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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4">897a8148</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2018-12-23T14:39:45Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.13.2+ds</pre>
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<h4>6 changed files:</h4>
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<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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<a href="#2a1e1b6414ed603b06fec0cdbe3def87a6de5920">
ariba/tb.py
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<li class="file-stats">
<a href="#4b78fa5767d377d1fc130725caf805bf47f3e4c4">
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ariba/tb_data/panel.20181221.json
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ariba/tb_data/panel.20181221.txt
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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/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4#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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<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/ariba/tree/HEAD)</span></span>
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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">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.13.1...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">
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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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> Update python min version <span class="p">[</span><span class="nv" style="color: teal;">\#247</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/247</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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<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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.13.1](https://github.com/sanger-pathogens/ariba/tree/v2.13.1) (2018-11-16)</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">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.13.0...v2.13.1</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">
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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;">**Closed issues:**</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> resfinder line breaks problem <span class="p">[</span><span class="nv" style="color: teal;">\#236</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/236</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">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></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 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="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>
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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> Include tb<span class="se" style="color: #d14;">\_</span>data dir in release <span class="p">[</span><span class="nv" style="color: teal;">\#244</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/244</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="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.13.0](https://github.com/sanger-pathogens/ariba/tree/v2.13.0) (2018-11-16)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.12.1...v2.13.0</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">-</span> Updated to 2.12.1 problems with resfinder <span class="p">[</span><span class="nv" style="color: teal;">\#237</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/237</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">-</span> Antibiotic resistance/susceptibility panel? <span class="p">[</span><span class="nv" style="color: teal;">\#232</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/232</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">-</span> Ariba fails when using virulencefinder db <span class="p">[</span><span class="nv" style="color: teal;">\#216</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/216</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">-</span> Ariba fails when using NFS directories for output <span class="p">[</span><span class="nv" style="color: teal;">\#203</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/203</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">-</span> Resfinder linebreaks <span class="p">[</span><span class="nv" style="color: teal;">\#243</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/243</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="LC35" class="line" lang="markdown"><span class="p">-</span> Tb amr <span class="p">[</span><span class="nv" style="color: teal;">\#242</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/242</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="LC36" class="line" lang="markdown"><span class="p">-</span> Do not use rmtree <span class="p">[</span><span class="nv" style="color: teal;">\#235</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/235</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="LC37" class="line" lang="markdown"><span class="p">-</span> Add to codecov <span class="p">[</span><span class="nv" style="color: teal;">\#234</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/234</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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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">-</span> Include conda and docker badges <span class="p">[</span><span class="nv" style="color: teal;">\#233</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/233</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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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.12.1](https://github.com/sanger-pathogens/ariba/tree/v2.12.1) (2018-06-15)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.12.0...v2.12.1</span><span class="p">)</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="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">-</span> PlasmidFinder databases have moved <span class="p">[</span><span class="nv" style="color: teal;">\#218</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/218</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="p">-</span> Add latest version of srst2<span class="se" style="color: #d14;">\_</span>argannot <span class="se" style="color: #d14;">\(</span>ARGannot<span class="se" style="color: #d14;">\_</span>r2.fasta<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: teal;">\#217</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/217</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="p">-</span> Necessity of spades executable? <span class="p">[</span><span class="nv" style="color: teal;">\#214</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/214</span><span class="p">)</span></span>
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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="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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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="p">-</span> Fix virulencefinder download <span class="p">[</span><span class="nv" style="color: teal;">\#228</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/228</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="LC52" class="line" lang="markdown"><span class="p">-</span> Update docker image to Ubuntu 17.10 and Ariba v.2.12.0 <span class="p">[</span><span class="nv" style="color: teal;">\#227</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/227</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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<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;">## [v2.12.0](https://github.com/sanger-pathogens/ariba/tree/v2.12.0) (2018-05-13)</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: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.11.1...v2.12.0</span><span class="p">)</span></span>
