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authorJustin Bedo <cu@cua0.org>2020-12-07 16:30:53 +1100
committerJustin Bedo <cu@cua0.org>2020-12-07 16:30:53 +1100
commit5cf9dcf15c3e384d02b81e81cb3e2c4a1de0efa4 (patch)
tree855679ee656b1f4ea3a155e861347fb8499b29fe /config.svg
parent0c566119872b385fe3eabef3ab308c02f71d65d2 (diff)
first draft
Diffstat (limited to 'config.svg')
-rw-r--r--config.svg223
1 files changed, 223 insertions, 0 deletions
diff --git a/config.svg b/config.svg
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+++ b/config.svg
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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ width="455.12238mm"
+ height="223.55347mm"
+ viewBox="0 0 455.12238 223.55347"
+ version="1.1"
+ id="svg7414"
+ inkscape:version="1.0.1 (3bc2e813f5, 2020-09-07)"
+ sodipodi:docname="config.svg">
+ <defs
+ id="defs7408">
+ <rect
+ x="-21.241243"
+ y="-44.831001"
+ width="289.90775"
+ height="229.43156"
+ id="rect9862" />
+ <rect
+ x="30.541494"
+ y="-13.458979"
+ width="413.88394"
+ height="334.50894"
+ id="rect9856" />
+ <marker
+ style="overflow:visible"
+ id="Arrow1Lend"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="Arrow1Lend"
+ inkscape:isstock="true">
+ <path
+ transform="matrix(-0.8,0,0,-0.8,-10,0)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1pt;stroke-opacity:1"
+ d="M 0,0 5,-5 -12.5,0 5,5 Z"
+ id="path9527" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ id="base"
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1.0"
+ inkscape:pageopacity="0.0"
+ inkscape:pageshadow="2"
+ inkscape:zoom="0.7"
+ inkscape:cx="759.14858"
+ inkscape:cy="391.12423"
+ inkscape:document-units="mm"
+ inkscape:current-layer="layer1"
+ inkscape:document-rotation="0"
+ showgrid="false"
+ fit-margin-top="0"
+ fit-margin-left="0"
+ fit-margin-right="0"
+ fit-margin-bottom="0"
+ inkscape:window-width="3436"
+ inkscape:window-height="1397"
+ inkscape:window-x="0"
+ inkscape:window-y="0"
+ inkscape:window-maximized="1" />
+ <metadata
+ id="metadata7411">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title></dc:title>
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <g
+ inkscape:label="Layer 1"
+ inkscape:groupmode="layer"
+ id="layer1"
+ transform="translate(143.30989,-31.132592)">
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:7.05556px;line-height:1.25;font-family:'TeX Gyre Heros';-inkscape-font-specification:'TeX Gyre Heros, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-feature-settings:normal;text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.264583"
+ x="-144.16017"
+ y="131.57629"
+ id="text8685"><tspan
+ sodipodi:role="line"
+ id="tspan8683"
+ x="-144.16017"
+ y="131.57629"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code';stroke-width:0.264583">{ bionix</tspan><tspan
+ sodipodi:role="line"
+ x="-144.16017"
+ y="140.63564"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code';stroke-width:0.264583"
+ id="tspan8687">, speed ? &quot;normal&quot;</tspan><tspan
+ sodipodi:role="line"
+ x="-144.16017"
+ y="149.69498"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code';stroke-width:0.264583"
+ id="tspan8689">, max-genotypes ? 0</tspan><tspan
+ sodipodi:role="line"
+ x="-144.16017"
+ y="158.75432"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code';stroke-width:0.264583"
+ id="tspan8691">, targets ? [] }:</tspan></text>
+ <path
+ style="fill:none;stroke:#000000;stroke-width:0.5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#Arrow1Lend)"
+ d="M -44.927083,142.90933 H 7.0016025"
+ id="path8699" />
+ <text
+ xml:space="preserve"
+ id="text9854"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:7.05556px;line-height:1.25;font-family:'TeX Gyre Heros';-inkscape-font-specification:'TeX Gyre Heros, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-feature-settings:normal;text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;white-space:pre;shape-inside:url(#rect9856);fill:#000000;fill-opacity:1;stroke:none" />
+ <text
+ xml:space="preserve"
+ id="text9860"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:7.05556px;line-height:1.25;font-family:'TeX Gyre Heros';-inkscape-font-specification:'TeX Gyre Heros, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-feature-settings:normal;text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;white-space:pre;shape-inside:url(#rect9862);fill:#000000;fill-opacity:1;stroke:none"
+ transform="translate(46.491085,75.595238)"><tspan
+ x="-21.242188"
+ y="-38.416574"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">{
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="-29.357233"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> options.octopus.call = {
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="-20.297893"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> speed = mkOption {
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="-11.238554"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> type = types.enum [ &quot;normal&quot; &quot;fast&quot; &quot;very-fast&quot; ];
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="-2.179214"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> default = &quot;normal&quot;;
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="6.8801255"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> };
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="15.939465"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="24.998805"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> max-genotypes = mkOption {
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="34.058144"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> type = types.int;
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="43.117484"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> default = 0;
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="52.176825"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> description = &quot;Maximum number of candidate genotypes. If </tspan></tspan><tspan
+ x="-21.242188"
+ y="61.236166"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">zero then flag is not passed to octopus.&quot;
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="70.295508"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> };
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="79.354849"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="88.414191"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> targets = mkOption {
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="97.473532"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> type = types.either (types.listOf types.str) types.path;
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="106.53287"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> default = [];
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="115.59222"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> description = &quot;either a list of genomic regions to call or a </tspan></tspan><tspan
+ x="-21.242188"
+ y="124.65156"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">file containing a list of genomic regions to call&quot;;
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="133.7109"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> example = ''
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="142.77024"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> targets = [ &quot;chr1&quot; &quot;chr2:0-1,000&quot; ];
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="151.82958"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> '';
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="160.88892"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> };
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="169.94826"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> };
+</tspan></tspan><tspan
+ x="-21.242188"
+ y="179.00761"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">...</tspan></tspan></text>
+ </g>
+</svg>