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Fix documentation
1 parent d498c42 commit c14b824

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‎abif.nimble‎

Lines changed: 3 additions & 1 deletion
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@@ -95,7 +95,9 @@ task docs, "Generate documentation":
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exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abimerge.nim"
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exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abimetadata.nim"
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exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abichromatogram.nim"
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else:
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echo "Nim >=2.0.0 is required to build the docs!"
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task buildbin, "Build all binaries to bin/ directory":
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exec "mkdir -p bin"
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exec "nim c -d:release --opt:speed -o:bin/abif src/abif.nim"

‎docs/abi2fq.html‎

Lines changed: 36 additions & 31 deletions
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‎docs/abi2fq.idx‎

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nimTitle abi2fq abi2fq.html module src/abi2fq 0
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nim Config abi2fq.html#Config object Config 41
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nim printHelp abi2fq.html#printHelp proc printHelp() 53
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nim parseCommandLine abi2fq.html#parseCommandLine proc parseCommandLine(): Config 75
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nim trimSequence abi2fq.html#trimSequence,string,seq[int],int,int proc trimSequence(sequence: string; qualities: seq[int]; windowSize: int;\n threshold: int): tuple[seq: string, qual: seq[int]] 145
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nim writeFastq abi2fq.html#writeFastq,string,seq[int],string,string,bool proc writeFastq(sequence: string; qualities: seq[int]; name: string;\n outFile: string = ""; fasta: bool = false) 195
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nim main abi2fq.html#main proc main() 226

‎docs/abichromatogram.html‎

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@@ -12,10 +12,10 @@
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<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">
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<!-- CSS -->
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<link rel="stylesheet" type="text/css" href="nimdoc.out.css">
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<link rel="stylesheet" type="text/css" href="nimdoc.out.css?v=2.0.8">
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<!-- JS -->
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<script type="text/javascript" src="dochack.js"></script>
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<script type="text/javascript" src="dochack.js?v=2.0.8"></script>
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</head>
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<body>
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<div class="document" id="documentId">
@@ -124,8 +124,7 @@ <h1><a class="toc-backref" href="#7">Types</a></h1>
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<span class="Identifier">peaks</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">seq</span><span class="Other">[</span><span class="Identifier">int</span><span class="Other">]</span> <span class="Comment">## Base call peak positions</span>
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<span class="Identifier">sequence</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">string</span> <span class="Comment">## Called sequence</span>
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<span class="Identifier">traceLen</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">int</span> <span class="Comment">## Total length of trace in data points</span>
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<span class="Identifier">baseColors</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">Table</span><span class="Other">[</span><a href="abichromatogram.html#Channel"><span class="Identifier">Channel</span></a><span class="Other">,</span> <span class="Identifier">string</span><span class="Other">]</span> <span class="Comment">## Color mapping for each nucleotide base</span>
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</pre></dt>
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<span class="Identifier">baseColors</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">Table</span><span class="Other">[</span><a href="abichromatogram.html#Channel"><span class="Identifier">Channel</span></a><span class="Other">,</span> <span class="Identifier">string</span><span class="Other">]</span> <span class="Comment">## Color mapping for each nucleotide base</span></pre></dt>
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<dd>
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Processed trace data ready for visualization
@@ -137,8 +136,7 @@ <h1><a class="toc-backref" href="#7">Types</a></h1>
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<div id="TraceDataPoint">
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<dt><pre><a href="abichromatogram.html#TraceDataPoint"><span class="Identifier">TraceDataPoint</span></a> <span class="Other">=</span> <span class="Keyword">object</span>
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<span class="Identifier">position</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">int</span> <span class="Comment">## X position (scan number)</span>
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<span class="Identifier">values</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">Table</span><span class="Other">[</span><a href="abichromatogram.html#Channel"><span class="Identifier">Channel</span></a><span class="Other">,</span> <span class="Identifier">int</span><span class="Other">]</span> <span class="Comment">## Intensity value for each channel (scaled 0-1000)</span>
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</pre></dt>
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<span class="Identifier">values</span><span class="Operator">*</span><span class="Other">:</span> <span class="Identifier">Table</span><span class="Other">[</span><a href="abichromatogram.html#Channel"><span class="Identifier">Channel</span></a><span class="Other">,</span> <span class="Identifier">int</span><span class="Other">]</span> <span class="Comment">## Intensity value for each channel (scaled 0-1000)</span></pre></dt>
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<dd>
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A single data point in the trace with values for each channel
@@ -157,7 +155,7 @@ <h1><a class="toc-backref" href="#7">Types</a></h1>
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<div class="twelve-columns footer">
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<span class="nim-sprite"></span>
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<br>
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<small style="color: var(--hint);">Made with Nim. Generated: 2025-04-26 09:58:57 UTC</small>
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<small style="color: var(--hint);">Made with Nim. Generated: 2025-04-29 10:45:02 UTC</small>
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</div>
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</div>
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</div>

‎docs/abichromatogram.idx‎

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nimTitle abichromatogram abichromatogram.html module src/abichromatogram 0
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nim A abichromatogram.html#A Channel.A 44
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nim C abichromatogram.html#C Channel.C 44
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nim G abichromatogram.html#G Channel.G 44
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nim T abichromatogram.html#T Channel.T 44
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nim Channel abichromatogram.html#Channel enum Channel 44
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nim TraceDataPoint abichromatogram.html#TraceDataPoint object TraceDataPoint 48
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nim TraceData abichromatogram.html#TraceData object TraceData 53

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