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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/aegean">Debian Med / aegean</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724">96c39eb4</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-10-05T16:03:28Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.16.0+dfsg</pre>
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<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
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<li class="file-stats">
<a href="#b95a728693c46323e1013c6df90fee3a8946db8d">
data/gff3/aech-dachsous-out.gff3
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<li class="file-stats">
<a href="#2b3789d33470dbaf5310571369d6a0abdbe7d258">
data/gff3/mrot-cst-out-cds.gff3
</a>
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<li class="file-stats">
<a href="#85de023616dc087200958e491d7e57f4f600eae6">
data/gff3/nvit-exospindle-out.gff3
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<li class="file-stats">
<a href="#fb02388ff1cda5574840ba863aa99ff6ac397571">
data/misc/amel-ogs-vs-ncbi-parseval-html/index.html
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<li class="file-stats">
<a href="#30bc223017fc826e9a388a948b93524f6d2924a6">
data/scripts/miloci.py
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<li class="file-stats">
<a href="#ecc80e754a71b298becce20c1285590b9e37d1b3">
src/core/AgnCompareReportHTML.c
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<li class="file-stats">
<a href="#351ec13c34b6d7b38544895e2819575257d0b1a8">
src/core/AgnLocusRefineStream.c
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<li class="file-stats">
<a href="#67738a6019a928039a6c3a327bff17202ebdaba7">
src/core/AgnUtils.c
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,13 @@</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">All notable changes to this project will be documented in this file.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">This project adheres to <span class="p">[</span><span class="nv" style="color: teal;">Semantic Versioning</span><span class="p">](</span><span class="sx" style="color: #d14;">http://semver.org/</span><span class="p">)</span>.</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.16.0] - 2016-05-09</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> Outer gene in intron gene cases now designated as a ciLocus.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> ciLoci are now exempt from merging into miLoci.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">-</span> Fixes to how polycistrons and other edge cases are handled.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.15.2] - 2016-03-17</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">
<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">v0.1<span class="idiff left right">5.2</span> stable</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">v0.1<span class="idiff left right">6.0</span> stable</span></pre>
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<li id="b95a728693c46323e1013c6df90fee3a8946db8d">
<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#b95a728693c46323e1013c6df90fee3a8946db8d"><strong>data/gff3/aech-dachsous-out.gff3</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">#!annotation-source NCBI Acromyrmex echinatior Annotation Release 100</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1190754 1200781 . . . child_gene=1;child_mRNA=2;riil=769;effective_length=10028;iLocus_type=siLocus</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1200782 1201550 . . . fg_orient=FR;effective_length=769;iLocus_type=iiLocus</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1201551 1566216 . . . <span class="idiff left right">effective_length=364666;iiLocus_exception=complex-overlap-3;liil=769;riil=8884;iLocus_type=siLocus</span>;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1201551 1566216 . . . <span class="idiff left right">iLocus_type=ciLocus;effective_length=364666;iiLocus_exception=complex-overlap-3;liil=769;riil=8884</span>;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1216473 1219475 . . . iiLocus_exception=intron-gene;liil=0;riil=0;iLocus_type=siLocus;child_gene=1;child_mRNA=2</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1537022 1540189 . . . liil=0;riil=0;iLocus_type=niLocus;child_gene=1;child_ncRNA=1</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">NW_011626563.1 AEGeAn::LocusPocus locus 1566217 1575100 . . . fg_orient=RR;effective_length=8884;iLocus_type=iiLocus</span>
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<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#2b3789d33470dbaf5310571369d6a0abdbe7d258"><strong>data/gff3/mrot-cst-out-cds.gff3</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,5 +6,5 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#!genome-build-accession NCBI_Assembly:GCF_000220905.1</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">#!annotation-date 7 April 2015</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">#!annotation-source NCBI Megachile rotundata Annotation Release 101</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">NW_003797177.1 AEGeAn::LocusPocus locus 9652 19311 . . . <span class="idiff left right">effective_length=9660;iLocus_type=siLocus</span>;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">NW_003797177.1 AEGeAn::LocusPocus locus 9652 19311 . . . <span class="idiff left right">iLocus_type=ciLocus;effective_length=9660</span>;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">NW_003797177.1 AEGeAn::LocusPocus locus 11405 18146 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=4</span></pre>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">#!annotation-date 3 June 2014</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">#!annotation-source NCBI Nasonia vitripennis Annotation Release 101</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">NC_015867.2 AEGeAn::LocusPocus locus 370926 373152 . . . child_gene=1;child_mRNA=1;right_overlap=262;iiLocus_exception=delta-overlap-delta;riil=0;effective_length=1965;iLocus_type=siLocus</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . <span class="idiff left right">effective_length=6758;iLocus_type=siLocus</span>;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">NC_015867.2 AEGeAn::LocusPocus locus 372891 380536 . . . <span class="idiff left right">iLocus_type=ciLocus;effective_length=6758</span>;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">NC_015867.2 AEGeAn::LocusPocus locus 374998 378903 . . . iiLocus_exception=intron-gene;iLocus_type=siLocus;child_gene=1;child_mRNA=1</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">NC_015867.2 AEGeAn::LocusPocus locus 379649 381835 . . . left_overlap=888;liil=0;child_gene=1;child_mRNA=1;effective_length=2187;iLocus_type=siLocus</span></pre>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="html"> <span class="nt" style="color: navy;"></tbody></span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="html"> <span class="nt" style="color: navy;"><h2></span>Gene loci <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"tooltip"</span><span class="nt" style="color: navy;">></span>[?]<span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"tooltip_text"</span><span class="nt" style="color: navy;">></span>If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">target=</span><span class="s" style="color: #d14;">"_blank"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://aegean.readthedocs.<span class="idiff left right">org/en/refactor</span>/loci.html"</span><span class="nt" style="color: navy;">></span>this page<span class="nt" style="color: navy;"></a></span> for a formal definition of a locus annotation.<span class="nt" style="color: navy;"></span></span></h2></span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="html"> <span class="nt" style="color: navy;"><h2></span>Gene loci <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"tooltip"</span><span class="nt" style="color: navy;">></span>[?]<span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"tooltip_text"</span><span class="nt" style="color: navy;">></span>If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">target=</span><span class="s" style="color: #d14;">"_blank"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://aegean.readthedocs.<span class="idiff left right">io/en/latest</span>/loci.html"</span><span class="nt" style="color: navy;">></span>this page<span class="nt" style="color: navy;"></a></span> for a formal definition of a locus annotation.<span class="nt" style="color: navy;"></span></span></h2></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="html"> <span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"table_normal"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="html"> <span class="nt" style="color: navy;"><tr><td></span>shared<span class="nt" style="color: navy;"></td><td></span>7<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="html"> <span class="nt" style="color: navy;"><tr><td></span>unique to reference<span class="nt" style="color: navy;"></td><td></span>1<span class="nt" style="color: navy;"></td></tr></span></span>
