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-rw-r--r--autogen.pdfbin0 -> 17464 bytes
-rw-r--r--autogen.svg426
-rw-r--r--config.pdfbin0 -> 14672 bytes
-rw-r--r--config.svg223
-rw-r--r--redcap.pdfbin0 -> 13903 bytes
-rw-r--r--redcap.svg148
-rw-r--r--sfrc01042-gridss.pdfbin0 -> 24223 bytes
-rw-r--r--sfrc01042-gridss.svg3784
-rw-r--r--sfrc01042.pdfbin0 -> 79461 bytes
-rw-r--r--sfrc01042.svg5065
-rw-r--r--slides.tex101
11 files changed, 9726 insertions, 21 deletions
diff --git a/autogen.pdf b/autogen.pdf
new file mode 100644
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--- /dev/null
+++ b/autogen.pdf
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diff --git a/autogen.svg b/autogen.svg
new file mode 100644
index 0000000..0db0c5a
--- /dev/null
+++ b/autogen.svg
@@ -0,0 +1,426 @@
+<?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#"
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+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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+ sodipodi:docname="autogen.svg">
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+ style="overflow:visible"
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+ 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="path850" />
+ </marker>
+ <rect
+ x="-200.98668"
+ y="21.381561"
+ width="269.63922"
+ height="253.40543"
+ id="rect18" />
+ <rect
+ x="59.720238"
+ y="16.630953"
+ width="859.45923"
+ height="488.2782"
+ id="rect12" />
+ </defs>
+ <sodipodi:namedview
+ id="base"
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1.0"
+ inkscape:pageopacity="0.0"
+ inkscape:pageshadow="2"
+ inkscape:zoom="0.3789018"
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+ units="px" />
+ <metadata
+ id="metadata5">
+ <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(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
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></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'">SBJ00239,MDX190220,L1901031,SFRC01222,SFRC01222-S1
+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+ y="136.50645"><tspan
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+</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"
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diff --git a/config.pdf b/config.pdf
new file mode 100644
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diff --git a/config.svg b/config.svg
new file mode 100644
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+ xmlns:dc="http://purl.org/dc/elements/1.1/"
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+ rdf:about="">
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+ inkscape:label="Layer 1"
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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
+ 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)"
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+ <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
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+ 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'"> '';