Mercurial > repos > greg > mummer4_dnadiff
changeset 0:491b007eec5d draft default tip
Uploaded
| author | greg |
|---|---|
| date | Mon, 27 Feb 2023 20:02:43 +0000 |
| parents | |
| children | |
| files | .shed.yml all_fasta.loc.sample dnadiff.xml macros.xml test-data/1coords.txt test-data/1delta.txt test-data/all_fasta.loc test-data/delta.txt test-data/human_aqp3.fasta test-data/mcoords.txt test-data/mdelta.txt test-data/mouse_aqp3.fasta test-data/qdiff.txt test-data/rdiff.txt test-data/report.txt test-data/snps.txt tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 18 files changed, 618 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,10 @@ +name: mummer4_dnadiff +owner: greg +homepage_url: https://github.com/gregvonkuster/galaxy_tools +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/mummer4_dnadiff +description: Mummer4 dnadiff +long_description: | + MUMmer is a system for rapidly aligning entire genomes. The current version (release 4.x) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer. +categories: + - Sequence Analysis +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,15 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the tool-data/genome directory (a directory that contains a directory +#for each build). This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dnadiff.xml Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,133 @@ +<tool id="mummer_dnadiff" name="DNAdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Evaluate similarities/differences between two sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"> +<![CDATA[ + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.reference_sequence' reference.fa && + #else: + ln -f -s '$reference_source.reference_sequence.fields.path' reference.fa && + #end if + ln -s $query_sequence query.fa && + dnadiff 'reference.fa' 'query.fa' +]]> + </command> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Select a reference genome from your history or select a cached reference genome?"> + <option value="cached">Select a cached reference genome</option> + <option value="history">Select a reference genome from the history and build the index</option> + </param> + <when value="cached"> + <param name="reference_sequence" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No reference genomes are available"/> + </options> + <validator type="no_options" message="A cached reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="reference_sequence" type="data" format="fasta" label="Use the following dataset as the reference genome" help="You can upload a FASTA or multi-Fasta file to your history and use it as reference"/> + </when> + </conditional> + <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA"/> + <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files"> + <option value="yes">YES</option> + <option value="no">NO</option> + </param> + </inputs> + <outputs> + <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report"/> + <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta"> + <filter> report_only == 'no'</filter> + </data> + <data name="delta1" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" > + <filter> report_only == 'no' </filter> + </data> + <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" > + <filter> report_only == 'no' </filter> + </data> + <data name="coords1" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" > + <filter> report_only == 'no' </filter> + <actions> + <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]"/> + </actions> + </data> + <data name="mcoords" format="tabular" from_work_dir="out.mcoords" label="${tool.name} on ${on_string}: mcoords" > + <filter> report_only == 'no' </filter> + <actions> + <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]"/> + </actions> + </data> + <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" > + <filter> report_only == 'no' </filter> + <actions> + <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]"/> + </actions> + </data> + <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" > + <filter> report_only == 'no' </filter> + <actions> + <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length"/> + </actions> + </data> + <data name="qdiff" format="tabular" from_work_dir="out.qdiff" label="${tool.name} on ${on_string}: qdiff" > + <filter> report_only == 'no' </filter> + <actions> + <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length"/> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history"/> + <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/> + <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/> + <param