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GitLab

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<h3>

Michael R. Crusoe pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/python-gffutils">Debian Med / python-gffutils</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7">22db2456</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-01-01T11:45:45Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.10.1</pre>

</li>

</ul>

<h4>25 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#382bcb8cd1496c8d0d592bdeaaaa156299aed898">

gffutils.egg-info/PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#d3589e08517ba1ffed9a60087862e0a3374d8f12">

gffutils.egg-info/SOURCES.txt

</a>

</li>

<li class="file-stats">

<a href="#f150cef205dd7bcb93d9a71c4b130f69cc21b933">

gffutils.egg-info/requires.txt

</a>

</li>

<li class="file-stats">

<a href="#df96c16f1a237002b91943103cf457a7a8c81f1a">

gffutils/attributes.py

</a>

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<li class="file-stats">

<a href="#f2a5d823fb26fca72f2fe98667ba1c506c945f11">

gffutils/bins.py

</a>

</li>

<li class="file-stats">

<a href="#173d7c6b62d5dfce2fa12bb662e3d7272b1b3bc6">

gffutils/biopython_integration.py

</a>

</li>

<li class="file-stats">

<a href="#0fcebaeb967483b2aefccc38ee7038aeb57ed6b6">

gffutils/create.py

</a>

</li>

<li class="file-stats">

<a href="#82bd271c739c9bc8738fd7c0b57257d6db9d00a2">

gffutils/feature.py

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<li class="file-stats">

<a href="#04cef6b8c6f04a6fd3441ac29249595f331a082f">

gffutils/helpers.py

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<li class="file-stats">

<a href="#3b56c7dca7a21095a405dffc855f81a640cda2f3">

<span class="deleted-file">

−

gffutils/inspection.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#fddb19e520264cff8743df915666b073884bef60">

gffutils/interface.py

</a>

</li>

<li class="file-stats">

<a href="#4596c28d6a9f80cdb433781b12bc2aafe91349e1">

gffutils/iterators.py

</a>

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<li class="file-stats">

<a href="#03d1eb2b3cf6671d3e39cac6e5cc741a6ea809df">

<span class="new-file">

+

gffutils/merge_criteria.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#95b5bb48b2a3ee493756e3ff8ac8f419724555fd">

gffutils/parser.py

</a>

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<li class="file-stats">

<a href="#813e78223f55b4ca02a5f4aee6a78b722bd609a2">

gffutils/pybedtools_integration.py

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<li class="file-stats">

<a href="#526a837fe4cca54b4c1c2279c2e24d4e942f8efc">

<span class="new-file">

+

gffutils/test/data/synthetic.gff3

</span>

</a>

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<li class="file-stats">

<a href="#b0f2632c4b65d2dfee8f69f70f70e1c7237393ba">

<span class="new-file">

+

gffutils/test/synth_test_base.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#36b3b2505247623a7a10862d6932e78bcdde4d12">

gffutils/test/test.py

</a>

</li>

<li class="file-stats">

<a href="#5f2c425940451a5e93c7e86645cb918593f3a9d7">

gffutils/test/test_biopython_integration.py

</a>

</li>

<li class="file-stats">

<a href="#178bad6d457c689d13f5187e9574fb61b8ef0d06">

<span class="new-file">

+

gffutils/test/test_merge.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#d58e1dc1356251786c2151af57cce228ffb8d3a1">

<span class="new-file">

+

gffutils/test/test_merge_all.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#3261a65b84ab9332a3637d0e16a82bbad42280f1">

gffutils/version.py

</a>

</li>

<li class="file-stats">

<a href="#19359a61ae2446b51b549167b014da2fcf265768">

requirements.txt

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<li class="file-stats">

<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">

setup.cfg

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</li>

</ul>

<h4>Changes:</h4>

<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: gffutils</span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">9</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">10.1</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Work with GFF and GTF files in a flexible database framework</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/daler/gffutils</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6" 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">

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Ryan Dale</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="382bcb8cd1496c8d0d592bdeaaaa156299aed898">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#382bcb8cd1496c8d0d592bdeaaaa156299aed898"><strong>gffutils.egg-info/PKG-INFO</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: gffutils</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">9</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">10.1</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" 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">

4

</td>

<td class="diff-line-num new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Work with GFF and GTF files in a flexible database framework</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" 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">

5

</td>

<td class="diff-line-num new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/daler/gffutils</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6" 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">

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Ryan Dale</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="d3589e08517ba1ffed9a60087862e0a3374d8f12">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#d3589e08517ba1ffed9a60087862e0a3374d8f12"><strong>gffutils.egg-info/SOURCES.txt</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -16,9 +16,9 @@ gffutils/feature.py</td>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

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<td class="diff-line-num new_line" data-linenumber="16" 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">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">gffutils/gffwriter.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

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<td class="diff-line-num new_line" data-linenumber="17" 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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">gffutils/helpers.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

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<td class="diff-line-num new_line" data-linenumber="18" 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">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">gffutils/inspect.py</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">gffutils/inspection.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

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<td class="diff-line-num new_line" data-linenumber="19" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">gffutils/interface.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

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<td class="diff-line-num new_line" data-linenumber="20" 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">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">gffutils/iterators.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="22" 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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<td class="diff-line-num new new_line" data-linenumber="21" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">gffutils/merge_criteria.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

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<td class="diff-line-num new_line" data-linenumber="22" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">gffutils/parser.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

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<td class="diff-line-num new_line" data-linenumber="23" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">gffutils/pybedtools_integration.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

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<td class="diff-line-num new_line" data-linenumber="24" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">gffutils/version.py</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="36" 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">@@ -36,8 +36,11 @@ gffutils/test/feature_test.py</td>

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<td class="diff-line-num old_line" data-linenumber="36" 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">

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<td class="diff-line-num new_line" data-linenumber="36" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">gffutils/test/helpers_test.py</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" 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">

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<td class="diff-line-num new_line" data-linenumber="37" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">gffutils/test/parser_test.py</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="38" 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">

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<td class="diff-line-num new_line" data-linenumber="38" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">gffutils/test/performance_test.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="39" 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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<td class="diff-line-num new new_line" data-linenumber="39" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">gffutils/test/synth_test_base.py</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="39" 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">

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<td class="diff-line-num new_line" data-linenumber="40" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">gffutils/test/test.py</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line" data-linenumber="41" 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">

41

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">gffutils/test/test_biopython_integration.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">gffutils/test/test_merge.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">gffutils/test/test_merge_all.py</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="41" 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">

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<td class="diff-line-num new_line" data-linenumber="44" 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">

44

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">gffutils/test/data/F3-unique-3.v2.gff</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line" data-linenumber="45" 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">

45

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">gffutils/test/data/FBgn0031208.gff</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="43" 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">

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46

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">gffutils/test/data/FBgn0031208.gtf</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" 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="70" 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">@@ -67,6 +70,7 @@ gffutils/test/data/mouse_extra_comma.gff3</td>

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67

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">gffutils/test/data/ncbi_gff3.txt</span>

</pre>

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68

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<td class="diff-line-num new_line" data-linenumber="71" 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">

71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">gffutils/test/data/nonascii</span>

</pre>

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69

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<td class="diff-line-num new_line" data-linenumber="72" 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">

72

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">gffutils/test/data/random-chr.gff</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="73" 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">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">gffutils/test/data/synthetic.gff3</span>

</pre>

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70

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<td class="diff-line-num new_line" data-linenumber="74" 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">

74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">gffutils/test/data/unsanitized.gff</span>

</pre>

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71

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75

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">gffutils/test/data/wormbase_gff2.txt</span>

</pre>

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72

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76

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">gffutils/test/data/wormbase_gff2_alt.txt</span></pre>

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<td class="new_line diff-line-num" 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">\ No newline at end of file</td>

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<br>

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<li id="f150cef205dd7bcb93d9a71c4b130f69cc21b933">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#f150cef205dd7bcb93d9a71c4b130f69cc21b933"><strong>gffutils.egg-info/requires.txt</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pyfaidx</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">six</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">argh</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">argcomplete</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pyfaidx<span class="idiff left right">>=0.5.5.2</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="5" 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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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">six<span class="idiff left right">>=1.12.0</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="5" 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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<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">argh<span class="idiff left right">>=0.26.2</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" 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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<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">argcomplete<span class="idiff left right">>=1.9.4</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">simplejson</span></pre>

</td>

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</table>

<br>

</li>

<li id="df96c16f1a237002b91943103cf457a7a8c81f1a">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#df96c16f1a237002b91943103cf457a7a8c81f1a"><strong>gffutils/attributes.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" 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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<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" 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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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="python">    <span class="n" style="color: #333;">collectionsAbc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abc</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" 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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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" 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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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">    <span class="n" style="color: #333;">collectionsAbc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="8" 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">constants</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="9" 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">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="11" 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">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># collections.MutableMapping is apparently the best way to provide dict-like</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

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<td class="diff-line-num new_line" data-linenumber="12" 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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># interface (http://stackoverflow.com/a/3387975)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Attributes</span><span class="p">(</span><span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MutableMapping</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" 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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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Attributes</span><span class="p">(</span><span class="n" style="color: #333;">collections<span class="idiff left right">Abc</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MutableMapping</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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">

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<td class="diff-line-num new_line" data-linenumber="14" 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">

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<pre style="margin: 0;"> <span id="LC14" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="15" 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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="16" 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">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">        An Attributes object acts much like a dictionary.  However, values are</span></span>

</pre>

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<br>

</li>

<li id="f2a5d823fb26fca72f2fe98667ba1c506c945f11">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#f2a5d823fb26fca72f2fe98667ba1c506c945f11"><strong>gffutils/bins.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" 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="53" 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">@@ -53,6 +53,7 @@ OFFSETS = [</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for BED (0-based, half-open) or GFF (1-based, closed intervals)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="n" style="color: #333;">COORD_OFFSETS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'bed'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'gff'</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="55" 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">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">MAX_CHROM_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">29</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bins</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gff'</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python">    <span class="s" style="color: #d14;">"""</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">@@ -72,6 +73,15 @@ def bins(start, stop, fmt='gff', one=True):</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;">    fmt : 'gff' | 'bed'</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;">        This specifies 1-based start coords (gff) or 0-based start coords (bed)</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># For very large coordinates, return 1 which is "somewhere on the</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># chromosome".</span></span>

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<pre style="margin: 0;">+<span id="LC79" 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="n" style="color: #333;">MAX_CHROM_SIZE</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MAX_CHROM_SIZE</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">one</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">+<span id="LC82" 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="LC83" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">set</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="LC84" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Jump to highest resolution bin that will fit these coords (depending on</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># whether we have a BED or GFF-style coordinate).</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" 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="124" 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">@@ -114,6 +124,7 @@ def bins(start, stop, fmt='gff', one=True):</td>

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<td class="diff-line-num old_line" data-linenumber="114" 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">

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<td class="diff-line-num new_line" data-linenumber="124" 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">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># larger bin size)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" 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">

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<td class="diff-line-num new_line" data-linenumber="125" 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">

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<pre style="margin: 0;"> <span id="LC125" 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;">NEXT_SHIFT</span></span>

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<td class="diff-line-num old_line" data-linenumber="116" 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">

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<td class="diff-line-num new_line" data-linenumber="126" 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">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python">        <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="n" style="color: #333;">NEXT_SHIFT</span></span>

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<td class="diff-line-num new old_line" data-linenumber="117" 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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<td class="diff-line-num new new_line" data-linenumber="127" 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="LC127" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="117" 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">

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<td class="diff-line-num new_line" data-linenumber="128" 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">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bins</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" 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">

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<td class="diff-line-num new_line" data-linenumber="129" 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">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" 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">

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<td class="diff-line-num new_line" data-linenumber="130" 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">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" 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="225" 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">@@ -214,6 +225,12 @@ def test():</td>

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<td class="diff-line-num new_line" data-linenumber="225" 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">

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bins</span><span class="p">(</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;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="215" 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">

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<td class="diff-line-num new_line" data-linenumber="226" 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">

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bins</span><span class="p">(</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;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="216" 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">

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<td class="diff-line-num new_line" data-linenumber="227" 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">

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="217" 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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<td class="diff-line-num new new_line" data-linenumber="228" 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="LC228" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Juuuust fits inside the max chrom size</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="217" 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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<td class="diff-line-num new new_line" data-linenumber="229" 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="LC229" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bins</span><span class="p">(</span><span class="mi" style="color: #099;">536870910</span><span class="p">,</span> <span class="mi" style="color: #099;">536870911</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">8776</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="217" 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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<td class="diff-line-num new new_line" data-linenumber="230" 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="LC230" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="217" 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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<td class="diff-line-num new new_line" data-linenumber="231" 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="LC231" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Too big; falls back to 1.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="217" 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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<td class="diff-line-num new new_line" data-linenumber="232" 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="LC232" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">bins</span><span class="p">(</span><span class="mi" style="color: #099;">536870911</span><span class="p">,</span> <span class="mi" style="color: #099;">536870912</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="217" 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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<td class="diff-line-num new new_line" data-linenumber="233" 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="LC233" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="217" 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">

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<pre style="margin: 0;"> <span id="LC234" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python">    <span class="n" style="color: #333;">print_bin_sizes</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python">    <span class="n" style="color: #333;">test</span><span class="p">()</span></span></pre>

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<br>

</li>

<li id="173d7c6b62d5dfce2fa12bb662e3d7272b1b3bc6">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#173d7c6b62d5dfce2fa12bb662e3d7272b1b3bc6"><strong>gffutils/biopython_integration.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,7 +5,6 @@ objects.</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

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<td class="diff-line-num new_line" data-linenumber="7" 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqFeature</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqFeature</span><span class="p">,</span> <span class="n" style="color: #333;">FeatureLocation</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"BioPython must be installed to use this module"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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="78" 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">@@ -79,4 +78,4 @@ def from_seqfeature(s, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">    <span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'seqid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="80" 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">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">    <span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'frame'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" 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">

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<td class="diff-line-num new_line" data-linenumber="80" 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">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Feature</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">featuretype</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python">                   <span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="n" style="color: #333;">attributes</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="83" 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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<td class="diff-line-num new new_line" data-linenumber="81" 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="LC81" class="line" lang="python">                   <span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="n" style="color: #333;">attributes</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">id</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span></pre>

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</li>

<li id="0fcebaeb967483b2aefccc38ee7038aeb57ed6b6">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#0fcebaeb967483b2aefccc38ee7038aeb57ed6b6"><strong>gffutils/create.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" 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="48" 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">@@ -48,7 +48,7 @@ def deprecation_handler(kwargs):</td>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_DBCreator</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC50" 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;">data</span><span class="p">,</span> <span class="n" style="color: #333;">dbfn</span><span class="p">,</span> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">id_spec</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python">                 <span class="n" style="color: #333;">merge_strategy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">merge</span>'</span><span class="p">,</span> <span class="n" style="color: #333;">checklines</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="python">                 <span class="n" style="color: #333;">merge_strategy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">error</span>'</span><span class="p">,</span> <span class="n" style="color: #333;">checklines</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="52" 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">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">                 <span class="n" style="color: #333;">force_dialect_check</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">from_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">dialect</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">                 <span class="n" style="color: #333;">default_encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="54" 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">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">                 <span class="n" style="color: #333;">disable_infer_genes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" 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="97" 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">@@ -97,7 +97,6 @@ class _DBCreator(object):</td>

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<td class="diff-line-num old_line" data-linenumber="97" 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">

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<pre style="margin: 0;"> <span id="LC97" 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;">disable_infer_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">disable_infer_genes</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC98" 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;">disable_infer_transcripts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">disable_infer_transcripts</span></span>

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<td class="diff-line-num old_line" data-linenumber="99" 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">

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<td class="diff-line-num new_line" data-linenumber="99" 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">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC100" 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;">_autoincrements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="100" 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">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">force</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">dbfn</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">dbfn</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" 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="123" 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">@@ -124,7 +123,10 @@ class _DBCreator(object):</td>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">            <span class="n" style="color: #333;">force_dialect_check</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">force_dialect_check</span><span class="p">,</span> <span class="n" style="color: #333;">from_string</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">from_string</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">            <span class="n" style="color: #333;">dialect</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dialect</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">        <span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="128" 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="LC126" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'_autoincrements'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC127" 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;">_autoincrements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'_autoincrements'</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" 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;">_autoincrements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_verbose</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'debug'</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" 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="209" 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">@@ -207,11 +209,12 @@ class _DBCreator(object):</td>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="s" style="color: #d14;">            Raise error</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="211" 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">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"><span class="s" style="color: #d14;">        "warning"</span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;">            Log a warning</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="211" 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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<td class="diff-line-num new new_line" data-linenumber="212" 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="LC212" class="line" lang="python"><span class="s" style="color: #d14;">            Log a warning, which indicates that all future instances of the</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="213" 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="LC213" class="line" lang="python"><span class="s" style="color: #d14;">            same ID will be ignored</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="214" 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">

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;">        "merge":</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;">            Combine old and new attributes -- but only if everything else</span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;">            matches; otherwise error. <span class="idiff left right"> </span>This can be slow, but is thorough.</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;">            matches; otherwise error. This can be slow, but is thorough.</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;">        "create_unique":</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;">            Autoincrement based on the ID, always creating a new ID.</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">@@ -248,8 +251,8 @@ class _DBCreator(object):</td>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python">                             <span class="o" style="font-weight: 600;">%</span> <span class="p">([</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</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;">_candidate_merges</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)]))</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># If force_merge_fields was provided, don't pay attention to these</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># fields if they're different. <span class="idiff left right"> We are assuming attributes will be</span></span></span>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># different, hence the [:-1]</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># fields if they're different. <span class="idiff left right">We are assuming the attributes field</span></span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">will be </span>different, hence the [:-1]</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">            <span class="n" style="color: #333;">_gffkeys_to_check</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">                <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffkeys</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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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">                <span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</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;">force_merge_fields</span><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">@@ -379,7 +382,7 @@ class _DBCreator(object):</td>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_candidate_merges</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"><span class="s" style="color: #d14;">        Identifies those features that originally had the same ID as `f`</span></span>

