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Merge pull request #2961 from bgruening/vg
add initial version of vg
2 parents cd3b054 + a0ee9e8 commit fc3deb5

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Lines changed: 788 additions & 3 deletions

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‎.github/workflows/pr.yaml‎

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@@ -318,9 +318,8 @@ jobs:
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path: upload
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- name: Check status of combined status
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run: |
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stat=$(jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success" || true)
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if [[ "$(echo -n $stat | wc -l)" -gt "0" ]]; then
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echo "Unsuccessful tests found $(sort <<<$stat | uniq -c)"
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if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
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echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
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exit 1
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fi
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‎tools/vg/.shed.yml‎

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owner: iuc
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long_description: |
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Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg
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homepage_url: https://github.com/vgteam/vg
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type: unrestricted
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categories:
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- Sequence Analysis
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- Variant Analysis
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auto_tool_repositories:
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name_template: "{{ tool_id }}"
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description_template: "Wrapper for the vg tool: {{ tool_name }}"
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suite:
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name: "suite_vg"
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description: "variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods"
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type: repository_suite_definition

‎tools/vg/convert.xml‎

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<tool id="vg_convert" name="vg convert" version="@TOOL_VERSION@">
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<description></description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="requirements"/>
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<command detect_errors="exit_code"><![CDATA[
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ln -s '$infile' ./infile.${infile.ext} &&
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vg convert
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$output_format
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./infile.${infile.ext}
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> '$output'
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]]></command>
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<inputs>
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<param name="infile" type="data" format="vg,xg" label="Input file in vg or xg format" />
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<param name="output_format" type="select" label="Choose your output format">
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<option value="--xg-out">XG format (--xg-out)</option>
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<!--option value="- -odgi-out">odgi format (- -odgi-out)</option-->
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</param>
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</inputs>
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<outputs>
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<data name="output" format="odgi">
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<change_format>
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<when input="output_format" value="--xg-out" format="xg"/>
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</change_format>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="infile" value="hla.vg" ftype="vg" />
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<param name="output_format" value="--xg-out" />
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<output name="output" file="hla.xg" ftype="xg" compare="sim_size" />
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</test>
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<!--test>
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<param name="infile" value="x.vg" ftype="vg" />
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<param name="output_format" value="- -odgi-out" />
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<output name="output" file="x.odgi" ftype="odgi" compare="sim_size" />
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</test-->
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</tests>
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<help><![CDATA[
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variation graph (vg) convert module
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-----------------------------------
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This module is converting various variant graphs into each format.
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]]></help>
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<expand macro="citations" />
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</tool>

‎tools/vg/deconstruct.xml‎

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<tool id="vg_deconstruct" name="vg deconstruct" version="@TOOL_VERSION@">
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<description>construct a dynamic succinct variation graph</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="requirements"/>
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<command detect_errors="exit_code"><![CDATA[
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ln -s '$infile' ./infile.${infile.ext} &&
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vg deconstruct
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#if $path:
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--path '${','.join([$p for $p in $path])}'
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#end if
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#if $path_prefix
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--path-prefix '${','.join([$p for $p in $path_prefix])}'
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#end if
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#if $alt_prefix
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--alt-prefix '${','.join([$p for $p in $alt_prefix])}'
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#end if
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#if $snarls:
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--snarls '$snarls'
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#end if
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$path_traversals ## -e
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--threads=\${GALAXY_SLOTS:-1}
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./infile.${infile.ext}
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> '$output'
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]]></command>
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<inputs>
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<param name="infile" type="data" format="xg,odgi" label="Graph files" />
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<param argument="--path" type="text" value="" label="A reference path to deconstruct against"
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help="comma-separated list accepted">
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<sanitizer>
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<valid initial="string.printable">
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<remove value="&apos;"/>
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</valid>
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</sanitizer>
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</param>
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<param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference"
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help="comma-separated list accepted">
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<sanitizer>
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<valid initial="string.printable">
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<remove value="&apos;"/>
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</valid>
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</sanitizer>
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</param>
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<param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF"
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help="comma-separated list accepted">
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<sanitizer>
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<valid initial="string.printable">
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<remove value="&apos;"/>
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</valid>
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</sanitizer>
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</param>
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<param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true"
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help="from `vg snarls` to avoid recomputing" />
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<param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false"
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label="Only consider traversals that correspond to paths in the grpah" />
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</inputs>
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<outputs>
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<data name="output" format="vcf" />
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</outputs>
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<tests>
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<test>
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<param name="infile" value="hla.xg" />
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<param name="path" value="gi|568815592:29791752-29792749" />
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<param name="path_traversals" value="true" />
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<output name="output" file="hla_variants.vcf" />
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</test>
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</tests>
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<help><![CDATA[
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variation graph (vg) deconstruct module
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-----------------------------------
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Creates VCF records for Snarls present in a graph (relative to a chosen reference path).
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]]></help>
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<expand macro="citations">
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</expand>
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</tool>

‎tools/vg/macros.xml‎

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<?xml version="1.0"?>
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<macros>
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<xml name="requirements">
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">vg</requirement>
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</requirements>
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</xml>
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<token name="@TOOL_VERSION@">1.23.0</token>
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<xml name="citations">
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<citations>
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<yield />
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</citations>
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</xml>
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</macros>

‎tools/vg/test-data/hla.vg‎

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‎tools/vg/test-data/hla.xg‎

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‎tools/vg/test-data/hla_variants.vcf‎

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##fileformat=VCFv4.2
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##contig=<ID=gi|568815592:29791752-29792749,length=998>
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT gi|157734152:29563108-29564082 gi|528476637:29761569-29762543 gi|568815454:1057585-1058559 gi|568815529:1275535-1276509 gi|568815551:1054737-1055734 gi|568815561:1054328-1055325 gi|568815564:1054403-1055400 gi|568815567:1054737-1055711 gi|568815569:1097903-1098900
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gi|568815592:29791752-29792749 92 . G A 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 105 . C T 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 151 . CAG C 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 160 . A G 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 222 . G A 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 283 . C G 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 295 . TT CC 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 348 . G A 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 357 . G A 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 395 . T C 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 468 . T C 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 583 . G C 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 621 . G T 23 . . GT 0 1 0 0 0 0 0 1 0
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gi|568815592:29791752-29792749 660 . G A 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 824 . CGCGGGCGCCGTGGATGGAGCA C 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 982 . G A 23 . . GT 1 1 1 1 0 0 0 1 0
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gi|568815592:29791752-29792749 995 . C T 23 . . GT 1 1 1 1 0 0 0 1 0

‎tools/vg/test-data/snarls.pb‎

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