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<li id="30bc223017fc826e9a388a948b93524f6d2924a6">
<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#30bc223017fc826e9a388a948b93524f6d2924a6"><strong>data/scripts/miloci.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,29 +11,67 @@ import re</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Locus</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_rawdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">9</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="nd">@property</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">seqid</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="nd">@property</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">start</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="nd">@property</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">end</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="nd">@property</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ilocus_class</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">typematch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">'iLocus_type=([^;</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">]+)'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">typematch</span><span class="p">,</span> <span class="s" style="color: #d14;">'could not determine iLocus type: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_rawdata</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">typematch</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="nd">@property</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mergeable</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ilocus_class</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'siLocus'</span><span class="p">,</span> <span class="s" style="color: #d14;">'niLocus'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'iiLocus_exception=intron-gene'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">'ID=[^;</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">]+;*'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">'Name=[^;</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">]+;*'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"""Merge ajacent or overlapping gene-containing iLoci."""</span></span>
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16
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span>
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17
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">'ID=[^;</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">]+;*'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">'Name=[^;</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">]+;*'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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24
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">locus</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">:</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">9</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqid</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seqid</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">lstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">lend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">lstart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lstart</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">lend</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">numeric_attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">findall</span><span class="p">(</span><span class="s" style="color: #d14;">'([^;=]+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seqid</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">numeric_attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">findall</span><span class="p">(</span><span class="s" style="color: #d14;">'([^;=]+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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37
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key_value_pair</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">numeric_attrs</span><span class="p">:</span></span>
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38
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">'='</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">key_value_pair</span><span class="p">,</span> \</span>
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39
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">'malformed key/value pair </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">key_value_pair</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,8 +87,9 @@ def merge_iloci(loci):</td>
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49
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">attrs</span><span class="p">):</span></span>
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50
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">attrstring</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">';</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">gff3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="s" style="color: #d14;">'AEGeAn::miloci.py'</span><span class="p">,</span> <span class="s" style="color: #d14;">'locus'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">),</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="n" style="color: #333;">attrstring</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">gff3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">)),</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="n" style="color: #333;">attrstring</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">gff3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Locus</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_iloci</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,34 +98,28 @@ def parse_iloci(fp):</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> Output: merged iLoci; gene-containing iLoci that are adjacent or</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> overlapping are combined</span></span>
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61
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">prev_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">locus_buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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64
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span></span>
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66
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">locus</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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67
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">locus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Locus</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">locus_buffer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">locus_buffer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;">locus_buffer</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">locus_buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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68