name="report_only" value="no"/> + <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/> + <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/> + <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/> + <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/> + <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/> + <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/> + <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/> + <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/> + <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/> + </test> + <test> + <param name="reference_source_selector" value="cached"/> + <param name="reference_sequence" ftype="fasta" value="human_aqp3"/> + <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/> + <param name="report_only" value="no"/> + <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/> + <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/> + <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/> + <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/> + <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/> + <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/> + <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/> + <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/> + <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/> + </test> + </tests> + <help><![CDATA[ +This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species. + +**Output files:** + * report: Summary of alignments, differences and SNPs + * delta: Standard nucmer alignment output + * 1delta: 1-to-1 alignment from delta-filter -1 + * mdelta: M-to-M alignment from delta-filter -m + * 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta + * mcoords: M-to-M coordinates from show-coords -THrcl .mdelta + * snps: SNPs from show-snps -rlTHC .1delta + * rdiff: Classified ref breakpoints from show-diff -rH .mdelta + * qdiff: Classified qry breakpoints from show-diff -qH .mdelta + ]]></help> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,22 @@ +<macros> + <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">mumer4</xref> + </xrefs> + </xml> + <xml name="citation"> + <citations> + <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="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement> + <yield /> + </requirements> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1coords.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,2 @@ +74 223 43 194 150 152 87.50 6480 5460 2.31 2.78 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5080 5599 4148 4658 520 511 86.18 6480 5460 8.02 9.36 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1delta.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,20 @@ +/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 +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,1 @@ +human_aqp3 human_aqp3 human_aqp3 ${__HERE__}/human_aqp3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,20 @@ +/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 +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_aqp3.fasta Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,95 @@ +>NG_007476.1:4960-11439 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), RefSeqGene on chromosome 9 +AGCGCTCCTATAAAGGGAGCCACCAGCGCTGGAGGCCGCTGCTCGCTGCGCCACCGCCTCCCGCCACCCC +TGCCCGCCCGACAGCGCCGCCGCCTGCCCCGCCATGGGTCGACAGAAGGAGCTGGTGTCCCGCTGCGGGG +AGATGCTCCACATCCGCTACCGGCTGCTCCGACAGGCGCTGGCCGAGTGCCTGGGGACCCTCATCCTGGT +GGTGAGTGGAGGGAGCCGGGGAAGCCCTTCTCTCTCCAGCCCTTGCACTCCCCAAACTCTCACTTCCCCG +AAGGGGCTGTGTTTTCCAAGGTAGCCTGGACCCACCTCCCCAGCTGTGACCCCCACGCTTAACCGCGGAG +GATCAAGCTGACTTCCAAAGTCCTCTTCCCCACGGTTCTAACCCCCTCTCTGACAGCTCCGACTCTTGCC +AGAATGACAGCTGTTACTCCCCAGTGATAGTGCCGATCGTTTACCCTCCCACAAGTGACTCAGCCAACAG +GCTGGGGGCAGCGGTCACGCTTGCAGTCTGGGACAGCCAGCCACTTCCCCTGCCTCCCACACCCCTCCAG +ATTCCCAGAATCCCAGCCCCCAGATGTAGGGGAGGGGGCGGAGGCAAATGAGCCATTATTAGGTTATTTG +GGTCCTGGGTGTCTGGCCTCTAATGAATAATTAAGCCTCAAAAAGTCCAAAGGTTGAAGTGAGTGAGGAC +AGTTTGCACGAGTGGGGGCAGAGGGTGCAGGCCACATGGGCTGCGAACAGCGAAGTGGGAAGGGAGGCAG +ATTCTGACGGTAGAAGGGTGGGAGGAAGCTAGGCCCAGGCACAGAGGACGCGTGTCTAAAGTTGCTCACC +TGGTGCTCAGCGACTCCCAGGCCCTGTCTGTTATCCAGACAGATGCTGTCAGCGTCTGTGCAGAAGACGA +CAAGCATTCTGGTTACTCCCTGGCCTCTTGGTTACTCTGTGGGTTCTCTGAGTGAGCATTTCCCTGCCTG +AGTTACTCCTCAGTCCTAGTTACTCCTTGGTCACACCAGTTTCACCCTGGTTTTGTTCTGAGTGACTCTG +TTTGCACTTCTTAGGTCTGGCAGACCCACCAGTTATGTTCTATTTCCTGTCCCAGTTACTCTGATTTTTC +AGCCGCTCATGTGGTTACACCTGTTTTCCTCTGTGTTCAGTTGCTACATTGCAGTGAGTGGGTTACTCCG +TTCCTGCCCCAGCCCTGGGTAGTACAGACCAGCTGGCCCACTGTGGACTAGGAAGCCTAACTAAGGGCAA +GTAGGGATCCCCAAATGGTTGAGGATCAGGATCTATGGGCAGAGGAGGGCTGAAACCCACTTCTGGCTTC +CAAGAATAGGAAGTGGGGAAGCCACAGGGGGCATTTTATCCACAGCCTCCCATAAGATTAGTCGTCCTAT +CAGCCAGCCCTAGCCCCTCTCTCCTGTGCCAAGAAGGCAATAGGAGGTGGCCTTTATCACTCTCCTGCCT +CGGAGCCCTCACTCCTATCGGAGTCCTGAGTCCAGCCACCTGTTTTAGAGCAGCCAGGCTAGGGGAGGAT +GATGTCTTCTATTTTCCTAGAGGGGCCTCCTCATTCCCTCCCAAGTCTCAGTTCACTCTCTCACAAAGGA +GCCGTTAGTCCTCCCACTGAGCCCCAGGATCATCAGGCTTATCCCAGACCACAAAAGAAGAGTGTTAAAT +TTTAGGGGAAGGGTTGCAGACTCAGATGGATGTGAGGTATTGGATATCAGTGAGAAGCAGAACTTCAAGG +ACTGCATGAACTGGAGGGGCAGGCCTGGGGATCCCTTTGTAGTGGGTGAGTGCCTGCCTGCCTACCTGCG +TGTTGGGAGCCTAGGCCTGCAGTGGCAGAATCAGGGTTGGCTTTGGGGTGAGGAAAGCCCCTTTCTCTGA +GATACCTGGTGTGAGGGCAGGGGGCGGTGCTGGCCGAGAACTCAGGGCAGGGGTTGGGGGAGGAAGAGGA +AGATTAGCCCCAAGGTGGTGGAACTGGCTCTGACAGCTCCTCCCTCCAAGGCGTCCTGGGATGGAGCCAG +GTCTGAGCCTTTGGCAGGCAAGGAGCTGCTGCCAGGGCCTCCCAAGCAGGGCAGGGCGCCTCAGACCCTC +ACGTGCCTGTCTCCCACCACCCCTCCTCACACATACACCTGCAATCTCTGATCTTTGCTCTCACCTGCCT +GCACACCTTTGCCCCATGTCATTGCCGCTGGCTTCTCCGTTATCTCTTGGTCTTTCTGGGATGATAATCA +AAATGCTTAACTATCCAGTACAACAGGCACTGACCCGTCAGAATAAACAAGGTCTGTAGCACAGGTCCTG +GAAACTGCCTGCTCTGTGGGCATAAAACCTTTAGTTATGGGCAGGTGGGAGAGGAGACCAGGGCAAGGCA +TTGGAGCAGCTTTGAGGGACACTCAGGGGGCTCAGGGCAACAATGCTTTACAGCTGCTGCAGAAGTATTT +TCAGGCTTGAACAAGGGGAACAGACATAGTACGTTCTTTTTCTTTTTTAAATAGAGACAAAGTCTCACTA +TGTTGCCCAGGCTGTTCTCAAACTCCTGGGTTCAAGATCCTCCCATCTCAGCCTCCAAAGTGCTGGGATT +ACAGGTGTGAGCCACCACAGCTGGCTCCAGTATGTTCTATATTTGTAGAACACCAGGGCTCTTAGTCTCT +TTTAGTTCCCCCATTTTTGGCAGAAAGTTTAGAACCGATCTCCCCATTTCTACAGCCCTGGGTCCCGGGC +TGGGGATAGTGAGAGGAGCCACACAGATCCCTGTCTGTAGGACCTCCAAATCTGAGTGGGGAATCTGGAC +CCCTGAGAGCAGAGAGGTCATGGGTGGAGAGAGGAGACGCTGGGACAGGGACAGGTAAAGGAAGGGGAGG +TTGTTGAGGGGGACATGGTGAAGGCTGGGGCTCTGGCATCCTGGACTCAGGAGAAGTGGATTCAACCTCA +CTTCTGGTCTCCTCCCTATTTATTTATGCCGCCCATTGCCACCACTACCACCACCACATGAGCTTTTCTT +TTCAACTCTTTTTTTTTTTTTTTTGAGATGGAGTCCCGCTCTGTCGCCCAGGCTGAAGTGCAGTGGCGCA +ATCTTGGCTCACTGCAACATCTGCCTCCCATTTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG +GGATTACAGGCACCTGCCACCACGCCTGGCTAATTTTTGTACTTTTAGTAGAGATGGGGTTTCACTATGT +TGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTACCAAAGTGCTGGGATT +ACAGTGTGAGCCACTGCACCGGGCCTACATGAGCTTTTCTTTGGGGCAGCTGGGGGATGAGTGAGAGGCT +TCCCACCTTTATGGTCCAGGCCTGAAGGGCTGTGGAGAAACTTGTGCTAAGGTGAAAGCTGTTCCCCTAC +ACCTACGCCTGCTGAAATTCAAGGAAAATCAGTGAAGATGGTTCAGTCATCTTCTAGGATCCCAGTCGCA +GACCCTGCTTCCAGCCCTTTCCATAGGGCCCTCTCATATTAGAGTTGGGACAGTGGGGTGGGAAGGCATG +TGTCCTTTTTCTGGAAAGTGCAATTACAGCAGAAGGGGTTTGGGCTGGGTTCCAGGAAGCGCCTCTAGTC +CTCCCAGTGGTGGCGAGTGGGCATGTTGCTGGCTTCACCCCTTCCTTCTGGAGTGAGAGTTGCTGGTCCT +CACCCTCCCTGCCTGTTCTTCTTCCTGACAGATGTTTGGCTGTGGCTCCGTGGCCCAGGTTGTGCTCAGC +CGGGGCACCCACGGTGGTTTCCTCACCATCAACCTGGCCTTTGGCTTTGCTGTCACTCTGGGCATCCTCA +TCGCTGGCCAGGTCTCTGGTAAGGCCTTAACCCTGCCCCCAGCCCTTGGCCCTCAATAGCATTCCCACTA +GGTGTCCTGGCATTCCTAAGGGCAGGTCACAGCTGTGGCCTCTGCTTTGGCCCCTTGGGAAAGGAGGGTG +GAGAAGAAACTTGACACTTAGAACTTTCGACTCTCACCTTGGAATCAGAGATTATCAGCTGACCTGTTAC +ATAGACCAACCGCCATCCTGTGCAAGAAACCCCTCTCTGCACCCCTTCTCAGGGGACCCTAGCCTGCCGA +CTGTGGCAGGCTGCAGCTAATAGGTCCCTTGTCCCCTCTGCCCAGGGGCCCACCTGAACCCTGCCGTGAC +CTTTGCCATGTGCTTCCTGGCTCGTGAGCCCTGGATCAAGCTGCCCATCTACACCCTGGCACAGACGCTG +GGAGCCTTCTTGGGTGCTGGAATAGTTTTTGGGCTGTATTATGGTAAGCATTCCCCACCCTGTCCTCCTC +CACTACCCCCGTCCCTCTGTTCAGGACCTGCTGGCACCAGGCCTTTTGATGACAGACGGCTAGGACCTGC +CCAGGCCCCGGGCTCATGACTCACTCATTCACGCACAGGGTCAAGGTAGGGGGCACGAAGGGAAAGAAAC +AAGTTGGGCAATAACAGAGTCTCAGGCCCTCCACCCCACCCCACGCCACCCCCTCTGCCTGCTGCAATAC +AGCAGTATTGCTACTTACCCATAACTCATGGGAGGGTGGGGAGGGCACACCTGAGAGGGAAGTCTGGGCT +CAGGCCTCTCCCCCGACTCACTGTGTGTCTAATCTGTCACCAGATGCAATCTGGCACTTCGCCGACAACC +AGCTTTTTGTTTCGGGCCCCAATGGCACAGCCGGCATCTTTGCTACCTACCCCTCTGGACACTTGGATAT +GATCAATGGCTTCTTTGACCAGGTATGGGCTGGGGACGTGTGAGGGGAACGCAGGGAGGGGACCGAGTTG +CCTTGGTAGCTCATGGGCTGGTTGGGGGACAGGACTCCTCGACTGTAGCAGGGTTTCTCCAATCTGTGGG +GTAACCCGCATCAGAACATGGTGGCAAGTACTTACAAAACATGCGGCTCTCCAGCGGGTTCTTGTCACGC +AGACATTCTAGCACCATTGCTTTCAGGAGAAGAGCATGGGCGGGCGCTGACAAGAGTTTAAGAGCTAGAG +GGAAGACGGGGGATGGAAGGAGGGGTCAGAGAAAGGGAGGGAGCTGCAGCTCACCCTGTTCTCCCCACTC +CCCAGTTCATAGGCACAGCCTCCCTTATCGTGTGTGTGCTGGCCATTGTTGACCCCTACAACAACCCCGT +CCCCCGAGGCCTGGAGGCCTTCACCGTGGGCCTGGTGGTCCTGGTCATTGGCACCTCCATGGGCTTCAAC +TCCGGCTATGCCGTCAACCCTGCCCGGGACTTTGGCCCCCGCCTTTTTACAGCCCTTGCGGGCTGGGGCT +CTGCAGTCTTCACGTGAGTACAGCCCCCACCCAGCTCACCCCAGCCTGCCTCTCCTCTGCCCTGCCCCCC +ATGTCCCTGACTATGAGTGTCTGTCCCCCCAGGACCGGCCAGCATTGGTGGTGGGTGCCCATCGTGTCCC +CACTCCTGGGCTCCATTGCGGGTGTCTTCGTGTACCAGCTGATGATCGGCTGCCACCTGGAGCAGCCCCC +ACCCTCCAACGAGGAAGAGAATGTGAAGCTGGCCCATGTGAAGCACAAGGAGCAGATCTGAGTGGGCAGG +GGCCATCTCCCCACTCCGCTGCCCTGGCCTTGAGCATCCACTGACTGTCCAAGGGCCACTCCCAAGAAGC +CCCCTTCACGATCCACCCTTTCAGGCTAAGGAGCTCCCTATCTACCCTCACCCCACGAGACAGCCCCTTC +AGGATTTCCACTGGACCTTGCCCAAATAGCACCTTAGGCCACTGCCCCTAAGCTGGGGTGGAACCGGAAT +TTGGGTCAATACATCCTTTTGTCTCCCAAGGGAAGAGAATGGGCAGCAGGTATGTGTGTGTGTGCATGTG +TGTGCATGTGTGTGCATGTGTGTGCAGGGGTGTGTGTGTGTGGGGGGGGTTCCCAGATATTCAGGGCAAG +GGACCAGTCGGAAGGGATTCTGGCTATTGGGGGAGCCCAGAGACAGGGGAAGGCAGCCTGTCCATCTGTG +CATAAGGAGAGGAAAGTTCCAGGGTGTGTATGTTTCAGGGGCTTCACATGGAGGAGCTGCAGATAGATAT +GTGTTTCTGTGTATGTGTATGTCTGCCTTTTTTTCTAAGTGGGGGCTTCTACAGGCTTTTGGGAAGTAGG +GTGGATGTGGGTAGGGCTGGGAGGAGGGGGCCACAGCTTAGGTTTGGAGCTCTGGATGTACATACATAAG +TAGGAGCAGTGGGACGTGTTTCTGTCATAATGCAGGCATGAAGGGTGGAGTGAAGTCAGGTCATAAGTTT +CATGTTTGCTTTTGTTTTGTTTTGTTTTTAATGTATGTAGCAGATGTTACAGTCTTAGGGATCCGGGATG +GGAGACCCCACTTTAGAAAGGGTCGTCACTCCTTTAATCCTCTACTCAACAATGTACTCTTTTACTTTTA +TATTAAAAAAAATAAAATAAATATGTGCCTAAAACCTCCA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcoords.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,2 @@ +74 223 43 194 150 152 87.50 6480 5460 2.31 2.78 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5080 5599 4148 4658 520 511 86.18 6480 5460 8.02 9.36 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mdelta.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,20 @@ +/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 +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_aqp3.fasta Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,80 @@ +>NC_000070.6:c41098183-41092724 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J +ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCG +CGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTT +CGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTAT +CTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAG +TTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGA +CAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGG +AGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAA +CTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGG +TCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCG +GATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGA +TTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGT +CCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCT +CTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGG +CGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTG +ACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCA +GCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACA +TGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTC +CTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAA +GAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTA +TTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAA +AAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAA +AGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGT +TGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAG +GTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATA +AGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTG +GCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGAC +GGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGAC +CTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGC +ACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTT +GTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTC +TCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGA +AAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAG +TTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCC +CTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGG +ACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGA +GGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACA +TTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATG +ACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGG +CAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATT +TAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGT +CTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCAT +GTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGG +TGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCT +TGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAG +CATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACA +GCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTG +GAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAA +AGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACC +CCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGC +ACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCC +CGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGG +CCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGA +AACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATAT +GCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAAT +GGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACG +GCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGT +ATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTG +TAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAA +GCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGG +ACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCG +CCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTT +CACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCT +GCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTAC +AGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCA +GGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGT +GTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTG +GCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGA +GTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTC +CCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTC +CCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA +GAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACC +AAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAA +TGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTAT +GCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAG +AAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGAT +AGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATAC +ATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTT +AATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qdiff.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,3 @@ +NC_000070.6:c41098183-41092724 BRK 1 42 42 +NC_000070.6:c41098183-41092724 GAP 195 4147 3953 4856 -903 +NC_000070.6:c41098183-41092724 BRK 4659 5460 802
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdiff.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,3 @@ +NG_007476.1:4960-11439 BRK 1 73 73 +NG_007476.1:4960-11439 GAP 224 5079 4856 3953 903 +NG_007476.1:4960-11439 BRK 5600 6480 881
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,87 @@ +/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 +NUCMER + + [REF] [QRY] +[Sequences] +TotalSeqs 1 1 +AlignedSeqs 1(100.0000%) 1(100.0000%) +UnalignedSeqs 0(0.0000%) 0(0.0000%) + +[Bases] +TotalBases 6480 5460 +AlignedBases 670(10.3395%) 663(12.1429%) +UnalignedBases 5810(89.6605%) 4797(87.8571%) + +[Alignments] +1-to-1 2 2 +TotalLength 670 663 +AvgLength 335.0000 331.5000 +AvgIdentity 86.4791 86.4791 + +M-to-M 2 2 +TotalLength 670 663 +AvgLength 335.0000 331.5000 +AvgIdentity 86.4791 86.4791 + +[Feature Estimates] +Breakpoints 4 4 +Relocations 0 0 +Translocations 0 0 +Inversions 0 0 + +Insertions 3 3 +InsertionSum 5810 4797 +InsertionAvg 1936.6667 1599.0000 + +TandemIns 0 0 +TandemInsSum 0 0 +TandemInsAvg 0.0000 0.0000 + +[SNPs] +TotalSNPs 78 78 +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%) + +TotalGSNPs 1 1 +TA 0(0.0000%) 0(0.0000%) +TG 0(0.0000%) 0(0.0000%) +TC 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 +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%) +.A 0(0.0000%) 3(23.0769%) +.T 2(15.3846%) 0(0.0000%) + +TotalGIndels 0 0 +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%) +.T 0(0.0000%) 0(0.0000%)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snps.txt Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,91 @@ +79 C G 48 4 48 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +83 A C 52 1 52 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +84 G T 53 1 53 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +91 C T 60 7 60 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +98 . T 68 1 68 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +99 . G 70 1 70 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +122 C T 93 3 93 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +125 G A 96 3 96 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +128 T A 99 1 99 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +129 C A 100 1 100 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +130 C T 101 1 101 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +133 C T 104 3 104 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +136 C T 107 3 107 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +148 C T 119 12 119 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +169 C T 140 3 140 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +172 A C 143 3 143 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +184 C G 155 12 155 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +208 G T 179 11 179 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +219 G C 190 5 190 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5087 C G 4155 1 1306 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5088 A C 4156 1 1305 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5089 G C 4157 1 1304 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5096 C G 4164 3 1297 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5099 T C 4167 3 1294 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5104 C T 4172 3 1289 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5107 A C 4175 3 1286 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5110 . T 4179 3 1282 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5131 T G 4200 8 1261 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5139 C T 4208 8 1253 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5148 