tG\t4448\t1\t1013\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5388\tC\tA\t4449\t1\t1012\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5391\tA\t.\t4451\t3\t1010\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5396\tC\tT\t4456\t5\t1005\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5401\tC\tT\t4461\t2\t1000\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5403\tA\tT\t4463\t1\t998\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5404\tT\tC\t4464\t1\t997\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5405\tG\tC\t4465\t1\t996\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5406\tA\tG\t4466\t1\t995\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5411\tC\t.\t4470\t2\t991\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5413\tG\tC\t4472\t2\t989\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5418\tC\tT\t4477\t5\t984\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5426\tC\tT\t4485\t5\t976\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5431\tA\tG\t4490\t4\t971\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5435\tT\tC\t4494\t4\t967\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5447\tG\tA\t4506\t6\t955\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5453\tC\tT\t4512\t3\t949\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5456\tG\tC\t4515\t3\t946\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5471\tC\tT\t4530\t6\t931\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5477\tT\tC\t4536\t3\t925\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5480\tG\tT\t4539\t3\t922\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5501\tG\tC\t4560\t6\t901\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5507\tC\tT\t4566\t3\t895\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5510\tC\tT\t4569\t3\t892\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5539\tA\tC\t4598\t28\t863\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5567\tT\tC\t4626\t1\t835\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5568\tG\tA\t4627\t1\t834\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n+5573\tG\tA\t4632\t5\t829\t6480\t5460\t1\t1\tNG_007476.1:4960-11439\tNC_000070.6:c41098183-41092724\n' |