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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;">**Closed issues:**</span></span>
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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> Problems Task getref xxxxFinder and CARD <span class="p">[</span><span class="nv" style="color: teal;">\#211</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/211</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC61" 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="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> Remove spades warnings <span class="p">[</span><span class="nv" style="color: teal;">\#224</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/224</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="LC64" class="line" lang="markdown"><span class="p">-</span> Get srst2<span class="se" style="color: #d14;">\_</span>argannot latest version r2 by default <span class="p">[</span><span class="nv" style="color: teal;">\#223</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/223</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="LC65" class="line" lang="markdown"><span class="p">-</span> Getref xfinder bitbucket <span class="p">[</span><span class="nv" style="color: teal;">\#222</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/222</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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"><span class="p">-</span> virulencefinder and nucmer version fixes <span class="p">[</span><span class="nv" style="color: teal;">\#220</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/220</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="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="p">-</span> change path to license file <span class="p">[</span><span class="nv" style="color: teal;">\#219</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/219</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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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></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="gu" style="color: #800080; font-weight: 600;">## [v2.11.1](https://github.com/sanger-pathogens/ariba/tree/v2.11.1) (2018-02-26)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.11.0-1...v2.11.1</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="p">-</span> fix card db path <span class="p">[</span><span class="nv" style="color: teal;">\#213</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/213</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[eppinglen](https://github.com/eppinglen</span><span class="p">)</span>)</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.11.0-1](https://github.com/sanger-pathogens/ariba/tree/v2.11.0-1) (2018-02-02)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.11.0...v2.11.0-1</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.11.0](https://github.com/sanger-pathogens/ariba/tree/v2.11.0) (2018-02-02)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.10.4...v2.11.0</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="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="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"><span class="p">-</span> micplot requires X window <span class="p">[</span><span class="nv" style="color: teal;">\#176</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/176</span><span class="p">)</span></span>
</pre>
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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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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="p">-</span> Option to use Spades and multithreading for Bowtie2 and Spades <span class="p">[</span><span class="nv" style="color: teal;">\#210</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/210</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andreyto](https://github.com/andreyto</span><span class="p">)</span>)</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"></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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.10.4](https://github.com/sanger-pathogens/ariba/tree/v2.10.4) (2018-02-01)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.10.3...v2.10.4</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"></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> Fails to getref card <span class="p">[</span><span class="nv" style="color: teal;">\#206</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/206</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="p">-</span> dont require X to run ariba <span class="p">[</span><span class="nv" style="color: teal;">\#209</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/209</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="p">-</span> update readme <span class="p">[</span><span class="nv" style="color: teal;">\#208</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/208</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="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.10.3](https://github.com/sanger-pathogens/ariba/tree/v2.10.3) (2017-11-24)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.10.2...v2.10.3</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"></span>
</pre>
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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="gs" style="font-weight: 600;">**Closed issues:**</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
</pre>
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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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="p">-</span> CARD downloads now bz2 <span class="p">[</span><span class="nv" style="color: teal;">\#200</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/200</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC109" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="markdown"><span class="p">-</span> Mlst hetmin bug <span class="p">[</span><span class="nv" style="color: teal;">\#204</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/204</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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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC113" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.10.2](https://github.com/sanger-pathogens/ariba/tree/v2.10.2) (2017-11-08)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.10.1...v2.10.2</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="p">-</span> The meaning of the flag "ref<span class="se" style="color: #d14;">\_</span>seq<span class="se" style="color: #d14;">\_</span>choose<span class="se" style="color: #d14;">\_</span>fail" <span class="p">[</span><span class="nv" style="color: teal;">\#199</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/199</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="p">-</span> How ariba deal with reads mapped to multiple clusters <span class="p">[</span><span class="nv" style="color: teal;">\#198</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/198</span><span class="p">)</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"><span class="p">-</span> TypeError <span class="p">[</span><span class="nv" style="color: teal;">\#197</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/197</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="p">-</span> Test failures with bowtie2 2.3.2 <span class="p">[</span><span class="nv" style="color: teal;">\#190</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/190</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="p">-</span> Version bump 2.10.2 <span class="p">[</span><span class="nv" style="color: teal;">\#202</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/202</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="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"><span