| Previous changeset 4:bcd65de9725b (2021-11-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538 |
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modified:
macros.xml mummer.xml test-data/1delta.txt test-data/delta.txt test-data/mdelta.txt test-data/nucmer.txt test-data/report.txt |
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added:
test-data/out.bam test-data/out.cram test-data/out.sam |
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| diff -r bcd65de9725b -r 57f042937ba7 macros.xml --- a/macros.xml Sat Nov 27 09:59:44 2021 +0000 +++ b/macros.xml Mon Mar 18 12:41:39 2024 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token> <xml name="bio_tools"> <xrefs> - <xref type="bio.tools">mumer4</xref> + <xref type="bio.tools">mummer4</xref> </xrefs> </xml> <xml name="citation"> @@ -10,15 +10,16 @@ <citation type="doi">10.1371/journal.pcbi.1005944</citation> </citations> </xml> + <token name="@TOOL_VERSION@">4.0.0rc1</token> + <token name="@VERSION_SUFFIX@">3</token> + <token name="@PROFILE@">20.05</token> <xml name="gnuplot_requirement"> - <requirement type="package" version="5.4.1">gnuplot</requirement> + <requirement type="package" version="5.4.8">gnuplot</requirement> </xml> - <token name="@TOOL_VERSION@">4.0.0rc1</token> - <token name="@VERSION_SUFFIX@">2</token> - <token name="@PROFILE@">20.05</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement> + <requirement type="package" version="1.19.2">samtools</requirement> <yield /> </requirements> </xml> @@ -30,13 +31,13 @@ <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." > + <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default 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" + <param 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)" /> + <param 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> @@ -54,7 +55,7 @@ <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)" /> + <param 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> |
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| diff -r bcd65de9725b -r 57f042937ba7 mummer.xml --- a/mummer.xml Sat Nov 27 09:59:44 2021 +0000 +++ b/mummer.xml Mon Mar 18 12:41:39 2024 +0000 |
| [ |
| @@ -9,7 +9,7 @@ </expand> <command detect_errors="exit_code"> <![CDATA[ - mummer + mummer $anchoring -l '$min' $direction @@ -87,9 +87,9 @@ <option value="0">No</option> <option value="1">Yes</option> </param> - <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify" + <param 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" + <param 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" /> @@ -112,7 +112,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" /> <param name="options|advanced" value="defaults" /> @@ -128,7 +128,7 @@ mummer - -mumreference Compute maximal matches that are unique in the reference- sequence but not + -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 @@ -154,16 +154,16 @@ mummerplot - -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest + -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 + -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 + --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 |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/1delta.txt --- a/test-data/1delta.txt Sat Nov 27 09:59:44 2021 +0000 +++ b/test-data/1delta.txt Mon Mar 18 12:41:39 2024 +0000 |
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| @@ -1,4 +1,4 @@ -/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat +/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat NUCMER >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 74 223 43 194 19 19 0 |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/delta.txt --- a/test-data/delta.txt Sat Nov 27 09:59:44 2021 +0000 +++ b/test-data/delta.txt Mon Mar 18 12:41:39 2024 +0000 |
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| @@ -1,4 +1,4 @@ -/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat +/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat NUCMER >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 74 223 43 194 19 19 0 |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/mdelta.txt --- a/test-data/mdelta.txt Sat Nov 27 09:59:44 2021 +0000 +++ b/test-data/mdelta.txt Mon Mar 18 12:41:39 2024 +0000 |
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| @@ -1,4 +1,4 @@ -/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat +/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat NUCMER >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 74 223 43 194 19 19 0 |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/nucmer.txt --- a/test-data/nucmer.txt Sat Nov 27 09:59:44 2021 +0000 +++ b/test-data/nucmer.txt Mon Mar 18 12:41:39 2024 +0000 |
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| @@ -1,4 +1,4 @@ -reference.fa query.fa +/tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat NUCMER >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 74 223 43 194 19 19 0 |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/out.bam |
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| Binary file test-data/out.bam has changed |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/out.cram |
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| Binary file test-data/out.cram has changed |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/out.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.sam Mon Mar 18 12:41:39 2024 +0000 |
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| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:NG_007476.1:4960-11439 LN:6480 M5:dcb745df791cdf1218f74d62ab4e1507 UR:file:///tmp/tmp885k3_3o/files/8/f/5/dataset_8f5d35c8-47ee-4bac-87e6-449833607f46.dat +@PG ID:samtools PN:samtools VN:1.19.2 CL:samtools sort -o outsamheadsort outsamhead +@PG ID:samtools.1 PN:samtools PP:samtools VN:1.19.2 CL:samtools calmd outsamheadsort reference.fa +NC_000070.6:c41098183-41092724 0 NG_007476.1:4960-11439 74 10 42S25M1I1M1I124M5266S * 0 0 ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCGCGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTTCGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTATCTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAGTTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGACAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGGAGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAACTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGGTCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCGGATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGATTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGTCCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCTCTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGGCGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTGACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCAGCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACATGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTCCTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAAGAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTATTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAAAAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAAAGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGTTGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAGGTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATAAGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTGGCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGACGGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGACCTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGCACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTTGTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTCTCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGAAAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAGTTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCCCTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGGACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGAGGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACATTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATGACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGGCAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATTTAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGTCTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCATGTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGGTGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCTTGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAGCATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACAGCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTGGAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAAAGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACCCCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGCACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCCCGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGGCCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGAAACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATATGCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAATGGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACGGCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGTATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTGTAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAAGCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGGACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCGCCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTTCACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCTGCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTACAGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCAGGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGTGTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTGGCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGAGTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTCCCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTCCCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACCAAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAATGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTATGCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAGAAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGATAGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATACATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTTAATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG * NM:i:19 MD:Z:5C3A0G6C30C2G2T0C0C2C2C11C20C2A11C23G10G4 +NC_000070.6:c41098183-41092724 2048 NG_007476.1:4960-11439 5080 10 4147H31M1I239M5D2M2D20M1D11M1D19M1D188M802H * 0 0 GGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCGCCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTTCACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCTGCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTACAGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCAGGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGTGTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTGGCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAG * NM:i:72 MD:Z:7C0A0G6C2T4C2A23T7C8G8T8C2C8C2C5A11C5C26C17C2C23G8C2C5T2T2A5T2G11T1C19C5^CCCAG2^CA7C6T5^G0C6C0C2^A4C4C1A0T0G0A4^C1G4C7C4A3T11G5C2G14C5T2G20G5C2C28A27T0G4G26 |
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| diff -r bcd65de9725b -r 57f042937ba7 test-data/report.txt --- a/test-data/report.txt Sat Nov 27 09:59:44 2021 +0000 +++ b/test-data/report.txt Mon Mar 18 12:41:39 2024 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat +/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat NUCMER [REF] [QRY] @@ -39,49 +39,49 @@ [SNPs] TotalSNPs 78 78 +AT 2(2.5641%) 2(2.5641%) +AC 6(7.6923%) 5(6.4103%) +AG 2(2.5641%) 5(6.4103%) +TA 2(2.5641%) 2(2.5641%) TG 2(2.5641%) 5(6.4103%) TC 9(11.5385%) 28(35.8974%) -TA 2(2.5641%) 2(2.5641%) -GC 6(7.6923%) 6(7.6923%) -GA 5(6.4103%) 2(2.5641%) -GT 5(6.4103%) 2(2.5641%) CT 28(35.8974%) 9(11.5385%) CA 5(6.4103%) 6(7.6923%) CG 6(7.6923%) 6(7.6923%) -AT 2(2.5641%) 2(2.5641%) -AG 2(2.5641%) 5(6.4103%) -AC 6(7.6923%) 5(6.4103%) +GT 5(6.4103%) 2(2.5641%) +GA 5(6.4103%) 2(2.5641%) +GC 6(7.6923%) 6(7.6923%) TotalGSNPs 1 1 -TA 0(0.0000%) 0(0.0000%) +GT 0(0.0000%) 0(0.0000%) +GA 0(0.0000%) 0(0.0000%) +GC 0(0.0000%) 0(0.0000%) +CG 0(0.0000%) 0(0.0000%) +CT 0(0.0000%) 0(0.0000%) +CA 0(0.0000%) 1(100.0000%) +TC 0(0.0000%) 0(0.0000%) TG 0(0.0000%) 0(0.0000%) -TC 0(0.0000%) 0(0.0000%) +TA 0(0.0000%) 0(0.0000%) +AT 0(0.0000%) 0(0.0000%) AG 0(0.0000%) 0(0.0000%) AC 1(100.0000%) 0(0.0000%) -AT 0(0.0000%) 0(0.0000%) -GC 0(0.0000%) 0(0.0000%) -GA 0(0.0000%) 0(0.0000%) -GT 0(0.0000%) 0(0.0000%) -CT 0(0.0000%) 0(0.0000%) -CG 0(0.0000%) 0(0.0000%) -CA 0(0.0000%) 1(100.0000%) TotalIndels 13 13 +A. 3(23.0769%) 0(0.0000%) T. 0(0.0000%) 2(15.3846%) -G. 2(15.3846%) 1(7.6923%) C. 5(38.4615%) 0(0.0000%) -A. 3(23.0769%) 0(0.0000%) -.G 1(7.6923%) 2(15.3846%) -.C 0(0.0000%) 5(38.4615%) +G. 2(15.3846%) 1(7.6923%) .A 0(0.0000%) 3(23.0769%) .T 2(15.3846%) 0(0.0000%) +.C 0(0.0000%) 5(38.4615%) +.G 1(7.6923%) 2(15.3846%) TotalGIndels 0 0 +G. 0(0.0000%) 0(0.0000%) +C. 0(0.0000%) 0(0.0000%) T. 0(0.0000%) 0(0.0000%) A. 0(0.0000%) 0(0.0000%) -G. 0(0.0000%) 0(0.0000%) -C. 0(0.0000%) 0(0.0000%) -.A 0(0.0000%) 0(0.0000%) .C 0(0.0000%) 0(0.0000%) .G 0(0.0000%) 0(0.0000%) +.A 0(0.0000%) 0(0.0000%) .T 0(0.0000%) 0(0.0000%) |