first draft

11 files changed, 9726 insertions, 21 deletions

diff --git a/autogen.pdf b/autogen.pdf
new file mode 100644
index 0000000..fa9bb2d
--- /dev/null
+++ b/autogen.pdf
diff --git a/autogen.svg b/autogen.svg
new file mode 100644
index 0000000..0db0c5a
--- /dev/null
+++ b/autogen.svg
@@ -0,0 +1,426 @@
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+     id="base"
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+     id="metadata5">
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+         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(470.13962,-16.998291)">
+    <text
+       xml:space="preserve"
+       id="text10"
+       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(#rect12);fill:#000000;fill-opacity:1;stroke:none;"
+       transform="matrix(0.59766334,0,0,0.59766334,-205.02948,6.8390357)"><tspan
+         x="59.720703"
+         y="23.044364"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">with import ./milton-slurm.nix { };
+</tspan></tspan><tspan
+         x="59.720703"
+         y="32.103703"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">let
+</tspan></tspan><tspan
+         x="59.720703"
+         y="41.163043"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">  samples = [
+</tspan></tspan><tspan
+         x="59.720703"
+         y="50.22238"><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="59.720703"
+         y="59.281722"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      site = &quot;B1&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="68.341063"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      class = &quot;normals&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="77.400404"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      pdx = false;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="86.459746"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r1 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="95.519087"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;mz/Vf/SHA256E-s23731819040--c650db8ef7fcd00178178fd254970d989b1a964ee68b887f56ae0586683f7c0a.gz/SHA256E-s23731819040--c650db8ef7fcd00178178fd254970d989b1a964ee68b887f56ae0586683f7c0a.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="104.57843"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r2 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="113.63777"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;kz/Zq/SHA256E-s25775609303--bfe116906bddf9799ba78d78be56938b21910812bebcf947f0c56cfbd5fc650a.gz/SHA256E-s25775609303--bfe116906bddf9799ba78d78be56938b21910812bebcf947f0c56cfbd5fc650a.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="122.69711"><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="59.720703"
+         y="131.75645"><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="59.720703"
+         y="140.81579"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      site = &quot;B1&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="149.87513"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      class = &quot;normals&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="158.93447"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      pdx = false;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="167.99381"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r1 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="177.05315"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;V4/Wj/SHA256E-s17295801172--19e79e9018a60ea5715481973ff92194f6a218e5f04418303d99a2eafbaac7d9.gz/SHA256E-s17295801172--19e79e9018a60ea5715481973ff92194f6a218e5f04418303d99a2eafbaac7d9.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="186.11249"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r2 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="195.17184"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;j7/z8/SHA256E-s18960756093--07bdcea8a80adfbf021c9082b1de5dd9a27d7325ecbff0122b82d8654245ed20.gz/SHA256E-s18960756093--07bdcea8a80adfbf021c9082b1de5dd9a27d7325ecbff0122b82d8654245ed20.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="204.23118"><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="59.720703"
+         y="213.29052"><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="59.720703"
+         y="222.34986"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      site = &quot;S1&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="231.4092"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      class = &quot;tumours&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="240.46854"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      pdx = false;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="249.52788"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r1 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="258.58723"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;Fm/94/SHA256E-s4503271082--528808192a494d4e8dc98c0596ee8d04e45cd65c70957993ffdf6a8c2294dd51.gz/SHA256E-s4503271082--528808192a494d4e8dc98c0596ee8d04e45cd65c70957993ffdf6a8c2294dd51.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="267.64657"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r2 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="276.70589"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;q2/Zk/SHA256E-s4582653633--d32ee809bd7d19ed497938a7a5ee36117b8f3f1b43109482da174555bcb1a45e.gz/SHA256E-s4582653633--d32ee809bd7d19ed497938a7a5ee36117b8f3f1b43109482da174555bcb1a45e.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="285.76522"><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="59.720703"
+         y="294.82455"><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="59.720703"
+         y="303.88387"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      site = &quot;S1&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="312.9432"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      class = &quot;tumours&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="322.00252"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      pdx = false;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="331.06185"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r1 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="340.12118"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;Kf/w5/SHA256E-s34952768707--cc01c16aea8cdf162e439c8c7cb419bcb381efe95c071b9e6b97771b40f1eff8.gz/SHA256E-s34952768707--cc01c16aea8cdf162e439c8c7cb419bcb381efe95c071b9e6b97771b40f1eff8.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="349.1805"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r2 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="358.23983"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;Gg/gk/SHA256E-s37880355076--e10fc22839c91f8900ef98afd473361ef0dcb1882b92f87140a9000237fac0e6.gz/SHA256E-s37880355076--e10fc22839c91f8900ef98afd473361ef0dcb1882b92f87140a9000237fac0e6.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="367.29915"><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="59.720703"
+         y="376.35848"><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="59.720703"
+         y="385.41781"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      site = &quot;S1&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="394.47713"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      class = &quot;tumours&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="403.53646"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      pdx = false;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="412.59579"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r1 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="421.65511"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;xM/Q9/SHA256E-s38656117968--04dc46ef77fef4a5578d00d073682d433dfeb6337b905a2cc822b685e0cf61ea.gz/SHA256E-s38656117968--04dc46ef77fef4a5578d00d073682d433dfeb6337b905a2cc822b685e0cf61ea.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="430.71444"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">      r2 =