class="p">-</span> Changed card to utilise .tar.bz2 from .tar.gz <span class="p">[</span><span class="nv" style="color: teal;">\#201</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/201</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[JezSw](https://github.com/JezSw</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="p">-</span> correct spelling mistake <span class="p">[</span><span class="nv" style="color: teal;">\#195</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/195</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[EdwardBetts](https://github.com/EdwardBetts</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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"></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="gu" style="color: #800080; font-weight: 600;">## [v2.10.1](https://github.com/sanger-pathogens/ariba/tree/v2.10.1) (2017-08-14)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.10.0...v2.10.1</span><span class="p">)</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC132" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="p">-</span> Creation of custom variant database containing indels, both in-frame or frameshifts <span class="p">[</span><span class="nv" style="color: teal;">\#189</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/189</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"><span class="p">-</span> Clusters listed in debug.report.tsv not in report.tsv <span class="p">[</span><span class="nv" style="color: teal;">\#188</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/188</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="p">-</span> <span class="se" style="color: #d14;">\_\_</span>main<span class="se" style="color: #d14;">\_\_</span> error message <span class="p">[</span><span class="nv" style="color: teal;">\#187</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/187</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"><span class="p">-</span> Failed Cluster <span class="p">[</span><span class="nv" style="color: teal;">\#186</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/186</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"><span class="p">-</span> What about MLST not hosted at pubmlst.org? <span class="p">[</span><span class="nv" style="color: teal;">\#185</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/185</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"><span class="p">-</span> How to detect presence or absence of a sequence carrying a deletion <span class="p">[</span><span class="nv" style="color: teal;">\#184</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/184</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="p">-</span> Add curl <span class="p">[</span><span class="nv" style="color: teal;">\#194</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/194</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="LC144" class="line" lang="markdown"><span class="p">-</span> Bowtie2 version issues <span class="p">[</span><span class="nv" style="color: teal;">\#193</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/193</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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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"><span class="p">-</span> Fix utf-8 encoding problems <span class="p">[</span><span class="nv" style="color: teal;">\#192</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/192</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[aunderwo](https://github.com/aunderwo</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"><span class="p">-</span> Install specific release instead of master branch <span class="p">[</span><span class="nv" style="color: teal;">\#191</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/191</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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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.10.0](https://github.com/sanger-pathogens/ariba/tree/v2.10.0) (2017-06-28)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.9.4...v2.10.0</span><span class="p">)</span></span>
</pre>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC151" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="p">-</span> pubmlstget does not work with docker <span class="p">[</span><span class="nv" style="color: teal;">\#180</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/180</span><span class="p">)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="p">-</span> getref broken on CARD v1.1.8 <span class="p">[</span><span class="nv" style="color: teal;">\#178</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/178</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" 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="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"><span class="p">-</span> Reviewer issues <span class="p">[</span><span class="nv" style="color: teal;">\#182</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/182</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="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"><span class="p">-</span> Task expandflag <span class="p">[</span><span class="nv" style="color: teal;">\#181</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/181</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.9.4](https://github.com/sanger-pathogens/ariba/tree/v2.9.4) (2017-05-24)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.9.3...v2.9.4</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="p">-</span> problems with fermilite <span class="p">[</span><span class="nv" style="color: teal;">\#169</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/169</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"><span class="p">-</span> Card 1.1.8 <span class="p">[</span><span class="nv" style="color: teal;">\#179</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/179</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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"><span class="p">-</span> update AUTHORS and LICENSE <span class="p">[</span><span class="nv" style="color: teal;">\#177</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/177</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="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.9.3](https://github.com/sanger-pathogens/ariba/tree/v2.9.3) (2017-04-28)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.9.2...v2.9.3</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="p">-</span> Test failures with bowtie2 2.3.1 <span class="p">[</span><span class="nv" style="color: teal;">\#170</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/170</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" 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="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"><span class="p">-</span> Getmlst dots in names <span class="p">[</span><span class="nv" style="color: teal;">\#175</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/175</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="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.9.2](https://github.com/sanger-pathogens/ariba/tree/v2.9.2) (2017-04-27)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.9.1...v2.9.2</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