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">locusseqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'([^</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">]+)'</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqid</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locusseqid</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">locusseqid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">seqid</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">prev_loci</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;">prev_loci</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">prev_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locusseqid</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">';child_gene='</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">prev_loci</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mergeable</span><span class="p">:</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">locus_buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">locus</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">prev_loci</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">prev_loci</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">prev_loci</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">l<span class="idiff left">ine</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">re</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sub</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'ID=[^;</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">]+;*'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">''</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">line</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">re</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sub</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Name=[^;</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">]+;*'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">''</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">yield</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">prev_loci</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">prev_loci</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">locus_buffer</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">locus_buffer</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">locus_buffer</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">l<span class="idiff left">ocus</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">yield</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">locus</span></span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">locus_buffer</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">merge_iloci</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">locus_buffer</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#ecc80e754a71b298becce20c1285590b9e37d1b3"><strong>src/core/AgnCompareReportHTML.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -403,7 +403,7 @@ static void compare_report_html_footer(FILE *outstream)</td>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="c"> <span class="s" style="color: #d14;">" <p class=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">footer</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> <span class="s" style="color: #d14;">" Generated by <a href=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>AEGeAn %s (%s %s)</a>.<br /></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="c"> <span class="s" style="color: #d14;">"latest/contrib.html</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>AEGeAn authors</a>.<br /></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="s" style="color: #d14;">" </p></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">AGN_VERSION_LINK</span><span class="p">,</span> <span class="n" style="color: #333;">AGN_SEMANTIC_VERSION</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -712,7 +712,7 @@ static void compare_report_html_print_compclassfiles(AgnCompareReportHTML *rpt)</td>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="c"><span class="p">{</span></span>
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713
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="c"> <span class="n" style="color: #333;">GtArray</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compclassdata</span><span class="p">;</span></span>
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714
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="c"> <span class="n" style="color: #333;">GtUword</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="c"><span class="idiff left right"> </span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="c"></span>
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716
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="c"> <span class="n" style="color: #333;">compclassdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_hashmap_get</span><span class="p">(</span><span class="n" style="color: #333;">rpt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compclassdata</span><span class="p">,</span> <span class="s" style="color: #d14;">"perfect"</span><span class="p">);</span></span>
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717
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_array_size</span><span class="p">(</span><span class="n" style="color: #333;">compclassdata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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718
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -734,7 +734,7 @@ static void compare_report_html_print_compclassfiles(AgnCompareReportHTML *rpt)</td>
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734
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="c"> <span class="n" style="color: #333;">compare_report_html_seqfile_footer</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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735
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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736
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="c"> <span class="p">}</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="c"><span class="idiff left right"> </span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="c"></span>
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738
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="c"> <span class="n" style="color: #333;">compclassdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_hashmap_get</span><span class="p">(</span><span class="n" style="color: #333;">rpt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compclassdata</span><span class="p">,</span> <span class="s" style="color: #d14;">"mislabeled"</span><span class="p">);</span></span>
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739
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_array_size</span><span class="p">(</span><span class="n" style="color: #333;">compclassdata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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740
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -757,7 +757,7 @@ static void compare_report_html_print_compclassfiles(AgnCompareReportHTML *rpt)</td>
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757
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">compare_report_html_seqfile_footer</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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758
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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759
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="c"></span>
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761
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="c"> <span class="n" style="color: #333;">compclassdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_hashmap_get</span><span class="p">(</span><span class="n" style="color: #333;">rpt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compclassdata</span><span class="p">,</span> <span class="s" style="color: #d14;">"cds"</span><span class="p">);</span></span>
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762
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_array_size</span><span class="p">(</span><span class="n" style="color: #333;">compclassdata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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763
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="c"> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -779,7 +779,7 @@ static void compare_report_html_print_compclassfiles(AgnCompareReportHTML *rpt)</td>
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779
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="c"> <span class="n" style="color: #333;">compare_report_html_seqfile_footer</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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780
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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781
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781
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="c"> <span class="p">}</span></span>
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782
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="c"><span class="idiff left right"> </span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="c"></span>
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783
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="c"> <span class="n" style="color: #333;">compclassdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_hashmap_get</span><span class="p">(</span><span class="n" style="color: #333;">rpt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compclassdata</span><span class="p">,</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">);</span></span>
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784
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_array_size</span><span class="p">(</span><span class="n" style="color: #333;">compclassdata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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785
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -801,7 +801,7 @@ static void compare_report_html_print_compclassfiles(AgnCompareReportHTML *rpt)</td>
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801
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="c"> <span class="n" style="color: #333;">compare_report_html_seqfile_footer</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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802
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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803
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="c"> <span class="p">}</span></span>
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804
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="c"><span class="idiff left right"> </span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="c"></span>
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805
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="c"> <span class="n" style="color: #333;">compclassdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_hashmap_get</span><span class="p">(</span><span class="n" style="color: #333;">rpt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compclassdata</span><span class="p">,</span> <span class="s" style="color: #d14;">"utr"</span><span class="p">);</span></span>
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806
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_array_size</span><span class="p">(</span><span class="n" style="color: #333;">compclassdata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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807
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -823,7 +823,7 @@ static void compare_report_html_print_compclassfiles(AgnCompareReportHTML *rpt)</td>
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823
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="c"> <span class="n" style="color: #333;">compare_report_html_seqfile_footer</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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824
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824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outstream</span><span class="p">);</span></span>
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825
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="c"> <span class="p">}</span></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="c"> <span class="n" style="color: #333;">compclassdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_hashmap_get</span><span class="p">(</span><span class="n" style="color: #333;">rpt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compclassdata</span><span class="p">,</span> <span class="s" style="color: #d14;">"nonmatch"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_array_size</span><span class="p">(</span><span class="n" style="color: #333;">compclassdata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="c"> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1127,7 +1127,7 @@ static void compare_report_html_summary_annot(AgnCompInfo *info,</td>
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="c"> <span class="s" style="color: #d14;">" <h2>Gene loci <span class=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">tooltip</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>[?]<span class=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">tooltip_text</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>If a gene "</span></span>
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="c"> <span class="s" style="color: #d14;">"annotation overlaps with another gene annotation, those annotations are associated "</span></span>
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="c"> <span class="s" style="color: #d14;">"with the same gene locus. See <a target=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">_blank</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> "</span></span>
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<pre style="margin: 0;">-<span id="LC1130" class="line" lang="c"> <span class="s" style="color: #d14;">"href=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">http://aegean.readthedocs.<span class="idiff left right">org/en/refactor</span>/loci.html</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span></span>
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="c"> <span class="s" style="color: #d14;">"href=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">http://aegean.readthedocs.<span class="idiff left right">io/en/latest</span>/loci.html</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span></span>
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="c"> <span class="s" style="color: #d14;">"this page</a> for a formal definition of a locus annotation.</span></span></h2></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="c"> <span class="s" style="color: #d14;">" <table class=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">table_normal</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="c"> <span class="s" style="color: #d14;">" <tr><td>shared</td><td>%lu</td></tr></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<li id="351ec13c34b6d7b38544895e2819575257d0b1a8">
<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#351ec13c34b6d7b38544895e2819575257d0b1a8"><strong>src/core/AgnLocusRefineStream.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -311,6 +311,8 @@ static bool refine_locus_check_intron_genes(AgnLocusRefineStream *stream,</td>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c"> <span class="n" style="color: #333;">GtStr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_genome_node_get_seqid</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gn1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c"> <span class="n" style="color: #333;">AgnLocus</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">locus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_locus_new</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">agn_locus_add_feature</span><span class="p">(</span><span class="n" style="color: #333;">locus</span><span class="p">,</span> <span class="n" style="color: #333;">fn1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"> <span class="n" style="color: #333;">gt_feature_node_add_attribute</span><span class="p">((</span><span class="n" style="color: #333;">GtFeatureNode</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">locus</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="c"> <span class="s" style="color: #d14;">"ciLocus"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> <span class="n" style="color: #333;">gt_genome_node_ref</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gn1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">gt_array_add</span><span class="p">(</span><span class="n" style="color: #333;">iloci</span><span class="p">,</span> <span class="n" style="color: #333;">locus</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -408,11 +410,14 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,</td>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numloci</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;">GtGenomeNode</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">gn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_array_get</span><span class="p">(</span><span class="n" style="color: #333;">iloci</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="c"> <span class="n" style="color: #333;">GtFeatureNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_feature_node_cast</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gn</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;">coding_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_locus_num_mrnas</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gn</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="c"> <span class="n" style="color: #333;">coding_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_typecheck_count</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="n" style="color: #333;">agn_typecheck_cds</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">test_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_<span class="idiff left">locus_num_mrnas</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">gn</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">test_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_<span class="idiff left">typecheck_count</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fn</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">agn_typecheck_cds</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">same_coding_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coding_status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">test_status</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">same_coding_status</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -467,7 +472,10 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,</td>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ilenfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">gt_str_get</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="c"> <span class="n" style="color: #333;">gt_feature_node_add_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">,</span> <span class="n" style="color: #333;">typestr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_feature_node_get_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c"> <span class="n" style="color: #333;">gt_feature_node_add_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">,</span> <span class="n" style="color: #333;">typestr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"> <span class="p">}</span></span>
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numloci</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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473
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -489,7 +497,7 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,</td>
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489
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">GtFeatureNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_feature_node_cast</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gn1</span><span class="p">);</span></span>
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490
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">GtFeatureNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_feature_node_cast</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gn2</span><span class="p">);</span></span>
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491
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">cds1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_<span class="idiff left">locus_num_mrnas</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">gn1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">cds1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_<span class="idiff left">typecheck_count</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fn1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">agn_typecheck_cds</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span>;</span></span>
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493
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cds1</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span></span>
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494
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="c"> <span class="p">{</span></span>
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495
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"> <span class="n" style="color: #333;">gt_feature_node_add_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn1</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">,</span> <span class="s" style="color: #d14;">"siLocus"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -624,7 +632,10 @@ static void locus_refine_stream_extend(AgnLocusRefineStream *stream,</td>
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624
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c"> <span class="p">{</span></span>
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625
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ciLocus"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">gt_feature_node_add_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">,</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_feature_node_get_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">gt_feature_node_add_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"iLocus_type"</span><span class="p">,</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/aegean/commit/96c39eb486a856f52e9770b7a0fde07bef032724#67738a6019a928039a6c3a327bff17202ebdaba7"><strong>src/core/AgnUtils.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -269,6 +269,9 @@ bool agn_overlap_ilocus(GtGenomeNode *f1, GtGenomeNode *f2,</td>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_str_cmp</span><span class="p">(</span><span class="n" style="color: #333;">seqid1</span><span class="p">,</span> <span class="n" style="color: #333;">seqid2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">GtRange</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_genome_node_get_range</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">GtRange</span> <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_genome_node_get_range</span><span class="p">(</span><span class="n" style="color: #333;">f2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c"></span>
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272
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">by_cds</span><span class="p">)</span></span>
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273
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> <span class="p">{</span></span>
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274
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="n" style="color: #333;">GtRange</span> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">agn_feature_node_get_cds_range</span><span class="p">((</span><span class="n" style="color: #333;">GtFeatureNode</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">f1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -286,13 +289,18 @@ bool agn_overlap_ilocus(GtGenomeNode *f1, GtGenomeNode *f2,</td>
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286
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"> <span class="p">{</span></span>
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287
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Both have coding sequences, use those instead of the complete feature</span></span>
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288
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// coordinates.</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gt_range_compare</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Polycistrons belong together</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"> <span class="p">}</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c"></span>
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289
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt_range_overlap_delta</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c2</span><span class="p">,</span> <span class="n" style="color: #333;">minoverlap</span><span class="p">);</span></span>
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290
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="p">}</span></span>
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291
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c"> <span class="p">}</span></span>
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292
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Either we are not in CDS mode, or the features don't have a CDS.</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">GtRange</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_genome_node_get_range</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;">GtRange</span> <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt_genome_node_get_range</span><span class="p">(</span><span class="n" style="color: #333;">f2</span><span class="p">);</span></span>
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296
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt_range_overlap_delta</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">minoverlap</span><span class="p">);</span></span>
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297
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"><span class="p">}</span></span>
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c"></span>
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