</pre>

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382

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<td class="diff-line-num new_line old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"><span class="s" style="color: #d14;">        (according to the id_spec), <span class="idiff left right"> </span>but were modified because of duplicate</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="385" 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="LC385" class="line" lang="python"><span class="s" style="color: #d14;">        (according to the id_spec), but were modified because of duplicate</span></span>

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<td class="diff-line-num new_line" data-linenumber="386" 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">

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"><span class="s" style="color: #d14;">        IDs.</span></span>

</pre>

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384

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<td class="diff-line-num new_line" data-linenumber="387" 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">

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">        <span class="n" style="color: #333;">candidates</span> <span class="o" style="font-weight: 600;">=</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;">_get_feature</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="486" 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -486,7 +489,7 @@ class _DBCreator(object):</td>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'CREATE INDEX seqidstartendstrand ON features (seqid, start, end, strand)'</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="490" 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">

490

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># speeds computation 1000x in some cases</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Running ANALY<span class="idiff left right">S</span>E features"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="492" 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="LC492" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Running ANALY<span class="idiff left right">Z</span>E features"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="493" 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">

493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'ANALYZE features'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="494" 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">

494

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="492" 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">

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<td class="diff-line-num new_line" data-linenumber="495" 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">

495

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<pre style="margin: 0;"> <span id="LC495" 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;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">commit</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="505" 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="508" 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">@@ -505,6 +508,7 @@ class _DBCreator(object):</td>

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505

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<td class="diff-line-num new_line" data-linenumber="508" 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">

508

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<pre style="margin: 0;"> <span id="LC508" 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;">_update_relations</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="509" 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">

509

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<pre style="margin: 0;"> <span id="LC509" 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;">_finalize</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="510" 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">

510

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO: not sure this is used anywhere</span></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">iterator</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC513" 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;">_populate_from_lines</span><span class="p">(</span><span class="n" style="color: #333;">iterator</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC514" 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;">_update_relations</span><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">@@ -645,29 +649,29 @@ class _GFFDBCreator(_DBCreator):</td>

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<pre style="margin: 0;"> <span id="LC649" 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="LC650" class="line" lang="python">            <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.gffutils'</span></span>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python">        <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">suffix</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python">        <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC649" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC650" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Here we look for "grandchildren" -- for each ID, get the child</span></span>

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># (parenthetical subquery below); then for each of those get *its*</span></span>

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># child (main query below).</span></span>

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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Results are written to temp file so that we don't read and write at</span></span>

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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># the same time, which would slow things down considerably.</span></span>

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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC657" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'SELECT id FROM features'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">parent</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC659" class="line" lang="python">            <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>

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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"><span class="s" style="color: #d14;">                       SELECT child FROM relations WHERE parent IN</span></span>

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python"><span class="s" style="color: #d14;">                       (SELECT child FROM relations WHERE parent = ?)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"><span class="s" style="color: #d14;">                       '''</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">grandchild</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c2</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC664" class="line" lang="python">                <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">((</span><span class="n" style="color: #333;">parent</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">grandchild</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python">        <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fout</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Here we look for "grandchildren" -- for each ID, get the child</span></span>

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># (parenthetical subquery below); then for each of those get *its*</span></span>

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># child (main query below).</span></span>

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Results are written to temp file so that we don't read and write at</span></span>

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># the same time, which would slow things down considerably.</span></span>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python">            <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'SELECT id FROM features'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">parent</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python">                <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>

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<td class="diff-line-num new new_line" data-linenumber="664" 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="LC664" class="line" lang="python"><span class="s" style="color: #d14;">                           SELECT child FROM relations WHERE parent IN</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"><span class="s" style="color: #d14;">                           (SELECT child FROM relations WHERE parent = ?)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"><span class="s" style="color: #d14;">                           '''</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="667" 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="LC667" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">grandchild</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="668" 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="LC668" class="line" lang="python">                    <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">((</span><span class="n" style="color: #333;">parent</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">grandchild</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">relations_generator</span><span class="p">():</span></span>

</pre>

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668

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<td class="diff-line-num new_line old" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC668" 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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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669

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="python">                <span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">child</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>

</pre>

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670

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<td class="diff-line-num new_line old" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="672" 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">

672

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<pre style="margin: 0;">+<span id="LC672" 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;">fin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="673" 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="LC673" class="line" lang="python">                    <span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">child</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>

</pre>

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python">                    <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"></span>

</pre>

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672

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<td class="diff-line-num new_line" data-linenumber="676" 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">

676

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">executemany</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="673" 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">

673

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<td class="diff-line-num new_line" data-linenumber="677" 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">

677

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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python">            <span class="s" style="color: #d14;">'''</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="720" 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="724" 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">@@ -720,7 +724,7 @@ class _GTFDBCreator(_DBCreator):</td>

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<td class="diff-line-num old_line" data-linenumber="720" 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">

720

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<td class="diff-line-num new_line" data-linenumber="724" 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">

724

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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python">                    <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="721" 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">

721

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<td class="diff-line-num new_line" data-linenumber="725" 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">

725

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC725" class="line" lang="python">                        <span class="s" style="color: #d14;">"It appears you have a transcript feature in your GTF "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="722" 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">

722

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<td class="diff-line-num new_line" data-linenumber="726" 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">

726

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">                        <span class="s" style="color: #d14;">"file. You may want to use the "</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

723

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<td class="diff-line-num new_line old" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python">                        <span class="s" style="color: #d14;">"`disable_infer_transcripts` "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="724" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="727" 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">

727

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC727" class="line" lang="python">                        <span class="s" style="color: #d14;">"`disable_infer_transcripts<span class="idiff left right">=True</span>` "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="724" 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">

724

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<td class="diff-line-num new_line" data-linenumber="728" 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">

728

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC728" class="line" lang="python">                        <span class="s" style="color: #d14;">"option to speed up database creation"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="725" 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">

725

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<td class="diff-line-num new_line" data-linenumber="729" 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">

729

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC729" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="726" 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">

726

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<td class="diff-line-num new_line" data-linenumber="730" 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">

730

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC730" class="line" lang="python">                    <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'gene'</span> <span class="ow" style="font-weight: 600;">and</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="729" 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="733" 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">@@ -729,7 +733,7 @@ class _GTFDBCreator(_DBCreator):</td>

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<td class="diff-line-num old_line" data-linenumber="729" 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">

729

</td>

<td class="diff-line-num new_line" data-linenumber="733" 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">

733

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC733" class="line" lang="python">                    <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="730" 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">

730

</td>

<td class="diff-line-num 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">

734

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC734" class="line" lang="python">                        <span class="s" style="color: #d14;">"It appears you have a gene feature in your GTF "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="731" 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">

731

</td>

<td class="diff-line-num new_line" data-linenumber="735" 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">

735

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC735" class="line" lang="python">                        <span class="s" style="color: #d14;">"file. You may want to use the "</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

732

</td>

<td class="diff-line-num new_line old" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC732" class="line" lang="python">                        <span class="s" style="color: #d14;">"`disable_infer_genes` "</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="733" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="736" 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">

736

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC736" class="line" lang="python">                        <span class="s" style="color: #d14;">"`disable_infer_genes<span class="idiff left right">=True</span>` "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="733" 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">

733

</td>

<td class="diff-line-num new_line" data-linenumber="737" 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">

737

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC737" class="line" lang="python">                        <span class="s" style="color: #d14;">"option to speed up database creation"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num 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">

734

</td>

<td class="diff-line-num new_line" data-linenumber="738" 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">

738

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC738" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="735" 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">

735

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<td class="diff-line-num new_line" data-linenumber="739" 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">

739

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC739" class="line" lang="python">            <span class="n" style="color: #333;">lines_seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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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">@@ -838,101 +842,64 @@ class _GTFDBCreator(_DBCreator):</td>

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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python">            <span class="n" style="color: #333;">suffix</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;">_keep_tempfiles</span></span>

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<pre style="margin: 0;"> <span id="LC843" 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="LC844" class="line" lang="python">            <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.gffutils'</span></span>

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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python">        <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">suffix</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

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<pre style="margin: 0;">-<span id="LC842" class="line" lang="python">        <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC843" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC844" 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;">_tmpfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span></span>

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<pre style="margin: 0;"> <span id="LC845" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC846" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># This takes some explanation...</span></span>

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<pre style="margin: 0;">-<span id="LC847" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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848

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC848" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># First, the nested subquery gets the level-1 parents of</span></span>

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC849" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># self.subfeature featuretypes.  For an on-spec GTF file,</span></span>

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<pre style="margin: 0;">-<span id="LC850" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># self.subfeature = "exon". So this subquery translates to getting the</span></span>

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<pre style="margin: 0;">-<span id="LC851" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># distinct level-1 parents of exons -- which are transcripts.</span></span>

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<pre style="margin: 0;">-<span id="LC852" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC853" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># OK, so this first subquery is now a list of transcripts; call it</span></span>

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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># "firstlevel".</span></span>

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<pre style="margin: 0;">-<span id="LC855" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC856" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Then join firstlevel on relations, but the trick is to now consider</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

857

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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># each transcript a *child* -- so that relations.parent (on the first</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

858

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># line of the query) will be the first-level parent of the transcript</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

859

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># (the gene).</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

860

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<pre style="margin: 0;">-<span id="LC860" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

861

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

862

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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># The result is something like:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

863

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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

864

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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#   transcript1     gene1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

865

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC865" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#   transcript2     gene1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

866

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC866" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#   transcript3     gene2</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

867

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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

868

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC868" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Note that genes are repeated; below we need to ensure that only one</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

869

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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC869" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># is added.  To ensure this, the results are ordered by the gene ID.</span></span>

</pre>

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870

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<pre style="margin: 0;">-<span id="LC870" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

871

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<pre style="margin: 0;">-<span id="LC871" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># By the way, we do this even if we're only looking for transcripts or</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

872

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<pre style="margin: 0;">-<span id="LC872" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># only looking for genes.</span></span>

</pre>

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846

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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python">        <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">suffix</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="847" 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="LC847" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fout</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="848" 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">

848

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<pre style="margin: 0;">+<span id="LC848" 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;">_tmpfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span></span>

</pre>

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849

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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="850" 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">

850

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<pre style="margin: 0;">+<span id="LC850" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># This takes some explanation...</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="851" 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">

851

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="852" 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">

852

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># First, the nested subquery gets the level-1 parents of</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="853" 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">

853

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># self.subfeature featuretypes.  For an on-spec GTF file,</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="854" 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">

854

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># self.subfeature = "exon". So this subquery translates to getting the</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="855" 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">

855

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<pre style="margin: 0;">+<span id="LC855" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># distinct level-1 parents of exons -- which are transcripts.</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="856" 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">

856

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="857" 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">

857

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># OK, so this first subquery is now a list of transcripts; call it</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="858" 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">

858

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<pre style="margin: 0;">+<span id="LC858" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># "firstlevel".</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="859" 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">

859

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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="860" 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">

860

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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Then join firstlevel on relations, but the trick is to now consider</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="861" 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">

861

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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># each transcript a *child* -- so that relations.parent (on the first</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="873" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="862" 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">

862

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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># line of the query) will be the first-level parent of the transcript</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="873" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="863" 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">

863

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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># (the gene).</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="864" 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">

864

</td>

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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="873" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="865" 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">

865

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<pre style="margin: 0;">+<span id="LC865" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="873" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="866" 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">

866

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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># The result is something like:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="867" 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">

867

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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#   transcript1     gene1</span></span>

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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#   transcript2     gene1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC870" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#   transcript3     gene2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC871" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC872" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Note that genes are repeated; below we need to ensure that only one</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC873" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># is added.  To ensure this, the results are ordered by the gene ID.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># By the way, we do this even if we're only looking for transcripts or</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># only looking for genes.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC874" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC875" class="line" lang="python">            <span class="s" style="color: #d14;">'''</span></span>

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<pre style="margin: 0;">-<span id="LC876" class="line" lang="python"><span class="s" style="color: #d14;">            SELECT DISTINCT firstlevel.parent, relations.parent</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC877" class="line" lang="python"><span class="s" style="color: #d14;">            FROM (</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python"><span class="s" style="color: #d14;">                SELECT DISTINCT parent</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"><span class="s" style="color: #d14;">                FROM relations</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"><span class="s" style="color: #d14;">                JOIN features ON features.id = relations.child</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC881" class="line" lang="python"><span class="s" style="color: #d14;">                WHERE features.featuretype = ?</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC882" class="line" lang="python"><span class="s" style="color: #d14;">                AND relations.level = 1</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC883" class="line" lang="python"><span class="s" style="color: #d14;">            )</span></span>

</pre>

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884

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<pre style="margin: 0;">-<span id="LC884" class="line" lang="python"><span class="s" style="color: #d14;">            AS firstlevel</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

885

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC885" class="line" lang="python"><span class="s" style="color: #d14;">            JOIN relations ON firstlevel.parent = child</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

886

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC886" class="line" lang="python"><span class="s" style="color: #d14;">            WHERE relations.level = 1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

887

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC887" class="line" lang="python"><span class="s" style="color: #d14;">            ORDER BY relations.parent</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

888

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC888" class="line" lang="python"><span class="s" style="color: #d14;">            '''</span><span class="p">,</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;">subfeature</span><span class="p">,))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

889

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC889" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

890

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC890" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Now we iterate through those results (using a new cursor) to infer</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

891

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC891" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># the extent of transcripts and/or genes.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

892

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC892" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

893

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<pre style="margin: 0;">-<span id="LC893" class="line" lang="python">        <span class="n" style="color: #333;">last_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

894

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC894" class="line" lang="python">        <span class="n" style="color: #333;">n_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

895

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC895" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">transcript_id</span><span class="p">,</span> <span class="n" style="color: #333;">gene_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

896

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC896" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

897

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC897" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">disable_infer_transcripts</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

898

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC898" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># transcript extent</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

899

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC899" class="line" lang="python">                <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

900

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC900" class="line" lang="python">                    <span class="s" style="color: #d14;">'''</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

901

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC901" class="line" lang="python"><span class="s" style="color: #d14;">                    SELECT MIN(start), MAX(end), strand, seqid</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

902

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC902" class="line" lang="python"><span class="s" style="color: #d14;">                    FROM features</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

903

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC903" class="line" lang="python"><span class="s" style="color: #d14;">                    JOIN relations ON</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

904

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</td>

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<pre style="margin: 0;">-<span id="LC904" class="line" lang="python"><span class="s" style="color: #d14;">                    features.id = relations.child</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

905

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC905" class="line" lang="python"><span class="s" style="color: #d14;">                    WHERE parent = ? AND featuretype == ?</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

906

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC906" class="line" lang="python"><span class="s" style="color: #d14;">                    '''</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_id</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;">subfeature</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

907

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC907" class="line" lang="python">                <span class="n" style="color: #333;">transcript_start</span><span class="p">,</span> <span class="n" style="color: #333;">transcript_end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetchone</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

908

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC908" class="line" lang="python">                <span class="n" style="color: #333;">transcript_attributes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

909

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC909" 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;">transcript_key</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333;">transcript_id</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

910

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC910" 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;">gene_key</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

911

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC911" class="line" lang="python">                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

912

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<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC912" class="line" lang="python">                <span class="n" style="color: #333;">transcript_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bins</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

913

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC913" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_start</span><span class="p">,</span> <span class="n" style="color: #333;">transcript_end</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

914

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC914" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

915

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC915" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Write out to file; we'll be reading it back in shortly.  Omit</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

916

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC916" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># score, frame, source, and extra since they will always have</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

917

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC917" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># the same default values (".", ".", "gffutils_derived", and []</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

918

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC918" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># respectively)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

919

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC919" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

920

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC920" class="line" lang="python">                <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="p">[</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

921

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC921" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_id</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

922

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC922" class="line" lang="python">                    <span class="n" style="color: #333;">seqid</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

923

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC923" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_start</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

924

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC924" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_end</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

925

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC925" class="line" lang="python">                    <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

926

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC926" class="line" lang="python">                    <span class="s" style="color: #d14;">'transcript'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

927

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC927" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_bin</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

928

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC928" class="line" lang="python">                    <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_jsonify</span><span class="p">(</span><span class="n" style="color: #333;">transcript_attributes</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

929

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC929" class="line" lang="python">                <span class="p">]))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

930

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC930" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

931

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC931" class="line" lang="python">                <span class="n" style="color: #333;">n_features</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

932

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC932" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

933

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC933" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">disable_infer_genes</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

934

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC934" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Infer gene extent, but only if we haven't done so already</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

935

</td>

<td class="diff-line-num new_line old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC935" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">last_gene_id</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="878" 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">

878

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC878" class="line" lang="python">            <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="879" 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">

879

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC879" class="line" lang="python">                <span class="s" style="color: #d14;">'''</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="880" 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">

880

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"><span class="s" style="color: #d14;">                SELECT DISTINCT firstlevel.parent, relations.parent</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="881" 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">

881

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"><span class="s" style="color: #d14;">                FROM (</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="882" 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">

882

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"><span class="s" style="color: #d14;">                    SELECT DISTINCT parent</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="883" 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">

883

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"><span class="s" style="color: #d14;">                    FROM relations</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="884" 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">

884

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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"><span class="s" style="color: #d14;">                    JOIN features ON features.id = relations.child</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="885" 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">

885

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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python"><span class="s" style="color: #d14;">                    WHERE features.featuretype = ?</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="886" 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">

886

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC886" class="line" lang="python"><span class="s" style="color: #d14;">                    AND relations.level = 1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="887" 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">

887

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<pre style="margin: 0;">+<span id="LC887" class="line" lang="python"><span class="s" style="color: #d14;">                )</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="888" 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">

888

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<pre style="margin: 0;">+<span id="LC888" class="line" lang="python"><span class="s" style="color: #d14;">                AS firstlevel</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="889" 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">

889

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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"><span class="s" style="color: #d14;">                JOIN relations ON firstlevel.parent = child</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="890" 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">

890

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<pre style="margin: 0;">+<span id="LC890" class="line" lang="python"><span class="s" style="color: #d14;">                WHERE relations.level = 1</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="891" 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">

891

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"><span class="s" style="color: #d14;">                ORDER BY relations.parent</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="892" 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">

892

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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"><span class="s" style="color: #d14;">                '''</span><span class="p">,</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;">subfeature</span><span class="p">,))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="893" 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">

893

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="894" 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">

894

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<pre style="margin: 0;">+<span id="LC894" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Now we iterate through those results (using a new cursor) to infer</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="895" 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">

895

</td>

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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># the extent of transcripts and/or genes.</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="896" 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">

896

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="897" 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">

897

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC897" class="line" lang="python">            <span class="n" style="color: #333;">last_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="898" 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">

898

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC898" class="line" lang="python">            <span class="n" style="color: #333;">n_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="899" 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">

899

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC899" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">transcript_id</span><span class="p">,</span> <span class="n" style="color: #333;">gene_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="900" 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">

900

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC900" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="901" 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">

901

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC901" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">disable_infer_transcripts</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="936" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="902" 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">

902

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC902" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># transcript extent</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="936" 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">

936

</td>

<td class="diff-line-num new_line" data-linenumber="903" 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">

903

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC903" class="line" lang="python">                    <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="937" 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">

937

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<td class="diff-line-num new_line" data-linenumber="904" 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">

904

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<pre style="margin: 0;"> <span id="LC904" class="line" lang="python">                        <span class="s" style="color: #d14;">'''</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="938" 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">

938

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<td class="diff-line-num new_line" data-linenumber="905" 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">

905

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<pre style="margin: 0;"> <span id="LC905" class="line" lang="python"><span class="s" style="color: #d14;">                        SELECT MIN(start), MAX(end), strand, seqid</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="940" 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="907" 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">@@ -940,26 +907,61 @@ class _GTFDBCreator(_DBCreator):</td>

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<td class="diff-line-num old_line" data-linenumber="940" 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">

940

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<td class="diff-line-num new_line" data-linenumber="907" 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">

907

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<pre style="margin: 0;"> <span id="LC907" class="line" lang="python"><span class="s" style="color: #d14;">                        JOIN relations ON</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="941" 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">

941

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<td class="diff-line-num new_line" data-linenumber="908" 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">

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<pre style="margin: 0;"> <span id="LC908" class="line" lang="python"><span class="s" style="color: #d14;">                        features.id = relations.child</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="942" 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">

942

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<td class="diff-line-num new_line" data-linenumber="909" 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">

909

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<pre style="margin: 0;"> <span id="LC909" class="line" lang="python"><span class="s" style="color: #d14;">                        WHERE parent = ? AND featuretype == ?</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

943

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<td class="diff-line-num new_line old" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC943" class="line" lang="python"><span class="s" style="color: #d14;">                        '''</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">gene_id</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;">subfeature</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

944

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<td class="diff-line-num new_line old" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC944" class="line" lang="python">                    <span class="n" style="color: #333;">gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">gene_end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetchone</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

945

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<td class="diff-line-num new_line old" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC945" class="line" lang="python">                    <span class="n" style="color: #333;">gene_attributes</span> <span class="o" style="font-weight: 600;">=</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;">gene_key</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

946

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<td class="diff-line-num new_line old" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC946" class="line" lang="python">                    <span class="n" style="color: #333;">gene_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bins</span><span class="p">(</span><span class="n" style="color: #333;">gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">gene_end</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="910" 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">

910

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<pre style="margin: 0;">+<span id="LC910" class="line" lang="python"><span class="s" style="color: #d14;">                        '''</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_id</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;">subfeature</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="911" 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">

911

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<pre style="margin: 0;">+<span id="LC911" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_start</span><span class="p">,</span> <span class="n" style="color: #333;">transcript_end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetchone</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="912" 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">

912

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<pre style="margin: 0;">+<span id="LC912" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_attributes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="913" 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">

913

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<pre style="margin: 0;">+<span id="LC913" 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;">transcript_key</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333;">transcript_id</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="914" 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">

914

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<pre style="margin: 0;">+<span id="LC914" 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;">gene_key</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="915" 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">

915

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<pre style="margin: 0;">+<span id="LC915" class="line" lang="python">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="916" 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">

916

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<pre style="margin: 0;">+<span id="LC916" class="line" lang="python">                    <span class="n" style="color: #333;">transcript_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bins</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="917" 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">

917

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC917" class="line" lang="python">                        <span class="n" style="color: #333;">transcript_start</span><span class="p">,</span> <span class="n" style="color: #333;">transcript_end</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="918" 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">

918

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC918" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="919" 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">

919

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC919" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Write out to file; we'll be reading it back in shortly.  Omit</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="920" 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">

920

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC920" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># score, frame, source, and extra since they will always have</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="921" 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">

921

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC921" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># the same default values (".", ".", "gffutils_derived", and []</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="947" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="922" 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">

922

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC922" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># respectively)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="947" 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">

947

</td>

<td class="diff-line-num new_line" data-linenumber="923" 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">

923

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC923" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="948" 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">

948

</td>

<td class="diff-line-num new_line" data-linenumber="924" 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">

924

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC924" class="line" lang="python">                    <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="p">[</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

949

</td>

<td class="diff-line-num new_line old" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC949" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">gene</span>_id</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="950" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="925" 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">

925

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC925" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">transcript</span>_id</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="950" 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">

950

</td>

<td class="diff-line-num new_line" data-linenumber="926" 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">

926

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC926" class="line" lang="python">                        <span class="n" style="color: #333;">seqid</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

951

</td>

<td class="diff-line-num new_line old" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC951" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">gene</span>_start</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

952

</td>

<td class="diff-line-num new_line old" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC952" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">gene</span>_end</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="953" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="927" 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">

927

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC927" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">transcript</span>_start</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="953" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="928" 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">

928

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC928" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">transcript</span>_end</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="953" 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">

953

</td>

<td class="diff-line-num new_line" data-linenumber="929" 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">

929

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC929" class="line" lang="python">                        <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

954

</td>

<td class="diff-line-num new_line old" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC954" class="line" lang="python">                        <span class="s" style="color: #d14;">'<span class="idiff left right">gene</span>'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

955

</td>

<td class="diff-line-num new_line old" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC955" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">gene</span>_bin</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

956

</td>

<td class="diff-line-num new_line old" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC956" class="line" lang="python">                        <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_jsonify</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">gene</span>_attributes</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="957" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="930" 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">

930

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC930" class="line" lang="python">                        <span class="s" style="color: #d14;">'<span class="idiff left right">transcript</span>'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="957" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="931" 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">

931

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC931" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">transcript</span>_bin</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="957" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="932" 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">

932

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC932" class="line" lang="python">                        <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_jsonify</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">transcript</span>_attributes</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="957" 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">

957

</td>

<td class="diff-line-num new_line" data-linenumber="933" 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">

933

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC933" class="line" lang="python">                    <span class="p">]))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="958" 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">

958

</td>

<td class="diff-line-num new_line" data-linenumber="934" 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">

934

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC934" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

959

</td>

<td class="diff-line-num new_line old" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC959" class="line" lang="python">                <span class="n" style="color: #333;">last_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

960

</td>

<td class="diff-line-num new_line old" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC960" class="line" lang="python">                <span class="n" style="color: #333;">n_features</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="961" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="935" 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">

935

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC935" class="line" lang="python">                    <span class="n" style="color: #333;">n_features</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="961" 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">

961

</td>

<td class="diff-line-num new_line" data-linenumber="936" 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">

936

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC936" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

962

</td>

<td class="diff-line-num new_line old" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC962" class="line" lang="python">        <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="937" 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">

937

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC937" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">disable_infer_genes</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="938" 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">

938

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC938" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Infer gene extent, but only if we haven't done so already</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="939" 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">

939

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC939" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">last_gene_id</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="940" 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">

940

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC940" class="line" lang="python">                        <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="941" 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">

941

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC941" class="line" lang="python">                            <span class="s" style="color: #d14;">'''</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="942" 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">

942

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC942" class="line" lang="python"><span class="s" style="color: #d14;">                            SELECT MIN(start), MAX(end), strand, seqid</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="943" 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">

943

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC943" class="line" lang="python"><span class="s" style="color: #d14;">                            FROM features</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="944" 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">

944

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC944" class="line" lang="python"><span class="s" style="color: #d14;">                            JOIN relations ON</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="945" 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">

945

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC945" class="line" lang="python"><span class="s" style="color: #d14;">                            features.id = relations.child</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="946" 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">

946

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<pre style="margin: 0;">+<span id="LC946" class="line" lang="python"><span class="s" style="color: #d14;">                            WHERE parent = ? AND featuretype == ?</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="947" 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">

947

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC947" class="line" lang="python"><span class="s" style="color: #d14;">                            '''</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">gene_id</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;">subfeature</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="948" 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">

948

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC948" class="line" lang="python">                        <span class="n" style="color: #333;">gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">gene_end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetchone</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="949" 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">

949

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<pre style="margin: 0;">+<span id="LC949" class="line" lang="python">                        <span class="n" style="color: #333;">gene_attributes</span> <span class="o" style="font-weight: 600;">=</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;">gene_key</span><span class="p">:</span> <span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="950" 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">

950

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<pre style="margin: 0;">+<span id="LC950" class="line" lang="python">                        <span class="n" style="color: #333;">gene_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bins</span><span class="p">(</span><span class="n" style="color: #333;">gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">gene_end</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="951" 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">

951

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC951" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="952" 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">

952

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC952" class="line" lang="python">                        <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="953" 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">

953

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<pre style="margin: 0;">+<span id="LC953" class="line" lang="python">                            <span class="n" style="color: #333;">gene_id</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="954" 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">

954

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<pre style="margin: 0;">+<span id="LC954" class="line" lang="python">                            <span class="n" style="color: #333;">seqid</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="955" 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">

955

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC955" class="line" lang="python">                            <span class="n" style="color: #333;">gene_start</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="956" 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">

956

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC956" class="line" lang="python">                            <span class="n" style="color: #333;">gene_end</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="957" 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">

957

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC957" class="line" lang="python">                            <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="958" 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">

958

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC958" class="line" lang="python">                            <span class="s" style="color: #d14;">'gene'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="959" 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">

959

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC959" class="line" lang="python">                            <span class="n" style="color: #333;">gene_bin</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="960" 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">

960

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC960" class="line" lang="python">                            <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_jsonify</span><span class="p">(</span><span class="n" style="color: #333;">gene_attributes</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="961" 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">

961

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC961" class="line" lang="python">                        <span class="p">]))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="962" 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">

962

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC962" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="963" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="963" 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">

963

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC963" class="line" lang="python">                    <span class="n" style="color: #333;">last_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC964" class="line" lang="python">                    <span class="n" style="color: #333;">n_features</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC965" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC966" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">derived_feature_generator</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="967" 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">

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<pre style="margin: 0;"> <span id="LC967" class="line" lang="python">            <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="967" 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="969" 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">@@ -967,17 +969,18 @@ class _GTFDBCreator(_DBCreator):</td>

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<pre style="margin: 0;"> <span id="LC969" class="line" lang="python"><span class="s" style="color: #d14;">            """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC970" class="line" lang="python">            <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'parent'</span><span class="p">,</span> <span class="s" style="color: #d14;">'seqid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">,</span> <span class="s" style="color: #d14;">'end'</span><span class="p">,</span> <span class="s" style="color: #d14;">'strand'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="971" 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">

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<pre style="margin: 0;"> <span id="LC971" class="line" lang="python">                    <span class="s" style="color: #d14;">'featuretype'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bin'</span><span class="p">,</span> <span class="s" style="color: #d14;">'attributes'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC970" 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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC971" class="line" lang="python">                <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">,</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>

</pre>

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<pre style="margin: 0;">-<span id="LC972" class="line" lang="python">                <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'parent'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC973" class="line" lang="python">                <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'score'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC974" class="line" lang="python">                <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'source'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'gffutils_derived'</span></span>

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<pre style="margin: 0;">-<span id="LC975" class="line" lang="python">                <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'frame'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC976" class="line" lang="python">                <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'extra'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC977" class="line" lang="python">                <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'attributes'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_unjsonify</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'attributes'</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC978" class="line" lang="python">                <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Feature</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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979

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<td class="diff-line-num new_line old" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC979" class="line" lang="python">                <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</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;">_id_handler</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

980

</td>

<td class="diff-line-num new_line old" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC980" class="line" lang="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">f</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="972" 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">

972

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC972" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fin</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="973" 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">

973

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC973" 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;">fin</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="974" 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">

974

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC974" class="line" lang="python">                    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">,</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="975" 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">

975

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC975" class="line" lang="python">                    <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'parent'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="976" 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">

976

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC976" class="line" lang="python">                    <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'score'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="977" 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">

977

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC977" class="line" lang="python">                    <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'source'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'gffutils_derived'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="978" 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">

978

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC978" class="line" lang="python">                    <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'frame'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="979" 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">

979

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC979" class="line" lang="python">                    <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'extra'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="980" 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">

980

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC980" class="line" lang="python">                    <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'attributes'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_unjsonify</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'attributes'</span><span class="p">])</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="981" 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">

981

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC981" class="line" lang="python">                    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Feature</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="982" 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">

982

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC982" class="line" lang="python">                    <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</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;">_id_handler</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="981" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="983" 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">

983

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC983" class="line" lang="python">                    <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">f</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="981" 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">

981

</td>

<td class="diff-line-num new_line" data-linenumber="984" 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">

984

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC984" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="982" 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">

982

</td>

<td class="diff-line-num new_line" data-linenumber="985" 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">

985

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC985" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Drop the indexes so the inserts are faster</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="983" 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">

983

</td>

<td class="diff-line-num new_line" data-linenumber="986" 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">

986

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<pre style="margin: 0;"> <span id="LC986" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'DROP INDEX IF EXISTS relationsparent'</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1009" 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="1012" 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">@@ -1009,7 +1012,8 @@ class _GTFDBCreator(_DBCreator):</td>

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1009

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<td class="diff-line-num new_line" data-linenumber="1012" 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">

1012

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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_keep_tempfiles</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="1010" 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">

1010

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<td class="diff-line-num new_line" data-linenumber="1013" 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">

1013

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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1011" 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">

1011

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<td class="diff-line-num new_line" data-linenumber="1014" 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">

1014

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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1012

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<td class="diff-line-num new_line old" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO: recreate indexes?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1013" 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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<td class="diff-line-num new new_line" data-linenumber="1015" 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">

1015

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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO: recreate indexes? Typically the _finalize() method will be</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1013" 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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<td class="diff-line-num new new_line" data-linenumber="1016" 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">

1016

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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># called after this one, and indexes are created in _finalize().</span></span>

</pre>

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1013

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<td class="diff-line-num new_line" data-linenumber="1017" 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">

1017

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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="1014" 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">

1014

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<td class="diff-line-num new_line" data-linenumber="1018" 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">

1018

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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="python"></span>

</pre>

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1015

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1019

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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">dbfn</span><span class="p">,</span> <span class="n" style="color: #333;">id_spec</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<br>

</li>

<li id="82bd271c739c9bc8738fd7c0b57257d6db9d00a2">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#82bd271c739c9bc8738fd7c0b57257d6db9d00a2"><strong>gffutils/feature.py</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span></span>

</pre>

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2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">json</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">constants</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">helpers</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parser</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" 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="145" 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">@@ -145,7 +145,7 @@ class Feature(object):</td>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python">                <span class="n" style="color: #333;">attributes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_unjsonify</span><span class="p">(</span><span class="n" style="color: #333;">attributes</span><span class="p">,</span> <span class="n" style="color: #333;">isattributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># it's a string but not JSON: assume original attributes string.</span></span>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;"><span class="idiff left right">simple</span>json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">JSONDecodeError</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="149" 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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<td class="diff-line-num new new_line" data-linenumber="148" 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="LC148" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">JSONDecodeError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="150" 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">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># But Feature.attributes is still a dict</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python">                <span class="n" style="color: #333;">attributes</span><span class="p">,</span> <span class="n" style="color: #333;">_dialect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_split_keyvals</span><span class="p">(</span><span class="n" style="color: #333;">attributes</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="159" 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">@@ -159,7 +159,7 @@ class Feature(object):</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">extra</span><span class="p">,</span> <span class="n" style="color: #333;">six</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">string_types</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="161" 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">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">                <span class="n" style="color: #333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_unjsonify</span><span class="p">(</span><span class="n" style="color: #333;">extra</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;"><span class="idiff left right">simple</span>json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">JSONDecodeError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="163" 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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<td class="diff-line-num new new_line" data-linenumber="162" 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="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">JSONDecodeError</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="163" 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">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">                <span class="n" style="color: #333;">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extra</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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<td class="diff-line-num new_line" data-linenumber="164" 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">

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="165" 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">

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<td class="diff-line-num new_line" data-linenumber="165" 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">

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<pre style="margin: 0;"> <span id="LC165" 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;">seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqid</span></span>

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<br>

</li>

<li id="04cef6b8c6f04a6fd3441ac29249595f331a082f">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#04cef6b8c6f04a6fd3441ac29249595f331a082f"><strong>gffutils/helpers.py</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>

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<pre style="margin: 0;"> <span id="LC2" 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="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">json</span></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="256" 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">@@ -256,16 +256,16 @@ def _bin_from_dict(d):</td>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_jsonify</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">    <span class="s" style="color: #d14;">"""Use most compact form of JSON"""</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">dict_class</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">simple</span>json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_d</span><span class="p">,</span> <span class="n" style="color: #333;">separators</span><span class="o" style="font-weight: 600;">=</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>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">simple</span>json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">separators</span><span class="o" style="font-weight: 600;">=</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>

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<td class="diff-line-num new old_line" data-linenumber="261" 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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<td class="diff-line-num new new_line" data-linenumber="259" 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="LC259" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_d</span><span class="p">,</span> <span class="n" style="color: #333;">separators</span><span class="o" style="font-weight: 600;">=</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="261" 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="LC260" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">separators</span><span class="o" style="font-weight: 600;">=</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>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_unjsonify</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">isattributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">    <span class="s" style="color: #d14;">"""Convert JSON string to an ordered defaultdict."""</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isattributes</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python">        <span class="n" style="color: #333;">obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">simple</span>json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python">        <span class="n" style="color: #333;">obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dict_class</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">simple</span>json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_feature_to_fields</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">jsonify</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><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">@@ -318,7 +318,7 @@ def merge_attributes(attr1, attr2):</td>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python">    <span class="n" style="color: #333;">new_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">attr1</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python">    <span class="n" style="color: #333;">new_d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">attr2</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python">    <span class="n" style="color: #333;">new_d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">copy</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">deepcopy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">attr2</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#all of attr2 key : values just overwrote attr1, fix it</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python">                <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">v</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python">            <span class="n" style="color: #333;">new_d</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">list</span></span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">())</span></span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">sorted</span></span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dialect_compare</span><span class="p">(</span><span class="n" style="color: #333;">dialect1</span><span class="p">,</span> <span class="n" style="color: #333;">dialect2</span><span class="p">):</span></span>

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<li id="3b56c7dca7a21095a405dffc855f81a640cda2f3">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#3b56c7dca7a21095a405dffc855f81a640cda2f3"><strong>gffutils/inspection.py</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">iterators</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">interface</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>

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<pre style="margin: 0;">-<span id="LC4" 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="LC5" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">inspect</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">look_for</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'featuretype'</span><span class="p">,</span> <span class="s" style="color: #d14;">'chrom'</span><span class="p">,</span> <span class="s" style="color: #d14;">'attribute_keys'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python">                            <span class="s" style="color: #d14;">'feature_count'</span><span class="p">],</span> <span class="n" style="color: #333;">limit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">    Inspect a GFF or GTF data source.</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">    This function is useful for figuring out the different featuretypes found</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">    in a file (for potential removal before creating a FeatureDB).</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">    Returns a dictionary with a key for each item in `look_for` and</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">    a corresponding value that is a dictionary of how many of each unique item</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">    were found.</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">    There will always be a `feature_count` key, indicating how many features</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">    were looked at (if `limit` is provided, then `feature_count` will be the</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">    same as `limit`).</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">    For example, if `look_for` is ['chrom', 'featuretype'], then the result</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">    will be a dictionary like::</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">        {</span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;">            'chrom': {</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">                'chr1': 500,</span></span>

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29

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</td>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">                'chr2': 435,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">                'chr3': 200,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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</td>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;">                ...</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;">                ...</span></span>

</pre>

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33

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">            }.</span></span>

</pre>

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34

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

35

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">            'featuretype': {</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">                'gene': 150,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">                'exon': 324,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">                ...</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">            },</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;">            'feature_count': 5000</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;">        }</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;">    data : str, FeatureDB instance, or iterator of Features</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;">        If `data` is a string, assume it's a GFF or GTF filename.  If it's</span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">        a FeatureDB instance, then its `all_features()` method will be</span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;">        automatically called. Otherwise, assume it's an iterable of Feature</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;">        objects.</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;">    look_for : list</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;">        List of things to keep track of. Options are:</span></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="s" style="color: #d14;">            - any attribute of a Feature object, such as chrom, source, start,</span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;">              stop, strand.</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;">            - "attribute_keys", which will look at all the individual</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;">              attribute keys of each feature</span></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;">    limit : int</span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;">        Number of features to look at.  Default is no limit.</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;">    verbose : bool</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">        Report how many features have been processed.</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;">    -------</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;">    dict</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python">    <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python">    <span class="n" style="color: #333;">obj_attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">look_for</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</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;">'attribute_keys'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feature_count'</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">            <span class="n" style="color: #333;">obj_attrs</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;">i</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python">        <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counter</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">attr_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'attribute_keys'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">look_for</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iterators</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataIterator</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python">    <span class="n" style="color: #333;">feature_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\r</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s features inspected'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">feature_count</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obj_attr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">obj_attrs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python">            <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">obj_attr</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">([</span><span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">obj_attr</span><span class="p">)])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">attr_keys</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python">            <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">'attribute_keys'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">        <span class="n" style="color: #333;">feature_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">limit</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">feature_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">limit</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python">    <span class="n" style="color: #333;">new_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python">        <span class="n" style="color: #333;">new_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python">    <span class="n" style="color: #333;">new_results</span><span class="p">[</span><span class="s" style="color: #d14;">'feature_count'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature_count</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

105

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_results</span></span></pre>

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<br>

</li>

<li id="fddb19e520264cff8743df915666b073884bef60">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#fddb19e520264cff8743df915666b073884bef60"><strong>gffutils/interface.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="1" 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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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sqlite3</span></span>

</pre>

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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">@@ -6,10 +7,62 @@ import warnings</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bins</span></span>

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<td class="diff-line-num new_line" data-linenumber="8" 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">helpers</span></span>

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<td class="diff-line-num new_line" data-linenumber="9" 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">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">constants</span></span>

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<td class="diff-line-num new old_line" data-linenumber="9" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">merge_criteria</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mc</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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">

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<td class="diff-line-num new_line" data-linenumber="11" 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">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils.feature</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Feature</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

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<td class="diff-line-num new_line" data-linenumber="12" 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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FeatureNotFoundError</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

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<td class="diff-line-num new_line" data-linenumber="14" 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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">assign_child</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">child</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="python"><span class="s" style="color: #d14;">    Helper for add_relation()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="python"><span class="s" style="color: #d14;">    Sets 'Parent' attribute to parent['ID']</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="python"><span class="s" style="color: #d14;">    parent : Feature</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">        Parent Feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">    :param parent: parent Feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">    child : Feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="29" 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">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">        Child Feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;">    -------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="python"><span class="s" style="color: #d14;">    Child Feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="35" 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="LC35" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="python">    <span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Parent'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span><span class="p">[</span><span class="s" style="color: #d14;">'ID'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="37" 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">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">child</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="38" 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">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="39" 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">

39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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="LC40" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Reusable constant for FeatureDB.merge()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="41" 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">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">no_children</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="42" 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">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_finalize_merge</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">feature_children</span><span class="p">):</span></span>

</pre>

</td>

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44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;">    Helper for FeatureDB.merge() to update source and assign children property</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="47" 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">

47

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="48" 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">

48

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="49" 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="LC49" class="line" lang="python"><span class="s" style="color: #d14;">    feature : Feature</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="50" 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">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">        feature to finalise</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="51" 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">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="52" 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">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;">    feature_children</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="53" 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">

53

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;">        list of children to assign</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="54" 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">

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;">    </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" 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="LC55" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="56" 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="LC56" class="line" lang="python"><span class="s" style="color: #d14;">    -------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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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<td class="diff-line-num new new_line" data-linenumber="57" 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="LC57" class="line" lang="python"><span class="s" style="color: #d14;">    feature, modified</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" 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="LC59" 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;">feature_children</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>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python">        <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</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="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">source</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">feature_children</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" 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="LC61" class="line" lang="python">        <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature_children</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">        <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">no_children</span></span>

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<td class="diff-line-num new new_line" data-linenumber="64" 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="LC64" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">feature</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FeatureDB</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="LC67" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># docstring to be filled in for methods that call out to</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># helpers.make_query()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" 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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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">            <span class="s" style="color: #d14;">'''</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;">            SELECT base, n FROM autoincrements</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;">            '''</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC150" 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;">_autoincrements</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">dict</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC203" 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;">_autoincrements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">collections</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">defaultdict</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC205" 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;">set_pragmas</span><span class="p">(</span><span class="n" style="color: #333;">pragmas</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="604" 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="657" 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">@@ -604,17 +657,15 @@ class FeatureDB(object):</td>

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Only use bins if we have defined boundaries and completely_within is</span></span>

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># True. Otherwise you can't know how far away a feature stretches</span></span>

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<td class="diff-line-num new_line" data-linenumber="659" 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">

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># (which means bins are not computable ahead of time)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python">        <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">completely_within</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

608

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python">            <span class="n" style="color: #333;">_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bins</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

609

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># See issue #45</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

610

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC610" 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;">_bins</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">900</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

611

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python">                <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' or '</span> <span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'bin = ?'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">_bins</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

612

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python">                <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'AND ( </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;">_bin_clause</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

613

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python">                <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">_bins</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

614

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

615

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python">                <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

616

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

617

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC617" class="line" lang="python">            <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="618" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="662" 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">

662

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<pre style="margin: 0;">+<span id="LC662" 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="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MAX_CHROM_SIZE</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MAX_CHROM_SIZE</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="618" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="663" 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">

663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python">                <span class="n" style="color: #333;">_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bins</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="618" 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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<td class="diff-line-num new new_line" data-linenumber="664" 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">

664

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># See issue #45</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="618" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="665" 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">

665

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<pre style="margin: 0;">+<span id="LC665" 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;">_bins</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">900</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="618" 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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<td class="diff-line-num new new_line" data-linenumber="666" 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">

666

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python">                    <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' or '</span> <span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'bin = ?'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">_bins</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python">                    <span class="n" style="color: #333;">_bin_clause</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'AND ( </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;">_bin_clause</span></span>

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python">                    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">_bins</span></span>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python">        <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</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>

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python">            <span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_SELECT</span><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">@@ -662,11 +713,9 @@ class FeatureDB(object):</td>

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"><span class="s" style="color: #d14;">        Providing N features will return N - 1 new features.</span></span>

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"><span class="s" style="color: #d14;">        This method purposefully does *not* do any merging or sorting of</span></span>

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python"><span class="s" style="color: #d14;">        coordinates, so you may want to use :meth:`FeatureDB.merge` first.</span></span>

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC667" class="line" lang="python"><span class="s" style="color: #d14;">        The new features' attributes will be a merge of the neighboring</span></span>

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="python"><span class="s" style="color: #d14;">        features' attributes.  This is useful if you have provided a list of</span></span>

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="python"><span class="s" style="color: #d14;">        exons; the introns will then retain the transcript and/or gene parents.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python"><span class="s" style="color: #d14;">        coordinates, so you may want to use :meth:`FeatureDB.merge` first, or</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"><span class="s" style="color: #d14;">        when selecting features use the `order_by` kwarg, e.g.,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"><span class="s" style="color: #d14;">        `db.features_of_type('gene', order_by=('seqid', 'start'))`.</span></span>

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="727" 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">@@ -678,6 +727,14 @@ class FeatureDB(object):</td>

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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"><span class="s" style="color: #d14;">            then the featuretypes will be constructed from the neighboring</span></span>

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<td class="diff-line-num new_line" data-linenumber="728" 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">

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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"><span class="s" style="color: #d14;">            features, e.g., `inter_exon_exon`.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC729" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="730" 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="LC730" class="line" lang="python"><span class="s" style="color: #d14;">        merge_attributes : bool</span></span>

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<td class="diff-line-num new new_line" data-linenumber="731" 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="LC731" class="line" lang="python"><span class="s" style="color: #d14;">            If True, new features' attributes will be a merge of the neighboring</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="732" 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="LC732" class="line" lang="python"><span class="s" style="color: #d14;">            features' attributes.  This is useful if you have provided a list of</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="733" 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="LC733" class="line" lang="python"><span class="s" style="color: #d14;">            exons; the introns will then retain the transcript and/or gene</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="734" 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="LC734" class="line" lang="python"><span class="s" style="color: #d14;">            parents as a single item. Otherwise, if False, the attribute will</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="735" 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="LC735" class="line" lang="python"><span class="s" style="color: #d14;">            be a comma-separated list of values, potentially listing the same</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="736" 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="LC736" class="line" lang="python"><span class="s" style="color: #d14;">            gene ID twice.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="737" 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="LC737" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="738" 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">

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<pre style="margin: 0;"> <span id="LC738" class="line" lang="python"><span class="s" style="color: #d14;">        attribute_func : callable or None</span></span>

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<td class="diff-line-num new_line" data-linenumber="739" 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">

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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"><span class="s" style="color: #d14;">            If None, then nothing special is done to the attributes.  If</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="740" 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">

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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python"><span class="s" style="color: #d14;">            callable, then the callable accepts two attribute dictionaries and</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="762" 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">@@ -705,9 +762,21 @@ class FeatureDB(object):</td>

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<pre style="margin: 0;"> <span id="LC762" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">new_featuretype</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python">                <span class="n" style="color: #333;">new_featuretype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'inter_</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;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC764" class="line" lang="python">                    <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span></span>

</pre>

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709

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<td class="diff-line-num new_line old" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC709" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

710

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<td class="diff-line-num new_line old" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC710" class="line" lang="python">            <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="765" 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">

765

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<pre style="margin: 0;">+<span id="LC765" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="766" 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">

766

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<pre style="margin: 0;">+<span id="LC766" class="line" lang="python">                <span class="n" style="color: #333;">new_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="767" 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">

767

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<pre style="margin: 0;">+<span id="LC767" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="768" 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">

768

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<pre style="margin: 0;">+<span id="LC768" class="line" lang="python">                <span class="n" style="color: #333;">new_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="769" 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">

769

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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="770" 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">

770

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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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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<td class="diff-line-num new new_line" data-linenumber="771" 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">

771

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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># We've moved to a new chromosome.  For example, if we're</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="772" 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">

772

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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># getting intergenic regions from all genes, they will be on</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="773" 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">

773

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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># different chromosomes. We still assume sorted features, but</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="774" 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">

774

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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># don't complain if they're on different chromosomes -- just</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="775" 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">

775

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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># move on.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="776" 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">

776

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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python">                <span class="n" style="color: #333;">last_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="777" 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">

777

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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="778" 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">

778

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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="711" 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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<td class="diff-line-num new new_line" data-linenumber="779" 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">

779

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<pre style="margin: 0;">+<span id="LC779" class="line" lang="python">            <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_strand</span></span>

</pre>

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711

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<td class="diff-line-num new_line" data-linenumber="780" 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">

780

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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python">            <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span></span>

</pre>

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<td class="diff-line-num 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">

712

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<td class="diff-line-num new_line" data-linenumber="781" 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">

781

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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="713" 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">

713

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<td class="diff-line-num new_line" data-linenumber="782" 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">

782

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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Shrink</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" 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="817" 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">@@ -748,6 +817,7 @@ class FeatureDB(object):</td>

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<td class="diff-line-num old_line" data-linenumber="748" 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">

748

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<td class="diff-line-num new_line" data-linenumber="817" 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">

817

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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python">                    <span class="n" style="color: #333;">dialect</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="749" 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">

749

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<td class="diff-line-num new_line" data-linenumber="818" 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">

818

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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_feature_returner</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">fields</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="750" 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">

750

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<td class="diff-line-num new_line" data-linenumber="819" 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">

819

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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python">            <span class="n" style="color: #333;">interfeature_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="751" 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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<td class="diff-line-num new new_line" data-linenumber="820" 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">

820

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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python">            <span class="n" style="color: #333;">last_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="751" 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">

751

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<td class="diff-line-num new_line" data-linenumber="821" 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">

821

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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="752" 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">

752

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<td class="diff-line-num new_line" data-linenumber="822" 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">

822

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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">delete</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">,</span> <span class="n" style="color: #333;">make_backup</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="753" 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">

753

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<td class="diff-line-num 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">

823

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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="797" 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="867" 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">@@ -797,7 +867,19 @@ class FeatureDB(object):</td>

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<td class="diff-line-num old_line" data-linenumber="797" 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">

797

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<td class="diff-line-num new_line" data-linenumber="867" 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">

867

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<pre style="margin: 0;"> <span id="LC867" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="798" 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">

798

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<td class="diff-line-num new_line" data-linenumber="868" 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">

868

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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">make_backup</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="799" 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">

799

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<td class="diff-line-num new_line" data-linenumber="869" 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">

869

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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

800

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<td class="diff-line-num new_line old" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC800" class="line" lang="python"><span class="s" style="color: #d14;">        Update database with features in `data`.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="870" 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">

870

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<pre style="margin: 0;">+<span id="LC870" class="line" lang="python"><span class="s" style="color: #d14;">        Update the on-disk database with features in `data`.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="871" 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">

871

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<pre style="margin: 0;">+<span id="LC871" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="872" 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">

872

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<pre style="margin: 0;">+<span id="LC872" class="line" lang="python"><span class="s" style="color: #d14;">        WARNING: If you used any non-default kwargs for gffutils.create_db when</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="873" 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">

873

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<pre style="margin: 0;">+<span id="LC873" class="line" lang="python"><span class="s" style="color: #d14;">        creating the database in the first place (especially</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="874" 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="LC874" class="line" lang="python"><span class="s" style="color: #d14;">        `disable_infer_transcripts` or `disable_infer_genes`) then you should</span></span>

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python"><span class="s" style="color: #d14;">        use those same arguments here.</span></span>

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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC877" class="line" lang="python"><span class="s" style="color: #d14;">        The returned object is the same FeatureDB, but since it is pointing to</span></span>

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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python"><span class="s" style="color: #d14;">        the same database and that has been just updated, the new features can</span></span>

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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"><span class="s" style="color: #d14;">        now be accessed.</span></span>

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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"><span class="s" style="color: #d14;">        data : str, iterable, FeatureDB instance</span></span>

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"><span class="s" style="color: #d14;">            If FeatureDB, all data will be used. If string, assume it's</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">@@ -810,15 +892,15 @@ class FeatureDB(object):</td>

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<pre style="margin: 0;"> <span id="LC892" class="line" lang="python"><span class="s" style="color: #d14;">            makes a copy of the existing database and saves it with a .bak</span></span>

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<pre style="margin: 0;"> <span id="LC893" class="line" lang="python"><span class="s" style="color: #d14;">            extension.</span></span>

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"><span class="s" style="color: #d14;">        Notes</span></span>

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<pre style="margin: 0;">-<span id="LC814" class="line" lang="python"><span class="s" style="color: #d14;">        -----</span></span>

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<pre style="margin: 0;">-<span id="LC815" class="line" lang="python"><span class="s" style="color: #d14;">        Other kwargs are used in the same way as in gffutils.create_db; see the</span></span>

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<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;">        help for that function for details.</span></span>

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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"><span class="s" style="color: #d14;">        kwargs :</span></span>

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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"><span class="s" style="color: #d14;">            Additional kwargs are passed to gffutils.create_db; see the help</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="817" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="897" 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">

897

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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"><span class="s" style="color: #d14;">            for that function for details.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="817" 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">

817

</td>

<td class="diff-line-num new_line" data-linenumber="898" 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">

898

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC898" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="818" 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">

818

</td>

<td class="diff-line-num new_line" data-linenumber="899" 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">

899

</td>

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<pre style="margin: 0;"> <span id="LC899" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="819" 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">

819

</td>

<td class="diff-line-num new_line" data-linenumber="900" 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">

900

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<pre style="margin: 0;"> <span id="LC900" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

820

</td>

<td class="diff-line-num new_line old" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC820" class="line" lang="python"><span class="s" style="color: #d14;">        <span class="idiff left right">FeatureDB with updated features</span>.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="821" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="901" 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">

901

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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"><span class="s" style="color: #d14;">        <span class="idiff left right">Returns self but with the underlying database updated</span>.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="821" 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">

821

</td>

<td class="diff-line-num new_line" data-linenumber="902" 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">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="822" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="903" 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">

903

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC903" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="822" 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">

822

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<td class="diff-line-num new_line" data-linenumber="904" 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">

904

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<pre style="margin: 0;"> <span id="LC904" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">create</span></span>

</pre>

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<td class="diff-line-num 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">

823

</td>

<td class="diff-line-num new_line" data-linenumber="905" 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">

905

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC905" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">iterators</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="824" 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">

824

</td>

<td class="diff-line-num new_line" data-linenumber="906" 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">

906

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<pre style="margin: 0;"> <span id="LC906" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">make_backup</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="833" 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="915" 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">@@ -833,6 +915,7 @@ class FeatureDB(object):</td>

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<td class="diff-line-num old_line" data-linenumber="833" 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">

833

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<td class="diff-line-num new_line" data-linenumber="915" 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">

915

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC915" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="834" 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">

834

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<td class="diff-line-num new_line" data-linenumber="916" 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">

916

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<pre style="margin: 0;"> <span id="LC916" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Handle all sorts of input</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="835" 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">

835

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<td class="diff-line-num new_line" data-linenumber="917" 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">

917

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<pre style="margin: 0;"> <span id="LC917" class="line" lang="python">        <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iterators</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataIterator</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">_iterator_kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="836" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="918" 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">

918

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<pre style="margin: 0;">+<span id="LC918" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'_autoincrements'</span><span class="p">]</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;">_autoincrements</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="836" 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">

836

</td>

<td class="diff-line-num new_line" data-linenumber="919" 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">

919

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC919" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="837" 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">

837

</td>

<td class="diff-line-num new_line" data-linenumber="920" 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">

920

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC920" 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;">dialect</span><span class="p">[</span><span class="s" style="color: #d14;">'fmt'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'gtf'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="838" 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">

838

</td>

<td class="diff-line-num new_line" data-linenumber="921" 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">

921

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC921" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'id_spec'</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;">kwargs</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="849" 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="932" 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">@@ -849,10 +932,18 @@ class FeatureDB(object):</td>

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<td class="diff-line-num old_line" data-linenumber="849" 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">

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<td class="diff-line-num new_line" data-linenumber="932" 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">

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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="850" 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">

850

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<td class="diff-line-num new_line" data-linenumber="933" 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">

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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="851" 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">

851

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<td class="diff-line-num new_line" data-linenumber="934" 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">

934

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<pre style="margin: 0;"> <span id="LC934" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="852" 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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<td class="diff-line-num new new_line" data-linenumber="935" 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">

935

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<pre style="margin: 0;">+<span id="LC935" class="line" lang="python">        <span class="n" style="color: #333;">peek</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iterators</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">peek</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_iter</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="852" 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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<td class="diff-line-num new new_line" data-linenumber="936" 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">

936

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<pre style="margin: 0;">+<span id="LC936" 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;">peek</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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">db</span>  <span class="c1" style="color: #998; font-style: italic;"># If the file is empty then do nothing</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="852" 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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<td class="diff-line-num new new_line" data-linenumber="937" 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">

937

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<pre style="margin: 0;">+<span id="LC937" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="852" 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">

852

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<td class="diff-line-num new_line" data-linenumber="938" 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">

938

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<pre style="margin: 0;"> <span id="LC938" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_populate_from_lines</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="853" 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">

853

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<td class="diff-line-num new_line" data-linenumber="939" 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">

939

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<pre style="margin: 0;"> <span id="LC939" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_update_relations</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="854" 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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<td class="diff-line-num new new_line" data-linenumber="940" 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">

940

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC940" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="854" 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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<td class="diff-line-num new new_line" data-linenumber="941" 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">

941

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<pre style="margin: 0;">+<span id="LC941" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Note that the autoincrements gets updated here</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="854" 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">

854

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<td class="diff-line-num new_line" data-linenumber="942" 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">

942

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<pre style="margin: 0;"> <span id="LC942" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_finalize</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

855

</td>

<td class="diff-line-num new_line old" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC855" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">db</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="856" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="943" 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">

943

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<pre style="margin: 0;">+<span id="LC943" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="856" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="944" 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">

944

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<pre style="margin: 0;">+<span id="LC944" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Read it back in directly from the stored autoincrements table</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="856" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="945" 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">

945

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<pre style="margin: 0;">+<span id="LC945" 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;">_autoincrements</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="856" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="946" 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">

946

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<pre style="margin: 0;">+<span id="LC946" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="856" 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">

856

</td>

<td class="diff-line-num new_line" data-linenumber="947" 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">

947

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC947" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="857" 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">

857

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<pre style="margin: 0;"> <span id="LC948" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_relation</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="p">,</span> <span class="n" style="color: #333;">parent_func</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="858" 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">

858

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<td class="diff-line-num new_line" data-linenumber="949" 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">

949

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<pre style="margin: 0;"> <span id="LC949" class="line" lang="python">                     <span class="n" style="color: #333;">child_func</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1000" 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="1091" 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">@@ -1000,8 +1091,11 @@ class FeatureDB(object):</td>

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<td class="diff-line-num old_line" data-linenumber="1000" 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">

1000

</td>

<td class="diff-line-num new_line" data-linenumber="1091" 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">

1091

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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="python">            <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1001" 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">

1001

</td>

<td class="diff-line-num new_line" data-linenumber="1092" 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">

1092

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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">intron</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1002" 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">

1002

</td>

<td class="diff-line-num new_line" data-linenumber="1093" 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">

1093

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1093" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1003

</td>

<td class="diff-line-num new_line old" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_strand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1004" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1094" 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="LC1094" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">_old_</span>merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_strand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1004" 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">

1004

</td>

<td class="diff-line-num new_line" data-linenumber="1095" 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">

1095

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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1005" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1096" 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">

1096

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1096" class="line" lang="python"><span class="s" style="color: #d14;">        DEPRECATED, only retained here for backwards compatibility. Please use</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1005" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1097" 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">

1097

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1097" class="line" lang="python"><span class="s" style="color: #d14;">        merge().</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1005" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1098" 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">

1098

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1098" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1005" 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">

1005

</td>

<td class="diff-line-num new_line" data-linenumber="1099" 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">

1099

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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="python"><span class="s" style="color: #d14;">        Merge overlapping features together.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1006" 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">

1006

</td>

<td class="diff-line-num new_line" data-linenumber="1100" 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">

1100

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1100" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1007" 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">

1007

</td>

<td class="diff-line-num new_line" data-linenumber="1101" 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">

1101

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1101" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1095" 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="1189" 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">@@ -1095,6 +1189,197 @@ class FeatureDB(object):</td>

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<td class="diff-line-num old_line" data-linenumber="1095" 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">

1095

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<td class="diff-line-num new_line" data-linenumber="1189" 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">

1189

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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="python">            <span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1096" 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">

1096

</td>

<td class="diff-line-num new_line" data-linenumber="1190" 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">

1190

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1190" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_feature_returner</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">merged_feature</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1097" 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">

1097

</td>

<td class="diff-line-num new_line" data-linenumber="1191" 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">

1191

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1191" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1192" 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">

1192

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1192" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python">              <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_end_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="python">              <span class="n" style="color: #333;">multiline</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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1196

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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="python"><span class="s" style="color: #d14;">        Merge features matching criteria together</span></span>

</pre>

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1198

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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="python"><span class="s" style="color: #d14;">        Returned Features have a special property called 'children' that is</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="python"><span class="s" style="color: #d14;">        a list of the component features.  This only exists for the lifetime of</span></span>

</pre>

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1202

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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="python"><span class="s" style="color: #d14;">        the Feature instance.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="python"></span>

</pre>

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1204

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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1206" 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="LC1206" class="line" lang="python"><span class="s" style="color: #d14;">        features : iterable</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1207" 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="LC1207" class="line" lang="python"><span class="s" style="color: #d14;">            Iterable of Feature instances to merge</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1208" 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="LC1208" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1209" 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="LC1209" class="line" lang="python"><span class="s" style="color: #d14;">        merge_criteria : list</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="python"><span class="s" style="color: #d14;">            List of merge criteria callbacks. All must evaluate to True in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="python"><span class="s" style="color: #d14;">            order for a feature to be merged. See notes below on callback</span></span>

</pre>

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1212

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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="python"><span class="s" style="color: #d14;">            signature.</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1213" 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">

1213

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1213" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1214" 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">

1214

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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="python"><span class="s" style="color: #d14;">        multiline : bool</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1215" 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">

1215

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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="python"><span class="s" style="color: #d14;">            True to emit multiple features with the same ID attribute, False</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1216" 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">

1216

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1216" class="line" lang="python"><span class="s" style="color: #d14;">            otherwise.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1217" 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">

1217

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1217" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1218" 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">

1218

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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1219" 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">

1219

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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1220" 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">

1220

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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="python"><span class="s" style="color: #d14;">        Generator yielding merged Features</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1221" 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">

1221

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1221" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1222" 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">

1222

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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="python"><span class="s" style="color: #d14;">        Notes</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1223" 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">

1223

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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="python"><span class="s" style="color: #d14;">        -----</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1224" 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">

1224

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1224" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1225" 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">

1225

</td>

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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="python"><span class="s" style="color: #d14;">        See the `gffutils.merge_criteria` module (imported here as `mc`) for</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1226" 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">

1226

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1226" class="line" lang="python"><span class="s" style="color: #d14;">        existing callback functions. For writing custom callbacks, functions</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1227" 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">

1227

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1227" class="line" lang="python"><span class="s" style="color: #d14;">        must have the following signature::</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1228" 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">

1228

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1228" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1229" 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">

1229

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1229" class="line" lang="python"><span class="s" style="color: #d14;">            callback(</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1230" 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">

1230

</td>

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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="python"><span class="s" style="color: #d14;">                acc: gffutils.Feature,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1231" 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">

1231

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1231" class="line" lang="python"><span class="s" style="color: #d14;">                cur: gffutils.Feature,</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1232" 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">

1232

</td>

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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="python"><span class="s" style="color: #d14;">                components: [gffutils.Feature]</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="1233" 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">

1233

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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="python"><span class="s" style="color: #d14;">            ) -> bool</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1234" 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">

1234

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1234" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1235" 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">

1235

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1235" class="line" lang="python"><span class="s" style="color: #d14;">        Where:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1236" 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">

1236

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1236" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1237" 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">

1237

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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="python"><span class="s" style="color: #d14;">            - `acc`: current accumulated feature</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1238" 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">

1238

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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="python"><span class="s" style="color: #d14;">            - `cur`: candidate feature to merge</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1239" 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">

1239

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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="python"><span class="s" style="color: #d14;">            - `components`: list of features that compose acc</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1240" 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">

1240

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1240" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1241" 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">

1241

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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="python"><span class="s" style="color: #d14;">        The function should return True to merge `cur` into `acc`, False to set</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1242" 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">

1242

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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="python"><span class="s" style="color: #d14;">        `cur` to `acc` (that is, start a new merged feature).</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1243" 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">

1243

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1243" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1244" 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">

1244

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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1245" 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">

1245

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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="python"><span class="s" style="color: #d14;">        If merge criteria allows different feature types then the merged</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1246" 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">

1246

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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="python"><span class="s" style="color: #d14;">        features' feature types should have their featuretype property</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1247" 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">

1247

</td>

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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="python"><span class="s" style="color: #d14;">        reassigned to a more specific ontology value.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1248" 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">

1248

</td>

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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1249" 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">

1249

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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">merge_criteria</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1250" 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">

1250

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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1251" 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">

1251

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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="python">                <span class="n" style="color: #333;">merge_criteria</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">merge_criteria</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1252" 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">

1252

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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1253" 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">

1253

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1253" class="line" lang="python">                <span class="n" style="color: #333;">merge_criteria</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">merge_criteria</span><span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1254" 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">

1254

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1254" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1255" 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">

1255

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1255" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># To start, we create a merged feature of just the first feature.</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1256" 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">

1256

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1256" class="line" lang="python">        <span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">features</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1257" 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">

1257

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1257" class="line" lang="python">        <span class="n" style="color: #333;">last_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1258" 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">

1258

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1258" class="line" lang="python">        <span class="n" style="color: #333;">current_merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1259" 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">

1259

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1259" class="line" lang="python">        <span class="n" style="color: #333;">feature_children</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1260" 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">

1260

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1260" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1261" 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">

1261

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1261" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">features</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1262" 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">

1262

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1262" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">current_merged</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1263" 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">

1263

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1263" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">criteria</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">feature_children</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">criteria</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">merge_criteria</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1264" 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">

1264

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1264" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1265" 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">

1265

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1265" class="line" lang="python">                    <span class="n" style="color: #333;">feature_children</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1266" 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">

1266

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1266" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1267" 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">

1267

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1267" class="line" lang="python">                    <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">_finalize_merge</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">no_children</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1268" 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">

1268

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1268" class="line" lang="python">                    <span class="n" style="color: #333;">last_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1269" 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">

1269

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1269" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1270" 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">

1270

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1270" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1271" 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">

1271

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<pre style="margin: 0;">+<span id="LC1271" 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;">feature_children</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 class="c1" style="color: #998; font-style: italic;"># current_merged is last feature and unchecked</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1272" 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">

1272

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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">criteria</span><span class="p">(</span><span class="n" style="color: #333;">current_merged</span><span class="p">,</span> <span class="n" style="color: #333;">current_merged</span><span class="p">,</span> <span class="n" style="color: #333;">feature_children</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">criteria</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">merge_criteria</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1273" 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">

1273

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1273" class="line" lang="python">                    <span class="n" style="color: #333;">feature_children</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;">current_merged</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1274" 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">

1274

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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1275" 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">

1275

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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="python">                    <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">_finalize_merge</span><span class="p">(</span><span class="n" style="color: #333;">current_merged</span><span class="p">,</span> <span class="n" style="color: #333;">no_children</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1276" 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">

1276

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1276" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1277" 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">

1277

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1277" class="line" lang="python">                    <span class="n" style="color: #333;">last_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1278" 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">

1278

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1278" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1279" 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">

1279

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1279" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1280" 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">

1280

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1280" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">criteria</span><span class="p">(</span><span class="n" style="color: #333;">current_merged</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">feature_children</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">criteria</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">merge_criteria</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1281" 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">

1281

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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Criteria satisfied, merge</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1282" 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">

1282

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1282" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># TODO Test multiline records and iron out the following code</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1283" 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">

1283

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1283" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># if multiline and (feature.start > current_merged.end + 1 or feature.end + 1 < current_merged.start):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1284" 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">

1284

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1284" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#    # Feature is possibly multiline (discontiguous), keep ID but start new record</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1285" 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">

1285

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1285" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#    yield _finalize_merge(current_merged, feature_children)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1286" 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">

1286

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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#    current_merged = feature</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1287" 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">

1287

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1287" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#    feature_children = [feature]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1288" 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">

1288

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1288" class="line" lang="python"></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1289" 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">

1289

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<pre style="margin: 0;">+<span id="LC1289" 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;">feature_children</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1290" 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">

1290

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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Current merged is only child and merge is going to occur, make copy</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1291" 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">

1291

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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">(</span><span class="n" style="color: #333;">current_merged</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1292" 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">

1292

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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">current_merged</span><span class="p">[</span><span class="s" style="color: #d14;">'attributes'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1293" 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">

1293

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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">current_merged</span><span class="p">[</span><span class="s" style="color: #d14;">'extra'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1294" 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">

1294

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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">current_merged</span><span class="p">[</span><span class="s" style="color: #d14;">'dialect'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1295" 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">

1295

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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">current_merged</span><span class="p">[</span><span class="s" style="color: #d14;">'keep_order'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1296" 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">

1296

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1296" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">current_merged</span><span class="p">[</span><span class="s" style="color: #d14;">'sort_attribute_values'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1297" 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">

1297

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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</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;">_feature_returner</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">current_merged</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1298" 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">

1298

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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">last_id</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1299" 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">

1299

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1299" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Generate unique ID for new Feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1300" 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">

1300

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1300" 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;">_autoincrements</span><span class="p">[</span><span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1301" 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">

1301

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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="python">                        <span class="n" style="color: #333;">last_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1302" 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">

1302

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1302" 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;">_autoincrements</span><span class="p">[</span><span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1303" 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">

1303

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1303" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</span><span class="p">[</span><span class="s" style="color: #d14;">'ID'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_id</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1304" 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">

1304

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1304" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_id</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1305" 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">

1305

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1305" class="line" lang="python"></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1306" 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">

1306

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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="python">                <span class="n" style="color: #333;">feature_children</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;">feature</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1307" 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">

1307

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1307" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1308" 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">

1308

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1308" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Set mismatched properties to ambiguous values</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1309" 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">

1309

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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</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;">current_merged</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">):</span> <span class="n" style="color: #333;">current_merged</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="s" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1310" 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">

1310

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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">:</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1311" 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">

1311

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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span><span class="p">:</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1312" 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">

1312

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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span><span class="p">:</span> <span class="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"sequence_feature"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1313" 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">

1313

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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1314" 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">

1314

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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</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;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1315" 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">

1315

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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Extends prior, so set a new start position</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1316" 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">

1316

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1316" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</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;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1317" 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">

1317

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1317" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1318" 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">

1318

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1318" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</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="n" style="color: #333;">current_merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1319" 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">

1319

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1319" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Extends further, so set a new stop position</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1320" 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">

1320

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1320" class="line" lang="python">                    <span class="n" style="color: #333;">current_merged</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="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1321" 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">

1321

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1321" class="line" lang="python"></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1322" 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="LC1322" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1323" 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">

1323

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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">_finalize_merge</span><span class="p">(</span><span class="n" style="color: #333;">current_merged</span><span class="p">,</span> <span class="n" style="color: #333;">feature_children</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1324" 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">

1324

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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="python">                <span class="n" style="color: #333;">current_merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1325" 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">

1325

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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="python">                <span class="n" style="color: #333;">feature_children</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1326" 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">

1326

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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="python">                <span class="n" style="color: #333;">last_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1327" 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">

1327

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1327" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1328" 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">

1328

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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">current_merged</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1329" 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">

1329

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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">_finalize_merge</span><span class="p">(</span><span class="n" style="color: #333;">current_merged</span><span class="p">,</span> <span class="n" style="color: #333;">feature_children</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1330" 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">

1330

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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1331" 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">

1331

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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge_all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1332" 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">

1332

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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="python">                  <span class="n" style="color: #333;">merge_order</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'seqid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'featuretype'</span><span class="p">,</span> <span class="s" style="color: #d14;">'strand'</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1333" 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">

1333

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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="python">                  <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_end_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">),</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1334" 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">

1334

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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="python">                  <span class="n" style="color: #333;">featuretypes_groups</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1335" 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">

1335

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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="python">                  <span class="n" style="color: #333;">exclude_components</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1336" 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">

1336

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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1337" 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="LC1337" class="line" lang="python"><span class="s" style="color: #d14;">        Merge all features in database according to criteria.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1338" 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="LC1338" class="line" lang="python"><span class="s" style="color: #d14;">        Merged features will be assigned as children of the merged record.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1339" 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="LC1339" class="line" lang="python"><span class="s" style="color: #d14;">        The resulting records are added to the database.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1340" 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">

1340

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1340" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1341" 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">

1341

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1341" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1342" 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">

1342

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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1343" 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">

1343

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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="python"><span class="s" style="color: #d14;">        merge_order : list</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1344" 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">

1344

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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="python"><span class="s" style="color: #d14;">            Ordered list of columns with which to group features before evaluating criteria</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1345" 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">

1345

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1345" class="line" lang="python"><span class="s" style="color: #d14;">        merge_criteria : list</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1346" 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">

1346

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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="python"><span class="s" style="color: #d14;">            List of merge criteria callbacks. See merge().</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1347" 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">

1347

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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="python"><span class="s" style="color: #d14;">        featuretypes_groups : list</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1348" 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">

1348

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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="python"><span class="s" style="color: #d14;">            iterable of sets of featuretypes to merge together</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1349" 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">

1349

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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="python"><span class="s" style="color: #d14;">        exclude_components : bool</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1350" 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">

1350

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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="python"><span class="s" style="color: #d14;">            True: child features will be discarded. False to keep them.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1351" 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">

1351

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1351" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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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<td class="diff-line-num new new_line" data-linenumber="1352" 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">

1352

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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1353" 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">

1353

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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1354" 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">

1354

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1354" class="line" lang="python"><span class="s" style="color: #d14;">            list of merge features</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1355" 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">

1355

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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1356" 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">

1356

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1356" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1357" 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">

1357

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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">featuretypes_groups</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1358" 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">

1358

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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Can't be empty</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1359" 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">

1359

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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="python">            <span class="n" style="color: #333;">featuretypes_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1360" 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">

1360

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1360" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1361" 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">

1361

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1361" class="line" lang="python">        <span class="n" style="color: #333;">result_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1362" 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">

1362

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1362" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1363" 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">

1363

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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Merge features per featuregroup</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1364" 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">

1364

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1364" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">featuregroup</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">featuretypes_groups</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1365" 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">

1365

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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">merged</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;">merge</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;">all_features</span><span class="p">(</span><span class="n" style="color: #333;">featuretype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">featuregroup</span><span class="p">,</span> <span class="n" style="color: #333;">order_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">merge_order</span><span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1366" 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">

1366

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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="python">                                <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">merge_criteria</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1367" 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">

1367

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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># If feature is result of merge</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1368" 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">

1368

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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1369" 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">

1369

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<pre style="margin: 0;">+<span id="LC1369" 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;">_insert</span><span class="p">(</span><span class="n" style="color: #333;">merged</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;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cursor</span><span class="p">())</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1370" 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">

1370

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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">exclude_components</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1371" 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="LC1371" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Remove child features from DB</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1372" 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">

1372

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1372" 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;">delete</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1373" 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">

1373

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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1374" 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">

1374

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1374" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Add child relations to DB</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1375" 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">

1375

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1375" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">merged</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1376" 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">

1376

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<pre style="margin: 0;">+<span id="LC1376" 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;">add_relation</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">child_func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">assign_child</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1377" 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">

1377

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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="python">                    <span class="n" style="color: #333;">result_features</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;">merged</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1378" 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">

1378

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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1379" 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">

1379

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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span>  <span class="c1" style="color: #998; font-style: italic;"># Do nothing, feature is already in DB</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1380" 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">

1380

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1380" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1381" 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">

1381

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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result_features</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1098" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1382" 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">

1382

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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1098" 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">

1098

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<td class="diff-line-num new_line" data-linenumber="1383" 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">

1383

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<pre style="margin: 0;"> <span id="LC1383" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">children_bp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">child_featuretype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'exon'</span><span class="p">,</span> <span class="n" style="color: #333;">merge</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1099" 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">

1099

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<td class="diff-line-num new_line" data-linenumber="1384" 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">

1384

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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="python">                    <span class="n" style="color: #333;">ignore_strand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1100" 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">

1100

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<td class="diff-line-num new_line" data-linenumber="1385" 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">

1385

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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<br>

</li>

<li id="4596c28d6a9f80cdb433781b12bc2aafe91349e1">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#4596c28d6a9f80cdb433781b12bc2aafe91349e1"><strong>gffutils/iterators.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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="115" 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">@@ -115,6 +115,7 @@ class _FileIterator(_BaseIterator):</td>

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<td class="diff-line-num old_line" data-linenumber="115" 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">

115

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<td class="diff-line-num new_line" data-linenumber="115" 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">

115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;">    Subclass for iterating over features provided as a filename</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" 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">

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<td class="diff-line-num new_line" data-linenumber="116" 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">

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="117" 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">

117

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<td class="diff-line-num new_line" data-linenumber="117" 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">

117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open_function</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" 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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<td class="diff-line-num new new_line" data-linenumber="118" 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">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" 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">

118

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<td class="diff-line-num new_line" data-linenumber="119" 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">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" 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">

119

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<td class="diff-line-num new_line" data-linenumber="120" 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">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">            <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" 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">

120

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<td class="diff-line-num new_line" data-linenumber="121" 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">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" 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="131" 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">@@ -130,7 +131,7 @@ class _FileIterator(_BaseIterator):</td>

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<td class="diff-line-num old_line" data-linenumber="130" 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">

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<td class="diff-line-num new_line" data-linenumber="131" 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">

131

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<pre style="margin: 0;"> <span id="LC131" 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;">current_item_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>

</pre>

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131

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>

</pre>

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132

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'##FASTA'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python">                <span class="k" style="font-weight: 600;">r<span class="idiff left">aise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">StopIteratio</span>n</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="python">                <span class="k" style="font-weight: 600;">r<span class="idiff left right">etur</span>n</span></span>

</pre>

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134

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<td class="diff-line-num new_line" data-linenumber="135" 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">

135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" 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">

135

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<td class="diff-line-num new_line" data-linenumber="136" 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">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'##'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" 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">

136

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<td class="diff-line-num new_line" data-linenumber="137" 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">

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<pre style="margin: 0;"> <span id="LC137" 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;">_directive_handler</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="03d1eb2b3cf6671d3e39cac6e5cc741a6ea809df">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#03d1eb2b3cf6671d3e39cac6e5cc741a6ea809df"><strong>gffutils/merge_criteria.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Merge criteria used by FeatureDB merge() and merge_all()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils.feature</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Feature</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" 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="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur</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;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">strand</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="13" 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">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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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;">feature_type</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" 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">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" 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">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exact_coordinates_only</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">cur</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;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">overlap_end_inclusive</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</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;">cur</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;">acc</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="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">overlap_start_inclusive</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</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;">cur</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">acc</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="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" 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">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">overlap_any_inclusive</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</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;">cur</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;">acc</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="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">acc</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;">cur</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">acc</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="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="35" 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="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">overlap_end_threshold</span><span class="p">(</span><span class="n" style="color: #333;">threshold</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">partial</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="37" 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">

37

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</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;">cur</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;">acc</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="n" style="color: #333;">threshold</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="38" 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">

38

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">partial</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="39" 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">

39

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" 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">

40

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" 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">

41

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">overlap_start_threshold</span><span class="p">(</span><span class="n" style="color: #333;">threshold</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" 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">

42

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">partial</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" 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">

43

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">acc</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;">threshold</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">cur</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">acc</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="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="44" 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">

44

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">partial</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="48" 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="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">overlap_any_threshold</span><span class="p">(</span><span class="n" style="color: #333;">threshold</span><span class="p">):</span></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;">partial</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">components</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="n" style="color: #333;">acc</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;">threshold</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">cur</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">acc</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="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">acc</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;">cur</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;">acc</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="n" style="color: #333;">threshold</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">partial</span></span></pre>

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<br>

</li>

<li id="95b5bb48b2a3ee493756e3ff8ac8f419724555fd">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#95b5bb48b2a3ee493756e3ff8ac8f419724555fd"><strong>gffutils/parser.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" 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">@@ -152,6 +152,8 @@ def _reconstruct(keyvals, dialect, keep_order=False,</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Typically "=" for GFF3 or " " otherwise</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">                <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dialect</span><span class="p">[</span><span class="s" style="color: #d14;">'keyval separator'</span><span class="p">]</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;">key</span><span class="p">,</span> <span class="n" style="color: #333;">val_str</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC155" 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="LC156" class="line" lang="python">                <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span></span>

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<pre style="margin: 0;"> <span id="LC157" 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="LC158" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dialect</span><span class="p">[</span><span class="s" style="color: #d14;">'fmt'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'gtf'</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="159" 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">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">                <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dialect</span><span class="p">[</span><span class="s" style="color: #d14;">'keyval separator'</span><span class="p">]</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;">key</span><span class="p">,</span> <span class="s" style="color: #d14;">'""'</span><span class="p">])</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" 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="324" 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">@@ -322,6 +324,7 @@ def _split_keyvals(keyval_str, dialect=None):</td>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Pathological cases where values of a key have within them the key-val</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># separator, e.g.,</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#  Alias=SGN-M1347;ID=T0028;Note=marker name(s): T0028 SGN-M1347 |identity=99.58|escore=2e-126</span></span>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#                                                                         ^            ^</span></span>

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<pre style="margin: 0;"> <span id="LC328" 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="LC329" class="line" lang="python">            <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</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="LC330" class="line" lang="python">            <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dialect</span><span class="p">[</span><span class="s" style="color: #d14;">'keyval separator'</span><span class="p">]</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;">item</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>

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<br>

</li>

<li id="813e78223f55b4ca02a5f4aee6a78b722bd609a2">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#813e78223f55b4ca02a5f4aee6a78b722bd609a2"><strong>gffutils/pybedtools_integration.py</strong></a>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Module for integration with pybedtools</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pybedtools</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pybedtools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">featurefuncs</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">helpers</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_bedtool</span><span class="p">(</span><span class="n" style="color: #333;">iterator</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">    Convert any iterator into a pybedtools.BedTool object.</span></span>

</pre>

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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">@@ -22,7 +24,7 @@ def to_bedtool(iterator):</td>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tsses</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="n" style="color: #333;">merge_overlapping</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">attrs_sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python">          <span class="n" style="color: #333;">merge_kwargs</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">dict</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">o</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'distinct'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">as_bed6</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Fals</span>e</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">          <span class="n" style="color: #333;">merge_kwargs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">as_bed6</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bedtools_227_or_later</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Tru</span>e</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="28" 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">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">    Create 1-bp transcription start sites for all transcripts in the database</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">    and return as a sorted pybedtools.BedTool object pointing to a temporary</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="76" 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">@@ -74,13 +76,21 @@ def tsses(db, merge_overlapping=False, attrs=None, attrs_sep=":",</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;">        attributes is supplied, e.g. ["gene_id", "transcript_id"], then these</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;">        will be joined by `attr_join_sep` and then placed in the name field.</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;">    attrs_sep: str</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;">        If `as_bed6=True` or `merge_overlapping=True`, then use this character</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;">        to separate attributes in the name field of the output BED. If also</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;">        using `merge_overlapping=True`, you'll probably want this to be</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;">        different than `merge_sep` in order to parse things out later.</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;">    bedtools_227_or_later : bool</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;">        In version 2.27, BEDTools changed the output for merge. By default,</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;">        this function expects BEDTools version 2.27 or later, but set this to</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;">        False to assume the older behavior.</span></span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;">        For testing purposes, the environment variable</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;">        GFFUTILS_USES_BEDTOOLS_227_OR_LATER is set to either "true" or "false"</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;">        and is used to override this argument.</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 class="s" style="color: #d14;">    Examples</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;">    --------</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></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">@@ -146,7 +156,22 @@ def tsses(db, merge_overlapping=False, attrs=None, attrs_sep=":",</td>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python">    <span class="n" style="color: #333;">_merge_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'distinct'</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python">    <span class="n" style="color: #333;">_override</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'GFFUTILS_USES_BEDTOOLS_227_OR_LATER'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_override</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" 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">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_override</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'true'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="162" 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">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python">            <span class="n" style="color: #333;">bedtools_227_or_later</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="163" 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">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">_override</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'false'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="164" 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">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python">            <span class="n" style="color: #333;">bedtools_227_or_later</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="165" 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">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="166" 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">

166

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="167" 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">

167

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">                <span class="s" style="color: #d14;">"Unknown value for GFFUTILS_USES_BEDTOOLS_227_OR_LATER "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="168" 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">

168

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">                <span class="s" style="color: #d14;">"environment variable: {0}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">_override</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="169" 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">

169

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="170" 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">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bedtools_227_or_later</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="171" 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="LC171" class="line" lang="python">        <span class="n" style="color: #333;">_merge_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'distinct'</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'4,5,6'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="172" 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">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="173" 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="LC173" class="line" lang="python">        <span class="n" style="color: #333;">_merge_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'distinct'</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'4'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="174" 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="LC174" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" 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">

150

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<td class="diff-line-num new_line" data-linenumber="175" 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">

175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">merge_kwargs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="151" 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">

151

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<td class="diff-line-num new_line" data-linenumber="176" 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">

176

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python">        <span class="n" style="color: #333;">_merge_kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">merge_kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" 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">

152

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<td class="diff-line-num new_line" data-linenumber="177" 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">

177

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" 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="220" 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">@@ -195,18 +220,18 @@ def tsses(db, merge_overlapping=False, attrs=None, attrs_sep=":",</td>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python">        <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">each</span><span class="p">(</span><span class="n" style="color: #333;">to_bed</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">saveas</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">merge_overlapping</span><span class="p">:</span></span>

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">fix_merge</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff right">):</span></span></span>

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python">        <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">f</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">featurefuncs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">extend_fields</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pybedtools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Interval</span></span><span class="p"><span class="idiff right">(</span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python">                <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff right">,</span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff right">,</span></span></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stop</span></span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff right">]</span>,</span></span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python">                <span class="s" style="color: #d14;"><span class="idiff left right">'.'</span></span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span></span></span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left">x</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">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">merge</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">_merge_kwargs</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">each</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fix_merge</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">saveas</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="211" 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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<td class="diff-line-num new new_line" data-linenumber="223" 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">

223

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC223" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bedtools_227_or_later</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="224" 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">

224

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC224" class="line" lang="python">        <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">x</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">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">merge</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">_merge_kwargs</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="225" 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">

225

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="226" 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">

226

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC226" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">fix_merge</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff right">):</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="227" 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">

227

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC227" class="line" lang="python">                <span class="n" style="color: #333;">f</span><span class="idiff left"> </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">featurefuncs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">extend_fields</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="228" 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">

228

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC228" class="line" lang="python">                <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pybedtools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Interval</span></span><span class="p"><span class="idiff right">(</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="229" 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">

229

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">                <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">chrom</span></span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="230" 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">

230

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC230" class="line" lang="python">                <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">start</span></span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="231" 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">

231

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC231" class="line" lang="python">                <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stop</span></span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="232" 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">

232

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC232" class="line" lang="python">                <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff right">],</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="233" 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">

233

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC233" class="line" lang="python">                    <span class="s" style="color: #d14;">'.'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="234" 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">

234

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC234" class="line" lang="python">        <span class="idiff left">            </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">]</span>)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="211" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="235" 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">

235

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC235" class="line" lang="python">            <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">_merge_kwargs</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">saveas</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">each</span><span class="p">(</span><span class="n" style="color: #333;">fix_merge</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">saveas</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="211" 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">

211

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<td class="diff-line-num new_line" data-linenumber="236" 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">

236

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="212" 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">

212

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<td class="diff-line-num new_line" data-linenumber="237" 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">

237

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="526a837fe4cca54b4c1c2279c2e24d4e942f8efc">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#526a837fe4cca54b4c1c2279c2e24d4e942f8efc"><strong>gffutils/test/data/synthetic.gff3</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        5       15      .       .       .       ID=basic1</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        5       15      .       .       .       ID=discontig1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        20      30      .       .       .       ID=discontig1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        5       15      .       .       .       ID=perfect_overlap1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        16      20      .       .       .       ID=adjacent1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        16      16      .       .       .       ID=adjacent2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        1       4       .       .       .       ID=adjacent3</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">seq1  synthetic1      sequence_feature        4       4       .       .       .       ID=adjacent4</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        15      20      .       .       .       ID=overlap_end1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        1       5       .       .       .       ID=overlap_start1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        10      20      .       .       .       ID=overlap_past_end1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        10      20      .       +       .       ID=strand_plus1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        10      20      .       -       .       ID=strand_minus1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        35      40      .       .       .       ID=no_overlap1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">seq1 synthetic1      sequence_feature        21      29      .       .       .       ID=no_overlap2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">seq1 synthetic1      misc_feature    1       10      .       .       .       ID=different_type1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">seq1 synthetic2      sequence_feature        1       10      .       .       .       ID=different_source1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">seq2 synthetic1      sequence_feature        1       10      .       .       .       ID=different_seqid1</span></pre>

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</li>

<li id="b0f2632c4b65d2dfee8f69f70f70e1c7237393ba">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#b0f2632c4b65d2dfee8f69f70f70e1c7237393ba"><strong>gffutils/test/synth_test_base.py</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gffutils</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">synthetic_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'synthetic.gff3'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">num_synthetic_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">18</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">num_synthetic_overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">13</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestWithSynthDB</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" 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;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">synthetic_path</span><span class="p">,</span> <span class="s" style="color: #d14;">":memory:"</span><span class="p">,</span> <span class="n" style="color: #333;">merge_strategy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'create_unique'</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># type: gffutils.FeatureDB</span></span>

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<pre style="margin: 0;">+<span id="LC11" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_features</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">())</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_dump_db</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" 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;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_features</span><span class="p">()))</span></span></pre>

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<br>

</li>

<li id="36b3b2505247623a7a10862d6932e78bcdde4d12">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#36b3b2505247623a7a10862d6932e78bcdde4d12"><strong>gffutils/test/test.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">@@ -120,7 +120,7 @@ def test_update():</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Add attribute to each gene record</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">        <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_recs</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="LC122" class="line" lang="python">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">"new"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"new_value"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" 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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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="p">]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">merge_strategy</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'replace'</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" 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">

124

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<td class="diff-line-num new_line" data-linenumber="124" 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">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">        <span class="n" style="color: #333;">num_entries</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" 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">

125

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<td class="diff-line-num new_line" data-linenumber="125" 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">

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_features</span><span class="p">()))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" 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">

126

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<td class="diff-line-num new_line" data-linenumber="126" 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">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="621" 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="621" 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">@@ -621,6 +621,7 @@ def test_create_db_from_url():</td>

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<td class="diff-line-num old_line" data-linenumber="621" 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">

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<td class="diff-line-num new_line" data-linenumber="621" 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">

621

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="622" 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">

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<td class="diff-line-num new_line" data-linenumber="622" 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">

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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Serving test/data folder</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="623" 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">

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<td class="diff-line-num new_line" data-linenumber="623" 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">

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python">    <span class="n" style="color: #333;">served_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="624" 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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<td class="diff-line-num new new_line" data-linenumber="624" 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="LC624" class="line" lang="python">    <span class="n" style="color: #333;">savedir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="625" 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">

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python">    <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">served_folder</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="625" 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">

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<td class="diff-line-num new_line" data-linenumber="626" 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">

626

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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="626" 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">

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<td class="diff-line-num new_line" data-linenumber="627" 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">

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Starting SimpleHTTPServer in thread"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="654" 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="655" 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">@@ -654,6 +655,7 @@ def test_create_db_from_url():</td>

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<td class="diff-line-num new_line" data-linenumber="655" 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">

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Server shutdown.'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="655" 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">

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<td class="diff-line-num new_line" data-linenumber="656" 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">

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python">        <span class="n" style="color: #333;">httpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="656" 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">

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<td class="diff-line-num new_line" data-linenumber="657" 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">

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python">        <span class="n" style="color: #333;">server_thread</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="657" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="658" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC658" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">savedir</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="657" 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">

657

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<td class="diff-line-num new_line" data-linenumber="659" 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">

659

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="658" 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">

658

</td>

<td class="diff-line-num new_line" data-linenumber="660" 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">

660

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="659" 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">

659

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<td class="diff-line-num new_line" data-linenumber="661" 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">

661

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_empty_files</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="880" 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="882" 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">@@ -880,7 +882,7 @@ def test_tempfiles():</td>

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<td class="diff-line-num old_line" data-linenumber="880" 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">

880

</td>

<td class="diff-line-num new_line" data-linenumber="882" 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">

882

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<pre style="margin: 0;"> <span id="LC882" 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;">filelist</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 class="n" style="color: #333;">filelist</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="881" 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">

881

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<td class="diff-line-num new_line" data-linenumber="883" 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">

883

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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">filelist</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;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gffutils'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="882" 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">

882

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<td class="diff-line-num new_line" data-linenumber="884" 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">

884

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

883

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<td class="diff-line-num new_line old" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC883" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#...and another one for gff. This time, make sure the suffix<span class="idiff left right"> </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="884" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="885" 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">

885

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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#...and another one for gff. This time, make sure the suffix</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="884" 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">

884

</td>

<td class="diff-line-num new_line" data-linenumber="886" 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">

886

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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python">    <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="885" 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">

885

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<td class="diff-line-num new_line" data-linenumber="887" 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">

887

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python">        <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'FBgn0031208.gff'</span><span class="p">),</span> <span class="s" style="color: #d14;">':memory:'</span><span class="p">,</span> <span class="n" style="color: #333;">_keep_tempfiles</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="886" 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">

886

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<td class="diff-line-num new_line" data-linenumber="888" 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">

888

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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python">    <span class="n" style="color: #333;">filelist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">tempdir</span><span class="p">)</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1006" 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="1008" 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">@@ -1006,7 +1008,7 @@ def test_disable_infer():</td>

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<td class="diff-line-num old_line" data-linenumber="1006" 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">

1006

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<td class="diff-line-num new_line" data-linenumber="1008" 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">

1008

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1008" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1007" 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">

1007

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<td class="diff-line-num new_line" data-linenumber="1009" 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">

1009

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1009" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1008" 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">

1008

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<td class="diff-line-num new_line" data-linenumber="1010" 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">

1010

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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_deprecation_handler</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1009

</td>

<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1010" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1011" 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">

1011

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1011" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1010" 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">

1010

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<td class="diff-line-num new_line" data-linenumber="1012" 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">

1012

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1012" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1011" 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">

1011

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<td class="diff-line-num new_line" data-linenumber="1013" 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">

1013

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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO: when infer_gene_extent actually gets deprecated, test here.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1012" 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">

1012

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<td class="diff-line-num new_line" data-linenumber="1014" 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">

1014

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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="python">    <span class="n" style="color: #333;">assert_raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1141" 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="1143" 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">@@ -1141,7 +1143,7 @@ def test_unreasonable_unquoting():</td>

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<td class="diff-line-num old_line" data-linenumber="1141" 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">

1141

</td>

<td class="diff-line-num new_line" data-linenumber="1143" 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">

1143

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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'null'</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\x00</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1142" 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">

1142

</td>

<td class="diff-line-num new_line" data-linenumber="1144" 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">

1144

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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'comma'</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="s" style="color: #d14;">','</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1143" 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">

1143

</td>

<td class="diff-line-num new_line" data-linenumber="1145" 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">

1145

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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1144

</td>

<td class="diff-line-num new_line old" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1144" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Commas indicate<span class="idiff left right"> </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1145" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1146" 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">

1146

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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Commas indicate</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1145" 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">

1145

</td>

<td class="diff-line-num new_line" data-linenumber="1147" 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">

1147

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1147" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Parent'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'A,'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1146" 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">

1146

</td>

<td class="diff-line-num new_line" data-linenumber="1148" 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">

1148

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1148" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">s</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1147" 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">

1147

</td>

<td class="diff-line-num new_line" data-linenumber="1149" 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">

1149

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1149" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1174" 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="1176" 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">@@ -1174,6 +1176,145 @@ def test_db_unquoting():</td>

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<td class="diff-line-num old_line" data-linenumber="1174" 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">

1174

</td>

<td class="diff-line-num new_line" data-linenumber="1176" 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">

1176

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<pre style="margin: 0;"> <span id="LC1176" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'e'</span><span class="p">][</span><span class="s" style="color: #d14;">'Note'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">','</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1175" 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">

1175

</td>

<td class="diff-line-num new_line" data-linenumber="1177" 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">

1177

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1177" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'f'</span><span class="p">][</span><span class="s" style="color: #d14;">'Note'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">','</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1176" 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">

1176

</td>

<td class="diff-line-num new_line" data-linenumber="1178" 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">

1178

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1178" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1179" 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">

1179

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1179" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1180" 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">

1180

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1180" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_105</span><span class="p">():</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1181" 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">

1181

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1181" class="line" lang="python">    <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'FBgn0031208.gtf'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1182" 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">

1182

</td>

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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="python">    <span class="n" style="color: #333;">home</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="s" style="color: #d14;">'~'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1183" 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">

1183

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1183" class="line" lang="python">    <span class="n" style="color: #333;">newfn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">home</span><span class="p">,</span> <span class="s" style="color: #d14;">'.gffutils.test'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1184" 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">

1184

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1184" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">newfn</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fout</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1185" 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">

1185

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1185" class="line" lang="python">        <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1186" 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">

1186

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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="python">    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iterators</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataIterator</span><span class="p">(</span><span class="n" style="color: #333;">newfn</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1187" 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">

1187

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1187" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1188" 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">

1188

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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1189" 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">

1189

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1189" class="line" lang="python">    <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">newfn</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1190" 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">

1190

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1190" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1191" 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">

1191

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1191" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1192" 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">

1192

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1192" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_107</span><span class="p">():</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1193" 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">

1193

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1193" class="line" lang="python">    <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dedent</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1194" 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">

1194

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python">        <span class="s" style="color: #d14;">'''</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1195" 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">

1195

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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="python"><span class="s" style="color: #d14;">        chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">10</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">15</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID=b;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1196" 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">

1196

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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="python"><span class="s" style="color: #d14;">        chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID=a;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1197" 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">

1197

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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="python"><span class="s" style="color: #d14;">        chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">25</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">50</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID=c;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1198" 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">

1198

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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="python"><span class="s" style="color: #d14;">        chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">55</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">60</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID=d;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1199" 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">

1199

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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="python"><span class="s" style="color: #d14;">        '''</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1200" 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">

1200

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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="python">    <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1201" 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">

1201

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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fout</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1202" 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">

1202

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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="python">        <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1203" 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">

1203

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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="python">    <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">':memory:'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1204" 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">

1204

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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="python">    <span class="n" style="color: #333;">interfeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interfeatures</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1205" 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">

1205

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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features_of_type</span><span class="p">(</span><span class="s" style="color: #d14;">'gene'</span><span class="p">,</span> <span class="n" style="color: #333;">order_by</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'seqid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1206" 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">

1206

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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">interfeatures</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1207" 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">

1207

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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="python">            <span class="s" style="color: #d14;">'chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gffutils_derived</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">inter_gene_gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">9</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID=a,b;'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1208" 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">

1208

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1208" class="line" lang="python">            <span class="s" style="color: #d14;">'chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gffutils_derived</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">inter_gene_gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">16</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">54</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID=c,d;'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1209" 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">

1209

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1209" class="line" lang="python">    <span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1210" 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">

1210

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1210" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1211" 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">

1211

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1211" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1212" 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">

1212

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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_119</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1213" 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">

1213

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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># First file has these two exons with no ID:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1214" 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">

1214

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1214" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1215" 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">

1215

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1215" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   chr2L FlyBase exon  8193  8589  .  +  .  Parent=FBtr0300690</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1216" 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">

1216

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1216" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   chr2L FlyBase exon  7529  8116  .  +  .  Name=CG11023:1;Parent=FBtr0300689,FBtr0300690</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1217" 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">

1217

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1217" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1218" 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">

1218

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1218" class="line" lang="python">    <span class="n" style="color: #333;">db0</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'FBgn0031208.gff'</span><span class="p">),</span><span class="s" style="color: #d14;">':memory:'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1219" 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">

1219

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1219" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1220" 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">

1220

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1220" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># And this one, a bunch of reads with no IDs anywhere</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1221" 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">

1221

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1221" class="line" lang="python">    <span class="n" style="color: #333;">db1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'F3-unique-3.v2.gff'</span><span class="p">),</span><span class="s" style="color: #d14;">':memory:'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1222" 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">

1222

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1222" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1223" 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">

1223

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1223" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># When db1 is updated by db0</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1224" 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">

1224

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1224" class="line" lang="python">    <span class="n" style="color: #333;">db2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">db0</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1225" 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">

1225

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1225" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1226" 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">

1226

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1226" class="line" lang="python">        <span class="n" style="color: #333;">db2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1227" 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">

1227

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1227" class="line" lang="python">        <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">db1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1228" 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">

1228

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1228" class="line" lang="python">        <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'exon'</span><span class="p">:</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">'read'</span><span class="p">:</span> <span class="mi" style="color: #099;">112</span><span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1229" 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">

1229

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1229" class="line" lang="python">    <span class="p">),</span> <span class="n" style="color: #333;">db2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1230" 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">

1230

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1230" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1231" 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">

1231

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1231" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1232" 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">

1232

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1232" 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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">db0</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features_of_type</span><span class="p">(</span><span class="s" style="color: #d14;">'exon'</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1233" 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">

1233

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1233" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1234" 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">

1234

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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Now we update that with db0 again</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1235" 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">

1235

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1235" class="line" lang="python">    <span class="n" style="color: #333;">db3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">db0</span><span class="p">,</span> <span class="n" style="color: #333;">merge_strategy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'replace'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1236" 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">

1236

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1236" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1237" 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">

1237

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1237" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Using the "replace" strategy, we should have only gotten another 2 exons</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1238" 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">

1238

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1238" 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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">db3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features_of_type</span><span class="p">(</span><span class="s" style="color: #d14;">'exon'</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">8</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1239" 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">

1239

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1239" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1240" 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">

1240

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1240" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Make sure that the autoincrements for exons jumped by 2</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1241" 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">

1241

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1241" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1242" 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">

1242

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1242" class="line" lang="python">        <span class="n" style="color: #333;">db2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1243" 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">

1243

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1243" class="line" lang="python">        <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">db3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1244" 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">

1244

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1244" class="line" lang="python">        <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'exon'</span><span class="p">:</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="s" style="color: #d14;">'read'</span><span class="p">:</span> <span class="mi" style="color: #099;">112</span><span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1245" 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">

1245

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1245" class="line" lang="python">    <span class="p">),</span> <span class="n" style="color: #333;">db2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1246" 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">

1246

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1246" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1247" 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">

1247

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1247" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># More isolated test, merging two databases each created from the same file</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1248" 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">

1248

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1248" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># which itself contains only a single feature with no ID.</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1249" 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">

1249

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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="python">    <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1250" 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">

1250

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1250" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fout</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1251" 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">

1251

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1251" class="line" lang="python">        <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">10</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">15</span><span class="se" style="color: #d14;">\t</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1252" 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">

1252

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1252" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1253" 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">

1253

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1253" class="line" lang="python">    <span class="n" style="color: #333;">db4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.db'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1254" 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">

1254

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1254" class="line" lang="python">    <span class="n" style="color: #333;">db5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">':memory:'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1255" 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">

1255

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1255" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1256" 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">

1256

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1256" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'gene'</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1257" 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">

1257

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1257" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db5</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'gene'</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1258" 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">

1258

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1258" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1259" 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">

1259

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1259" class="line" lang="python">    <span class="n" style="color: #333;">db6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">db5</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1260" 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">

1260

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1260" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1261" 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">

1261

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1261" class="line" lang="python">    <span class="n" style="color: #333;">db7</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FeatureDB</span><span class="p">(</span><span class="n" style="color: #333;">db4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dbfn</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1262" 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">

1262

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1262" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1263" 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">

1263

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1263" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># both db4 and db6 should now have the same, updated autoincrements because</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1264" 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">

1264

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1264" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># they both point to the same db.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1265" 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">

1265

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1265" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">db4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'gene'</span><span class="p">:</span> <span class="mi" style="color: #099;">2</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1266" 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">

1266

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1266" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1267" 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">

1267

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1267" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># But db5 was created independently and should have unchanged autoincrements</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1268" 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">

1268

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1268" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db5</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'gene'</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1269" 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">

1269

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1269" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1270" 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">

1270

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1270" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># db7 was created from the database pointed to by both db4 and db6. This</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1271" 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">

1271

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1271" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># tests that when a FeatureDB is created it should have the</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1272" 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">

1272

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1272" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># correctly-updated autoincrements read from the db</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1273" 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">

1273

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1273" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db7</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_autoincrements</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'gene'</span><span class="p">:</span> <span class="mi" style="color: #099;">2</span><span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1274" 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">

1274

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1274" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1275" 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">

1275

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1275" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pr_131</span><span class="p">():</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1276" 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">

1276

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1276" class="line" lang="python">    <span class="n" style="color: #333;">db</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'FBgn0031208.gff'</span><span class="p">),</span><span class="s" style="color: #d14;">':memory:'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1277" 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">

1277

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1277" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1278" 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">

1278

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1278" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># previously would raise ValueError("No lines parsed -- was an empty</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1279" 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">

1279

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1279" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># file provided?"); now just does nothing</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1280" 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">

1280

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1280" class="line" lang="python">    <span class="n" style="color: #333;">db2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">([])</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1281" 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">

1281

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1281" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1282" 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">

1282

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1282" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1283" 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">

1283

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1283" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pr_133</span><span class="p">():</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1284" 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="LC1284" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Previously, merge_attributes would not deep-copy the values from the</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1285" 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="LC1285" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># second dict, and when the values are then modified, the second dict is</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1286" 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="LC1286" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># unintentionally modified.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1287" 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">

1287

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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="python">    <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1288" 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">

1288

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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="python">    <span class="n" style="color: #333;">d2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1289" 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">

1289

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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="python">    <span class="n" style="color: #333;">d1a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1290" 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">

1290

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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="python">    <span class="n" style="color: #333;">d2a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1291" 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">

1291

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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="python">    <span class="n" style="color: #333;">d3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">helpers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_attributes</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1292" 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">

1292

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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">d1a</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1293" 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">

1293

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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">d2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">d2a</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1294" 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">

1294

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1294" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1295" 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">

1295

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1295" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1296" 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="LC1296" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pr_139</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1297" 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="LC1297" class="line" lang="python">    <span class="n" style="color: #333;">db</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_db</span><span class="p">(</span><span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">example_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'FBgn0031208.gff'</span><span class="p">),</span><span class="s" style="color: #d14;">':memory:'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1298" 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">

1298

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1298" class="line" lang="python">    <span class="n" style="color: #333;">exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features_of_type</span><span class="p">(</span><span class="s" style="color: #d14;">'exon'</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1299" 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">

1299

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1299" class="line" lang="python">    <span class="n" style="color: #333;">inter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interfeatures</span><span class="p">(</span><span class="n" style="color: #333;">exons</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1300" 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">

1300

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1300" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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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<td class="diff-line-num new new_line" data-linenumber="1301" 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">

1301

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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># previously, the first exon's attributes would show up in subsequent merged features</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1302" 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">

1302

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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">exons</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;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Name'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</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;">inter</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Name'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1303" 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">

1303

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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">exons</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;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Name'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</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;">inter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Name'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1304" 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">

1304

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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">exons</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;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Name'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</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;">inter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'Name'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1305" 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">

1305

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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1306" 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">

1306

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1306" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1307" 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">

1307

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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pr_144</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1308" 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">

1308

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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># previously this would fail with:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1309" 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">

1309

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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#   UnboundLocalError: local variable 'part' referenced before assignment</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1310" 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">

1310

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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="python">    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Feature</span><span class="p">(</span><span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">''</span><span class="p">]})</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1311" 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">

1311

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1311" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1312" 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">

1312

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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Make sure everything got converted correctly</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1313" 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">

1313

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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">''</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1314" 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">

1314

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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".   .       .       .       .       .       .       .       a"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1315" 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">

1315

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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="python">    <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gffutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_from_line</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1316" 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">

1316

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1316" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1177" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1317" 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">

1317

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1317" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1177" 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">

1177

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<td class="diff-line-num new_line" data-linenumber="1318" 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">

1318

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<pre style="margin: 0;"> <span id="LC1318" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1178" 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">

1178

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<td class="diff-line-num new_line" data-linenumber="1319" 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">

1319

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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># this test case fails</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1179" 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">

1179

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<td class="diff-line-num new_line" data-linenumber="1320" 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">

1320

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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#test_attributes_modify()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1181" 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="1322" 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">@@ -1181,3 +1322,6 @@ if __name__ == "__main__":</td>

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<td class="diff-line-num old_line" data-linenumber="1181" 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">

1181

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<td class="diff-line-num new_line" data-linenumber="1322" 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">

1322

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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#test_random_chr()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1182" 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">

1182

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<td class="diff-line-num new_line" data-linenumber="1323" 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">

1323

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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#test_nonascii()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1183" 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">

1183

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<td class="diff-line-num new_line" data-linenumber="1324" 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">

1324

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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="python">    <span class="n" style="color: #333;">test_iterator_update</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1184" 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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<td class="diff-line-num new new_line" data-linenumber="1325" 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">

1325

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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1184" 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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<td class="diff-line-num new new_line" data-linenumber="1326" 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">

1326

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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1184" 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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<td class="diff-line-num new new_line" data-linenumber="1327" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1327" class="line" lang="python"></span></pre>

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<li id="5f2c425940451a5e93c7e86645cb918593f3a9d7">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#5f2c425940451a5e93c7e86645cb918593f3a9d7"><strong>gffutils/test/test_biopython_integration.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,5 +14,6 @@ def test_roundtrip():</td>

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14

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<td class="diff-line-num new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_seqfeature</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" 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">

15

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<td class="diff-line-num new_line" data-linenumber="15" 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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">location</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;">position</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">feature</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">location</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="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" 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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<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line" data-linenumber="18" 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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_seqfeature</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">dialect</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dialect</span><span class="p">,</span> <span class="n" style="color: #333;">keep_order</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">feature</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f</span></span></pre>

</td>

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</li>

<li id="178bad6d457c689d13f5187e9574fb61b8ef0d06">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#178bad6d457c689d13f5187e9574fb61b8ef0d06"><strong>gffutils/test/test_merge.py</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">merge_criteria</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mc</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils.test.synth_test_base</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestWithSynthDB</span><span class="p">,</span> <span class="n" style="color: #333;">num_synthetic_features</span><span class="p">,</span> <span class="n" style="color: #333;">num_synthetic_overlap</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestMerge</span><span class="p">(</span><span class="n" style="color: #333;">TestWithSynthDB</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_merge_and_compare</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">expected_merge_children</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">        <span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</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;">db</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ids</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">        <span class="n" style="color: #333;">features_backup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">features</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">        <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">features</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python">        <span class="n" style="color: #333;">m_dump</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">merged</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Ensure db wasn't modified</span></span>

</pre>

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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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_features</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">features_backup</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">expected</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;">db</span><span class="p">[</span><span class="n" style="color: #333;">actual</span><span class="p">],</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">expected</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;">db</span><span class="p">[</span><span class="n" style="color: #333;">actual</span><span class="p">]]))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Ensure input Features not modified</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">features_backup</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Ensure output matches expected</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" 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;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">expected_merge_children</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">m_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" 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="LC26" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">expected_merge_children</span><span class="p">,</span> <span class="n" style="color: #333;">merged</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" 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="LC27" class="line" lang="python">            <span class="n" style="color: #333;">c_dump</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" 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;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">expected</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" 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;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">expected</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'.'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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<pre style="margin: 0;">+<span id="LC32" 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;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'.'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" 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">

35

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<pre style="margin: 0;">+<span id="LC35" 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;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="37" 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">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">expected</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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">

38

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<pre style="margin: 0;">+<span id="LC38" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" 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">

40

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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="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</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;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="41" 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">

41

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<pre style="margin: 0;">+<span id="LC41" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</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 class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" 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;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">actual</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" 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">

44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</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;">featuretype</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<pre style="margin: 0;">+<span id="LC46" 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;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" 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">

47

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="48" 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">

48

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<pre style="margin: 0;">+<span id="LC48" 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;">assertEqual</span><span class="p">(</span><span class="s" style="color: #d14;">'sequence_feature'</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">featuretype</span><span class="p">,</span> <span class="n" style="color: #333;">c_dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" 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">

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="50" 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">

50

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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="n" style="color: #333;">merged</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="51" 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">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>

</pre>

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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;">test_defaults</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" 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="LC53" class="line" lang="python">        <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_features</span><span class="p">(</span><span class="n" style="color: #333;">order_by</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'seqid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'featuretype'</span><span class="p">,</span> <span class="s" style="color: #d14;">'strand'</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="python">        <span class="n" style="color: #333;">dump</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">merged</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="55" 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">

55

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<pre style="margin: 0;">+<span id="LC55" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_features</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="56" 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="LC56" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="57" 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="LC57" class="line" lang="python">        <span class="n" style="color: #333;">merged_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="58" 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">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">merged</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="59" 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">

59

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" 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">

60

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC60" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_overlap</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="61" 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">

61

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">                <span class="n" style="color: #333;">merged_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="62" 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">

62

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="63" 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">

63

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC63" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">merged_count</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="64" 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">

64

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="65" 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">

65

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="66" 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">

66

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">        <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</span><span class="p">([]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="67" 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">

67

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC67" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="68" 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">

68

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC68" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_features</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="69" 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">

69

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC69" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="70" 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">

70

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="71" 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">

71

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_one</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="72" 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">

72

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">],</span> <span class="p">[[]])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="73" 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">

73

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="74" 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">

74

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="75" 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">

75

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<pre style="margin: 0;">+<span id="LC75" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_overlap1'</span><span class="p">],</span> <span class="p">[[],[]])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" 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">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" 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">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_perfect_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="78" 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">

78

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<pre style="margin: 0;">+<span id="LC78" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'perfect_overlap1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'perfect_overlap1'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" 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">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" 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="LC80" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" 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">

81

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<pre style="margin: 0;">+<span id="LC81" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent1'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" 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">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" 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">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_any_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'overlap_start1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'overlap_start1'</span><span class="p">]],</span> <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_any_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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">

85

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<pre style="margin: 0;">+<span id="LC85" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'overlap_start1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'overlap_start1'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="86" 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">

86

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<pre style="margin: 0;">+<span id="LC86" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'adjacent1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent1'</span><span class="p">]],</span> <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_any_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="87" 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">

87

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<pre style="margin: 0;">+<span id="LC87" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'adjacent4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent4'</span><span class="p">]],</span> <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_any_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="88" 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">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" 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">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adjacent_len1</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent2'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent2'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'adjacent2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent2'</span><span class="p">]],</span> <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_any_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent3'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent3'</span><span class="p">]],</span> <span class="n" style="color: #333;">merge_criteria</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overlap_any_inclusive</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">feature_type</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'adjacent3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'adjacent3'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" class="line" lang="python"></span>

</pre>

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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;">test_end_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" 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="LC96" 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;">_merge_and_compare</span><span class="p">([</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'overlap_end1'</span><span class="p">],</span> <span class="p">[[</span><span class="s" style="color: #d14;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'overlap_end1'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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="LC98" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO test various feature orders</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="100" 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="LC100" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO test various merge criteria</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="102" 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="LC102" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO test multiline, this doesn't really work until gffutils better supports multiline features</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># TODO add test for PR #152</span></span></pre>

</td>

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<br>

</li>

<li id="d58e1dc1356251786c2151af57cce228ffb8d3a1">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#d58e1dc1356251786c2151af57cce228ffb8d3a1"><strong>gffutils/test/test_merge_all.py</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gffutils.test.synth_test_base</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestWithSynthDB</span><span class="p">,</span> <span class="n" style="color: #333;">num_synthetic_features</span><span class="p">,</span> <span class="n" style="color: #333;">num_synthetic_overlap</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestMerge_all</span><span class="p">(</span><span class="n" style="color: #333;">TestWithSynthDB</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaults</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python">        <span class="n" style="color: #333;">merged</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<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">

8

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<pre style="margin: 0;">+<span id="LC8" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_features</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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<pre style="margin: 0;">+<span id="LC9" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_overlap</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</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;">children</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" 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">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_empty</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" 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">

13

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<pre style="margin: 0;">+<span id="LC13" 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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_features</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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<pre style="margin: 0;">+<span id="LC15" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">0</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">        <span class="n" style="color: #333;">merged</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" 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">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">0</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">test_one</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">        <span class="n" style="color: #333;">features</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_features</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">        <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">features</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" 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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete</span><span class="p">(</span><span class="n" style="color: #333;">features</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">        <span class="n" style="color: #333;">merged</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" 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">

29

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" 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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete</span><span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_features</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</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;">'basic1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_overlap1'</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" 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">

35

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<pre style="margin: 0;">+<span id="LC35" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">2</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="python">        <span class="n" style="color: #333;">merged</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">2</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="40" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_merge_groups</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="python">        <span class="n" style="color: #333;">merged</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all</span><span class="p">(</span><span class="n" style="color: #333;">featuretypes_groups</span><span class="o" style="font-weight: 600;">=</span><span class="p">({</span><span class="s" style="color: #d14;">'sequence_feature'</span><span class="p">,</span> <span class="s" style="color: #d14;">'misc_feature'</span><span class="p">},))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_features</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="45" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" 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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_overlap</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</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;">children</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" 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">

48

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_exclude_components</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="49" 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">

49

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">        <span class="n" style="color: #333;">merged</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all</span><span class="p">(</span><span class="n" style="color: #333;">exclude_components</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="50" 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">

50

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">        <span class="n" style="color: #333;">dump</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;">_dump_db</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" 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">

51

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC51" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">6</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;">db</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_features_of_type</span><span class="p">(),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" 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">

52

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC52" 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;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="53" 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">

53

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_synthetic_overlap</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">merged</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;">children</span><span class="p">),</span> <span class="n" style="color: #333;">dump</span><span class="p">)</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3261a65b84ab9332a3637d0e16a82bbad42280f1">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#3261a65b84ab9332a3637d0e16a82bbad42280f1"><strong>gffutils/version.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.<span class="idiff left right">9</span>"</span></span></pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.<span class="idiff left right">10.1</span>"</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="19359a61ae2446b51b549167b014da2fcf265768">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyfaidx" rel="nofollow noreferrer noopener" target="_blank">pyfaidx</a></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/six" rel="nofollow noreferrer noopener" target="_blank">six</a></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/argh" rel="nofollow noreferrer noopener" target="_blank">argh</a></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/argcomplete" rel="nofollow noreferrer noopener" target="_blank">argcomplete</a></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyfaidx" rel="nofollow noreferrer noopener" target="_blank">pyfaidx</a><span class="idiff left right">>=0.5.5.2</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/six" rel="nofollow noreferrer noopener" target="_blank">six</a><span class="idiff left right">>=1.12.0</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/argh" rel="nofollow noreferrer noopener" target="_blank">argh</a><span class="idiff left right">>=0.26.2</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/argcomplete" rel="nofollow noreferrer noopener" target="_blank">argcomplete</a><span class="idiff left right">>=1.9.4</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" 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">

5

</td>

<td class="diff-line-num new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/simplejson" rel="nofollow noreferrer noopener" target="_blank">simplejson</a></span></pre>

</td>

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<br>

</li>

<li id="8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">

<a href="https://salsa.debian.org/med-team/python-gffutils/commit/22db24567b5c6f4809ea721fbfe575f1aee283c7#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">[egg_info]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">tag_build = </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">tag_date = 0</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">tag_svn_revision = 0</span>

</pre>

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5

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span></pre>

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