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Diffstat (limited to 'config.svg')
| -rw-r--r-- | config.svg | 223 |
1 files changed, 223 insertions, 0 deletions
diff --git a/config.svg b/config.svg new file mode 100644 index 0000000..5579b6e --- /dev/null +++ b/config.svg @@ -0,0 +1,223 @@ +<?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 ? "normal"</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 [ "normal" "fast" "very-fast" ]; +</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 = "normal"; +</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 = "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." +</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 = "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"; +</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 = [ "chr1" "chr2:0-1,000" ]; +</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> |