first draft

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 @@
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+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
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+       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"
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+         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
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+         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"
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+         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"
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+         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)"
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+    <text
+       xml:space="preserve"
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+       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"
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+           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'">    };
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+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">  };
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+           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>
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