G A 4217 9 1244 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5157 T C 4226 9 1235 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5166 C T 4235 3 1226 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5169 C T 4238 3 1223 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5178 C T 4247 3 1214 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5181 C G 4250 3 1211 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5187 A T 4256 6 1205 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5199 C T 4268 6 1193 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5205 C T 4274 6 1187 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5232 C A 4301 18 1160 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5250 C T 4319 3 1142 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5253 C T 4322 3 1139 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5277 G T 4346 9 1115 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5286 C A 4355 3 1106 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5289 C T 4358 3 1103 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5295 T C 4364 3 1097 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5298 T C 4367 3 1094 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5301 A C 4370 3 1091 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5307 T G 4376 3 1085 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5310 G T 4379 3 1082 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5322 T A 4391 2 1070 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5324 C A 4393 2 1068 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5344 C T 4413 6 1048 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5350 C . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5351 C . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5352 C . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5353 A . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5354 G . 4418 1 1043 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5357 C . 4420 1 1041 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5358 A . 4420 1 1041 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5366 C T 4428 7 1033 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5373 T C 4435 6 1026 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5379 G . 4440 1 1021 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5380 C T 4441 1 1020 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5387 C G 4448 1 1013 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5388 C A 4449 1 1012 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5391 A . 4451 3 1010 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5396 C T 4456 5 1005 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5401 C T 4461 2 1000 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5403 A T 4463 1 998 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5404 T C 4464 1 997 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5405 G C 4465 1 996 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5406 A G 4466 1 995 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5411 C . 4470 2 991 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5413 G C 4472 2 989 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5418 C T 4477 5 984 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5426 C T 4485 5 976 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5431 A G 4490 4 971 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5435 T C 4494 4 967 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5447 G A 4506 6 955 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5453 C T 4512 3 949 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5456 G C 4515 3 946 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5471 C T 4530 6 931 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5477 T C 4536 3 925 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5480 G T 4539 3 922 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5501 G C 4560 6 901 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5507 C T 4566 3 895 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5510 C T 4569 3 892 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5539 A C 4598 28 863 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5567 T C 4626 1 835 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5568 G A 4627 1 834 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5573 G A 4632 5 829 6480 5460 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under tool-data/genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Feb 27 20:02:43 2023 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under tool-data/genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables>