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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pymummer">Debian Med / python-pymummer</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed">786112ec</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-06-10T02:13:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.0</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
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+
CHANGELOG.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#61b883d0334940c60b10ad953797f3fed05283e4">
pymummer/snp.py
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<li class="file-stats">
<a href="#41e1310981fca6b755028385df0b3cd66e9bf7ad">
pymummer/tests/alignment_test.py
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<li class="file-stats">
<a href="#405913a15a7128bb8ec1a57171bac8d4121d8b1f">
pymummer/tests/snp_test.py
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<li class="file-stats">
<a href="#227886a778a831ee096b2c7e5b3cb07ccf2fb513">
pymummer/tests/variant_test.py
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<li class="file-stats">
<a href="#c0eff944f273f4a98493277d5ba62565a298467e">
pymummer/variant.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change Log</span></span>
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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="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [Unreleased](https://github.com/sanger-pathogens/pymummer/tree/HEAD)</span></span>
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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="markdown"></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.10.3...HEAD</span><span class="p">)</span></span>
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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="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> update README <span class="p">[</span><span class="nv" style="color: #008080;">\#29</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/29</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.10.3](https://github.com/sanger-pathogens/pymummer/tree/v0.10.3) (2017-08-21)</span></span>
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<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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.10.2...v0.10.3</span><span class="p">)</span></span>
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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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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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="markdown"></span>
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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="markdown"><span class="p">-</span> Add diagfactor <span class="se" style="color: #d14;">\(</span>-d<span class="se" style="color: #d14;">\)</span> and maxgap <span class="se" style="color: #d14;">\(</span>-g<span class="se" style="color: #d14;">\)</span> options for nucmer <span class="p">[</span><span class="nv" style="color: #008080;">\#28</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/28</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[Adamtaranto](https://github.com/Adamtaranto</span><span class="p">)</span>)</span>
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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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">-</span> update LICENSE <span class="p">[</span><span class="nv" style="color: #008080;">\#27</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/27</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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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="markdown"></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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.10.2](https://github.com/sanger-pathogens/pymummer/tree/v0.10.2) (2017-02-02)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.10.1...v0.10.2</span><span class="p">)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> MUMmer programs not found in path <span class="p">[</span><span class="nv" style="color: #008080;">\#21</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/issues/21</span><span class="p">)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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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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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> Ref qry translate vars not in matches <span class="p">[</span><span class="nv" style="color: #008080;">\#26</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/26</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.10.1](https://github.com/sanger-pathogens/pymummer/tree/v0.10.1) (2016-11-18)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.10.0...v0.10.1</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> Indels bug <span class="p">[</span><span class="nv" style="color: #008080;">\#25</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/25</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.10.0](https://github.com/sanger-pathogens/pymummer/tree/v0.10.0) (2016-11-15)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.9.0...v0.10.0</span><span class="p">)</span></span>
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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="markdown"></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="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">-</span> Show snps expose C option <span class="p">[</span><span class="nv" style="color: #008080;">\#24</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/24</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.9.0](https://github.com/sanger-pathogens/pymummer/tree/v0.9.0) (2016-10-17)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.8.1...v0.9.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p">-</span> Expose mincluster <span class="p">[</span><span class="nv" style="color: #008080;">\#23</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/23</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.1](https://github.com/sanger-pathogens/pymummer/tree/v0.8.1) (2016-08-23)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.8.0...v0.8.1</span><span class="p">)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.0](https://github.com/sanger-pathogens/pymummer/tree/v0.8.0) (2016-08-23)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.7.1...v0.8.0</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="p">-</span> Ref coords from qry coord <span class="p">[</span><span class="nv" style="color: #008080;">\#22</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/22</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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<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">
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.1](https://github.com/sanger-pathogens/pymummer/tree/v0.7.1) (2016-04-18)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.7.0...v0.7.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"><span class="p">-</span> Make <span class="se" style="color: #d14;">\_\_</span>version<span class="se" style="color: #d14;">\_\_</span> work <span class="p">[</span><span class="nv" style="color: #008080;">\#20</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/20</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.0](https://github.com/sanger-pathogens/pymummer/tree/v0.7.0) (2016-02-09)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.6.1...v0.7.0</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> Coords finding in matches <span class="p">[</span><span class="nv" style="color: #008080;">\#19</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/19</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></span>
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<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">
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.1](https://github.com/sanger-pathogens/pymummer/tree/v0.6.1) (2015-10-19)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.6.0...v0.6.1</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">-</span> Remove numpy dependency <span class="p">[</span><span class="nv" style="color: #008080;">\#18</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/18</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.0](https://github.com/sanger-pathogens/pymummer/tree/v0.6.0) (2015-10-14)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.5.0...v0.6.0</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">-</span> Convert to mspcrunch <span class="p">[</span><span class="nv" style="color: #008080;">\#17</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/17</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.0](https://github.com/sanger-pathogens/pymummer/tree/v0.5.0) (2015-10-09)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC90" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.4.0...v0.5.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> Msp crunch output <span class="p">[</span><span class="nv" style="color: #008080;">\#16</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/16</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="p">-</span> Add TravisCI support <span class="p">[</span><span class="nv" style="color: #008080;">\#15</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/15</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4.0](https://github.com/sanger-pathogens/pymummer/tree/v0.4.0) (2015-05-28)</span></span>
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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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.3.0...v0.4.0</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="p">-</span> Expose diagdiff to nucmer <span class="p">[</span><span class="nv" style="color: #008080;">\#14</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/14</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3.0](https://github.com/sanger-pathogens/pymummer/tree/v0.3.0) (2015-05-15)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.2.0...v0.3.0</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC107" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.2.0](https://github.com/sanger-pathogens/pymummer/tree/v0.2.0) (2015-05-15)</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.1.0...v0.2.0</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC110" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC112" class="line" lang="markdown"><span class="p">-</span> Reverse alignments <span class="p">[</span><span class="nv" style="color: #008080;">\#13</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/13</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="p">-</span> Fix constructing alignment from promer output <span class="p">[</span><span class="nv" style="color: #008080;">\#12</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/12</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="p">-</span> Add promer option; version bump <span class="p">[</span><span class="nv" style="color: #008080;">\#11</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/11</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.1.0](https://github.com/sanger-pathogens/pymummer/tree/v0.1.0) (2015-03-05)</span></span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/compare/v0.0.2...v0.1.0</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="p">-</span> minor version number incremented <span class="p">[</span><span class="nv" style="color: #008080;">\#10</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/10</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[nds](https://github.com/nds</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="p">-</span> Added --nosimplify toggle to nucmer command <span class="p">[</span><span class="nv" style="color: #008080;">\#9</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/9</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[nds](https://github.com/nds</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.0.2](https://github.com/sanger-pathogens/pymummer/tree/v0.0.2) (2015-02-02)</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="p">-</span> Change to pyfastaq; add to pypi <span class="p">[</span><span class="nv" style="color: #008080;">\#8</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/8</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_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="LC128" class="line" lang="markdown"><span class="p">-</span> put system call code in seprate module <span class="p">[</span><span class="nv" style="color: #008080;">\#7</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/7</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</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="markdown"><span class="p">-</span> Add snp<span class="se" style="color: #d14;">\_</span>file to list of modules <span class="p">[</span><span class="nv" style="color: #008080;">\#6</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/6</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p">-</span> Added documentation in README file <span class="p">[</span><span class="nv" style="color: #008080;">\#5</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/5</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[nds](https://github.com/nds</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="p">-</span> Add variant calling <span class="p">[</span><span class="nv" style="color: #008080;">\#4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/4</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"><span class="p">-</span> Added some doc lines <span class="p">[</span><span class="nv" style="color: #008080;">\#3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/3</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[nds](https://github.com/nds</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="p">-</span> Split into separate files <span class="p">[</span><span class="nv" style="color: #008080;">\#2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/2</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="p">-</span> Initial commit <span class="p">[</span><span class="nv" style="color: #008080;">\#1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/pull/1</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">pymummer</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># pymummer</span></span>
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3
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">Python3 wrapper for running MUMmer and parsing the output. </span>
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5
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/pymummer.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/pymummer)</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="gh" style="color: #999;">Installation</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;">------------</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Homebrew/LinuxBrew###</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/pymummer.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/pymummer) </span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/sanger-pathogens/pymummer/blob/master/LICENSE) </span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square</span><span class="p">)</span>](http://bioconda.github.io/recipes/pymummer/README.html) </span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Container ready</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/container-ready-brightgreen.svg</span><span class="p">)</span>](https://quay.io/repository/biocontainers/pymummer) </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
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<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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#introduction</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
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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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Required dependencies</span><span class="p">](</span><span class="sx" style="color: #d14;">#required-dependencies</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Homebrew/LinuxBrew</span><span class="p">](</span><span class="sx" style="color: #d14;">#homebrewlinuxbrew</span><span class="p">)</span></span>
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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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Using pip</span><span class="p">](</span><span class="sx" style="color: #d14;">#using-pip</span><span class="p">)</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Running the tests</span><span class="p">](</span><span class="sx" style="color: #d14;">#running-the-tests</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage (for developers)</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage-for-developers</span><span class="p">)</span></span>
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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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">pymummer nucmer class</span><span class="p">](</span><span class="sx" style="color: #d14;">#pymummer-nucmer-class</span><span class="p">)</span></span>
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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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">pymummer coords\_file class</span><span class="p">](</span><span class="sx" style="color: #d14;">#pymummer-coords_file-class</span><span class="p">)</span></span>
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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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">pymummer alignment class</span><span class="p">](</span><span class="sx" style="color: #d14;">#pymummer-alignment-class</span><span class="p">)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Feedback/Issues</span><span class="p">](</span><span class="sx" style="color: #d14;">#feedbackissues</span><span class="p">)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">Runs MUMmer and parses the output.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">pymummer has the following dependencies:</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Required dependencies</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">MUMmer</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mummer.sourceforge.net/manual/#installation</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">There are a number of ways to install pymummer and details are provided below. If you encounter an issue when installing pymummer please contact your local system administrator. If you encounter a bug please log it <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/issues</span><span class="p">)</span> or email us at path-help@sanger.ac.uk.</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Homebrew/LinuxBrew</span></span>
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12
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown">brew tap homebrew/python</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">brew install pymummer</span>
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15
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="p">```</span></span>
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16
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##Pip</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Pre-requisites###</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">The MUMmer package must be installed.</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">Instructions to install MUMmer can be found <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mummer.sourceforge.net/manual/#installation</span><span class="p">)</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"> </span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Installation###</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">Install with</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pip3 install pymummer</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using pip</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">pip3 install pymummer</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Running the tests</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown">The test can be run from the top level directory: </span>
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28
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">python setup.py test</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="gh" style="color: #999;">Usage (for developers)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage (for developers)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">Example showing how pymummer can be used to run nucmer on a fasta file and parse the output file to produce a set of alignment objects:</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>from pymummer import coords_file, alignment, nucmer</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>...</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>runner = nucmer.Runner(reference_file, query_file, results_file) </span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>runner.run()</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>file_reader = coords_file.reader(results_file)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>alignments = [coord for coord in file_reader if not coord.is_self_hit()] #Remove self hits</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span>...</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">pymummer nucmer class###</span></span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown">from pymummer import coords_file, alignment, nucmer</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">...</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">runner = nucmer.Runner(reference_file, query_file, results_file) </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">runner.run()</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">file_reader = coords_file.reader(results_file)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">alignments = [coord for coord in file_reader if not coord.is_self_hit()] #Remove self hits</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">...</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"> pymummer nucmer class</span></span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown">Wraps the <span class="sb" style="color: #d14;">`nucmer`</span>, <span class="sb" style="color: #d14;">`delta-filter`</span>, <span class="sb" style="color: #d14;">`show-coords`</span> and <span class="sb" style="color: #d14;">`show-snps`</span> commands. </span>
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46
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown">Arguments:</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">```</span></span>
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49
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown">__ref__ reference file </span>
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50
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown">__query__ query file </span>
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51
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">__outfile__ output file </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(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="77" style="width: 35px; color: rgba(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">@@ -56,26 +77,18 @@ __coords\_header__ print header in show-coords output (default True)</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown">__maxmatch__ maxmatch for nucmer (default False) </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown">__show\_snps__ run show-snps (default False) </span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown">__snps\_header__ print header in show-snps output (default True) </span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">```</span></span>
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59
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###pymummer promer class###</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown">[TODO]</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###pymummer coords_file class###</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### pymummer coords_file class</span></span>
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65
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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66
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">Parses the nucmer output and populate an alignment object for each hit in the output</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown"></span>
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68
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"> </span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">pymummer alignment class###</span></span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"> pymummer alignment class</span></span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">Check attributes of a hit, swap the reference and query, check if it's a self hit and so on</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown">Authors: Martin Hunt, Nishadi De Silva</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown">Affiliation: Wellcome Trust Sanger Institute, Hinxton, UK</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">pymummer is free software, licensed under <span class="p">[</span><span class="nv" style="color: #008080;">GPLv3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pymummer/blob/master/LICENSE</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"><span class="idiff left right">Email: path-help@sanger.ac.uk</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="idiff left right"> </span></span></pre>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">## Feedback/Issues</span></span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"><span class="idiff left">Please report any issues to the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">issues page</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/pymummer/issues</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> or email path-help@sanger.ac.uk.</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">\ No newline at end of file</td>
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<li id="61b883d0334940c60b10ad953797f3fed05283e4">
<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#61b883d0334940c60b10ad953797f3fed05283e4"><strong>pymummer/snp.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -18,6 +18,7 @@ class Snp:</td>
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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="p">.</span><span class="n" style="color: #333;">qry_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">l</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="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ref_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'1'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">'-1'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}[</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]]</span></span>
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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="p">.</span><span class="n" style="color: #333;">ref_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</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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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</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">@@ -36,6 +37,7 @@ class Snp:</td>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_pos</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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37
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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="p">.</span><span class="n" style="color: #333;">ref_length</span><span class="p">,</span></span>
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39
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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="p">.</span><span class="n" style="color: #333;">qry_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'-1'</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span></span>
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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="p">.</span><span class="n" style="color: #333;">ref_name</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_name</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="p">]])</span></span>
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<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#41e1310981fca6b755028385df0b3cd66e9bf7ad"><strong>pymummer/tests/alignment_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">@@ -159,16 +159,16 @@ class TestNucmer(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> def test_qry_coords_from_ref_coord_test_same_strand(self):</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> '''Test qry_coords_from_ref_coord on same strand'''</span></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"><span class="s" style="color: #d14;"> aln = alignment.Alignment('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">200</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">101</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mf" style="color: #099;">100.00</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">']))</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">T</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # snp</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">T</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # snp</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = variant.Variant(snp0)</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> snp1 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> snp2 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">141</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> snp1 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> snp2 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">141</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> del1 = variant.Variant(snp1)</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> del2 = variant.Variant(snp1)</span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> self.assertTrue(del2.update_indel(snp2))</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> snp3 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">50</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"><span class="s" style="color: #d14;"> snp4 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">51</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> snp5 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">G</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">52</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> snp3 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">50</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="s" style="color: #d14;"> snp4 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">51</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> snp5 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">G</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">52</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> ins1 = variant.Variant(snp3)</span></span>
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173
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"><span class="s" style="color: #d14;"> ins2 = variant.Variant(snp3)</span></span>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="s" style="color: #d14;"> self.assertTrue(ins2.update_indel(snp4))</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">@@ -209,16 +209,16 @@ class TestNucmer(unittest.TestCase):</td>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="s" style="color: #d14;"> def test_qry_coords_from_ref_coord_test_different_strand(self):</span></span>
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> '''Test qry_coords_from_ref_coord on different strand'''</span></span>
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"><span class="s" style="color: #d14;"> aln = alignment.Alignment('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">200</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">101</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mf" style="color: #099;">100.00</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">']))</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">T</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # snp</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">T</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # snp</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = variant.Variant(snp0)</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;"> snp1 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> snp2 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">141</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;"> snp1 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> snp2 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">141</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;"> del1 = variant.Variant(snp1)</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> del2 = variant.Variant(snp1)</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;"> self.assertTrue(del2.update_indel(snp2))</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;"> snp3 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">50</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;"> snp4 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">51</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"><span class="s" style="color: #d14;"> snp5 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">G</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">52</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;"> snp3 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">50</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;"> snp4 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">51</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"><span class="s" style="color: #d14;"> snp5 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">G</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">52</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"><span class="s" style="color: #d14;"> ins1 = variant.Variant(snp3)</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"><span class="s" style="color: #d14;"> ins2 = variant.Variant(snp3)</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"><span class="s" style="color: #d14;"> self.assertTrue(ins2.update_indel(snp4))</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">@@ -273,16 +273,16 @@ class TestNucmer(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> def test_ref_coords_from_qry_coord_test_same_strand(self):</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"><span class="s" style="color: #d14;"> '''Test ref_coords_from_qry_coord on same strand'''</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> aln = alignment.Alignment('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">101</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">200</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">100</span><span class="s" style="color: #d14;">', '</span><span class="mf" style="color: #099;">100.00</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">1</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">']))</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">T</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # snp</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">T</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # snp</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;"> snp0 = variant.Variant(snp0)</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> snp1 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> snp2 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">141</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> snp1 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">140</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> snp2 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">40</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">141</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from ref</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;"> del1 = variant.Variant(snp1)</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> del2 = variant.Variant(snp1)</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> self.assertTrue(del2.update_indel(snp2))</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> snp3 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">50</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;"> snp4 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">51</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"><span class="s" style="color: #d14;"> snp5 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">52</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">G</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> snp3 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">50</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">A</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;"> snp4 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">51</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">C</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"><span class="s" style="color: #d14;"> snp5 = snp.Snp('</span>\<span class="n" style="color: #333;">t</span><span class="s" style="color: #d14;">'.join(['</span><span class="mi" style="color: #099;">52</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">G</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">150</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;">300</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">x</span><span class="s" style="color: #d14;">', '</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">ref</span><span class="s" style="color: #d14;">', '</span><span class="n" style="color: #333;">qry</span><span class="s" style="color: #d14;">'])) # del from qry</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;"> ins1 = variant.Variant(snp3)</span></span>
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;"> ins2 = variant.Variant(snp3)</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;"> self.assertTrue(ins2.update_indel(snp4))</span></span>
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<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#405913a15a7128bb8ec1a57171bac8d4121d8b1f"><strong>pymummer/tests/snp_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">@@ -12,13 +12,13 @@ class TestSnp(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">'''Test __str__ with format with no -C option'''</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">l_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">]</span></span>
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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;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">l_in</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">1'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_str_with_c_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'''Test __str__ with format with -C option'''</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">l_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">l_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">-</span>1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC22" 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;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">l_in</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'187'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'269'</span><span class="p">,</span> <span class="s" style="color: #d14;">'654'</span><span class="p">,</span> <span class="s" style="color: #d14;">'853'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">-1'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>ref_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry_name'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span></pre>
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<li id="227886a778a831ee096b2c7e5b3cb07ccf2fb513">
<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#227886a778a831ee096b2c7e5b3cb07ccf2fb513"><strong>pymummer/tests/variant_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">@@ -25,33 +25,33 @@ class TestVariant(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_update_indel_no_change</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'''Test update_indel does nothing in the right cases'''</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">initial_vars</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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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;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">to_add</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'142'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'3000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'142'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'3000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry2'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'44'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry2'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'44'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'142'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'3000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'142'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'3000'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry2'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'44'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry2'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'44'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])),</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="p">]</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="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;">initial_vars</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_add</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="64" style="width: 35px; color: rgba(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">@@ -64,8 +64,8 @@ class TestVariant(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<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_update_indel_insertion</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">'''Test update_indel extends insertions correctly'''</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">insertion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">Variant</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])))</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">to_add</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</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 class="s" style="color: #d14;">'101'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">insertion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">Variant</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">-1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])))</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">to_add</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</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 class="s" style="color: #d14;">'101'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">-1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">insertion</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># coords stored zero-based, so subtract 1 from the real expected coords</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">expected</span><span class="p">.</span><span class="n" style="color: #333;">ref_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">41</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">@@ -84,8 +84,8 @@ class TestVariant(unittest.TestCase):</td>
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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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_update_indel_deletion</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'''Test update_indel extends deletions correctly'''</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">deletion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">Variant</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])))</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">to_add</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">x</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">deletion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">Variant</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'42'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">])))</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">to_add</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">Snp</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'43'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'100'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'300'</span><span class="p">,</span> <span class="s" style="color: #d14;">'400'</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qry'</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">deletion</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># coords stored zero-based, so subtract 1 from the real expected coords</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">expected</span><span class="p">.</span><span class="n" style="color: #333;">ref_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">41</span></span>
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<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#c0eff944f273f4a98493277d5ba62565a298467e"><strong>pymummer/variant.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,7 @@ class Variant:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">qry_pos</span></span>
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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="p">.</span><span class="n" style="color: #333;">qry_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">qry_length</span></span>
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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="p">.</span><span class="n" style="color: #333;">qry_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">qry_name</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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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;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</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">@@ -54,7 +55,8 @@ class Variant:</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_end</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="LC56" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_length</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_name</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_base</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_base</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;">'-1'</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span></span>
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58
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="p">])</span></span>
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59
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update_indel</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nucmer_snp</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">@@ -63,7 +65,8 @@ class Variant:</td>
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63
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">var_type</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="n" style="color: #333;">INS</span><span class="p">,</span> <span class="n" style="color: #333;">DEL</span><span class="p">]</span> \</span>
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64
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">var_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_variant</span><span class="p">.</span><span class="n" style="color: #333;">var_type</span> \</span>
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65
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qry_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_variant</span><span class="p">.</span><span class="n" style="color: #333;">qry_name</span> \</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ref_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_variant</span><span class="p">.</span><span class="n" style="color: #333;">ref_name</span><span class="p">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ref_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_variant</span><span class="p">.</span><span class="n" style="color: #333;">ref_name</span> \</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_variant</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span><span class="p">:</span></span>
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67
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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68
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">var_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">INS</span> \</span>
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69
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ref_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">new_variant</span><span class="p">.</span><span class="n" style="color: #333;">ref_start</span> \</span>
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<a href="https://salsa.debian.org/med-team/python-pymummer/-/commit/786112ec15d531568d96c2a8c829ff889e60b7ed#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(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">@@ -26,7 +26,7 @@ if not found_all_progs:</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'pymummer'</span><span class="p">,</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" 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;">'0.1<span class="idiff left right">0.3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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;">'0.1<span class="idiff left right">1.0</span>'</span><span class="p">,</span></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Wrapper for MUMmer'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Martin Hunt, Nishadi De Silva'</span><span class="p">,</span></span>
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