+</tspan></tspan><tspan
+         x="59.720703"
+         y="439.77376"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">        &quot;Jq/6j/SHA256E-s42454148279--ec5c092b13b76197e2659c51f11bf17c78b2caa44789c4fe006844f8bd15561e.gz/SHA256E-s42454148279--ec5c092b13b76197e2659c51f11bf17c78b2caa44789c4fe006844f8bd15561e.gz&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="448.83309"><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="59.720703"
+         y="457.89242"><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="59.720703"
+         y="466.95174"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">in import ./multisample.nix {
+</tspan></tspan><tspan
+         x="59.720703"
+         y="476.01107"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">  inherit bionix samples fetch;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="485.0704"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">  name = &quot;SFRC01247&quot;;
+</tspan></tspan><tspan
+         x="59.720703"
+         y="494.12972"><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="59.720703"
+         y="503.18905"><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>
+    <text
+       xml:space="preserve"
+       id="text16"
+       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(#rect18);fill:#000000;fill-opacity:1;stroke:none;"
+       transform="matrix(0.59766334,0,0,0.59766334,-350.2056,73.998447)"><tspan
+         x="-200.98633"
+         y="27.794364"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190227,L1901038,SFRC01247,SFRC01247-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="36.853703"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190227,L1901038_topup,SFRC01247,SFRC01247-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="45.913043"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190228,L1901026,SFRC01247,SFRC01247-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="54.97238"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190228,L1901039,SFRC01247,SFRC01247-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="64.031722"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190228,L1901039_topup,SFRC01247,SFRC01247-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="73.091063"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00239,MDX190220,L1901031,SFRC01222,SFRC01222-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="82.150404"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00239,MDX190220,L1901031_topup,SFRC01222,SFRC01222-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="91.209746"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00239,MDX190221,L1901032,SFRC01222,SFRC01222-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="100.26909"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00239,MDX190221,L1901032_topup,SFRC01222,SFRC01222-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="109.32843"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00240,MDX190222,L1901033,SFRC01228,SFRC01228-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="118.38777"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00240,MDX190222,L1901033_topup,SFRC01228,SFRC01228-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="127.44711"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00240,MDX190223,L1901034,SFRC01228,SFRC01228-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="136.50645"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00240,MDX190223,L1901034_topup,SFRC01228,SFRC01228-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="145.56579"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00268,PRJ200049,L2000061,SFRC01233,SFRC01233-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="154.62513"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00268,PRJ200050,L2000062,SFRC01233,SFRC01233-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="163.68447"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00284,PRJ200066,L2000102,SFRC01120,SFRC01120-A-E1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="172.74381"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00284,PRJ200067,L2000103,SFRC01120,SFRC01120-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="181.80315"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00304,PRJ200056,L2000153,SFRC01260,SFRC01260-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="190.86249"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00304,PRJ200202,L2000152,SFRC01260,SFRC01260-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="199.92184"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00307,PRJ200211,L2000166,SFRC01172,SFRC01172-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="208.98118"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00307,PRJ200212,L2000167,SFRC01172,SFRC01172-S1S3
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="218.04052"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00308,PRJ200213,L2000168,SFRC1265,SFRC1265-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="227.09986"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00308,PRJ200214,L2000169,SFRC1265,SFRC1265-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="236.1592"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00346,PRJ200267,L2000235,SFRC01273,PRJ200267-SFRC01273-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="245.21854"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00346,PRJ200268,L2000236,SFRC01273,PRJ200268-SFRC01273-S1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="254.27788"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00349,PRJ200304,L2000264,SFRC01232,SFRC01232-B1
+</tspan></tspan><tspan
+         x="-200.98633"
+         y="263.33721"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00349,PRJ200305,L2000265,SFRC01232,SFRC01232-S2
+</tspan></tspan></text>
+    <path
+       style="fill:#000000;fill-opacity:1;stroke:#000000;stroke-width:0.597664;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#Arrow1Lend)"
+       d="m -285.86987,160.15771 86.25809,-0.31946"
+       id="path22" />
+  </g>
+</svg>
diff --git a/config.pdf b/config.pdf
new file mode 100644
index 0000000..438cd47
--- /dev/null
+++ b/config.pdf
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">
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+     id="defs7408">
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+       x="-21.241243"
+       y="-44.831001"
+       width="289.90775"
+       height="229.43156"
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+       x="30.541494"
+       y="-13.458979"
+       width="413.88394"
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+       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"
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+    </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"
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+     inkscape:window-x="0"
+     inkscape:window-y="0"
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+  <metadata
+     id="metadata7411">
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+         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-specifi