</pre>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown"><span class="p">-</span> Curious output <span class="p">[</span><span class="nv" style="color: teal;">\#172</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/172</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown"><span class="p">-</span> How to input several fastq files for pooled assembly? <span class="p">[</span><span class="nv" style="color: teal;">\#171</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/171</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="markdown"><span class="p">-</span> Bowtie2.3.1 <span class="p">[</span><span class="nv" style="color: teal;">\#174</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/174</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="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.9.1](https://github.com/sanger-pathogens/ariba/tree/v2.9.1) (2017-04-07)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.9.0...v2.9.1</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"><span class="p">-</span> Failing to build wheel <span class="p">[</span><span class="nv" style="color: teal;">\#168</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/168</span><span class="p">)</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown"><span class="p">-</span> add VirulenceFinder <span class="p">[</span><span class="nv" style="color: teal;">\#165</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/165</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC204" 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="LC205" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown"><span class="p">-</span> Summary yes mutli het key error <span class="p">[</span><span class="nv" style="color: teal;">\#173</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/173</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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.9.0](https://github.com/sanger-pathogens/ariba/tree/v2.9.0) (2017-03-31)</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.8.1...v2.9.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"><span class="p">-</span> Ecoli no 1 profile warning <span class="p">[</span><span class="nv" style="color: teal;">\#163</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/163</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC214" class="line" lang="markdown"><span class="p">-</span> Failed building wheel for ariba <span class="p">[</span><span class="nv" style="color: teal;">\#161</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/161</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"><span class="p">-</span> getref CARD <span class="p">[</span><span class="nv" style="color: teal;">\#160</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/160</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC217" 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="LC218" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"><span class="p">-</span> Summary read depth column <span class="p">[</span><span class="nv" style="color: teal;">\#167</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/167</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="LC220" class="line" lang="markdown"><span class="p">-</span> new method <span class="se" style="color: #d14;">\_</span>get<span class="se" style="color: #d14;">\_</span>from<span class="se" style="color: #d14;">\_</span>virulencefinder <span class="p">[</span><span class="nv" style="color: teal;">\#166</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/166</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="221" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC221" class="line" lang="markdown"><span class="p">-</span> Fix bug in README subheading rendering <span class="p">[</span><span class="nv" style="color: teal;">\#164</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/164</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[fmaguire](https://github.com/fmaguire</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.8.1](https://github.com/sanger-pathogens/ariba/tree/v2.8.1) (2017-03-04)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.7.2...v2.8.1</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown"><span class="p">-</span> compilation problem: ku128<span class="se" style="color: #d14;">\_</span>v <span class="se" style="color: #d14;">\*</span>r = <span class="ni" style="color: purple;">&g-\>v.a\[idd\>\>1\].nei\[idd&1\];</span> <span class="p">[</span><span class="nv" style="color: teal;">\#159</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/159</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="p">-</span> error generating cluster <span class="p">[</span><span class="nv" style="color: teal;">\#157</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/157</span><span class="p">)</span></span>
</pre>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"><span class="p">-</span> --threads bug? <span class="p">[</span><span class="nv" style="color: teal;">\#155</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/155</span><span class="p">)</span></span>
</pre>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown"><span class="p">-</span> Mic plots <span class="p">[</span><span class="nv" style="color: teal;">\#162</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/162</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>
</pre>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC236" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.7.2](https://github.com/sanger-pathogens/ariba/tree/v2.7.2) (2017-02-02)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.7.1...v2.7.2</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC239" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"><span class="p">-</span> Require pymummer 0.10.2 <span class="p">[</span><span class="nv" style="color: teal;">\#158</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/158</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC243" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.7.1](https://github.com/sanger-pathogens/ariba/tree/v2.7.1) (2017-01-27)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.7.0...v2.7.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"><span class="p">-</span> Newick rooting bug <span class="p">[</span><span class="nv" style="color: teal;">\#156</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/156</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="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"><span class="p">-</span> Check BeautifulSoup version number <span class="p">[</span><span class="nv" style="color: teal;">\#154</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/154</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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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.7.0](https://github.com/sanger-pathogens/ariba/tree/v2.7.0) (2017-01-17)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.6.1...v2.7.0</span><span class="p">)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown"></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown"></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"><span class="p">-</span> Add megares <span class="p">[</span><span class="nv" style="color: teal;">\#153</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/153</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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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.6.1](https://github.com/sanger-pathogens/ariba/tree/v2.6.1) (2016-12-21)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.6.0...v2.6.1</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="markdown"><span class="p">-</span> Ignore additional columns in MLST profiles <span class="p">[</span><span class="nv" style="color: teal;">\#152</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/152</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.6.0](https://github.com/sanger-pathogens/ariba/tree/v2.6.0) (2016-12-20)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.5.1...v2.6.0</span><span class="p">)</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" 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="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown"><span class="p">-</span> Pubmlst <span class="p">[</span><span class="nv" style="color: teal;">\#151</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/151</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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.5.1](https://github.com/sanger-pathogens/ariba/tree/v2.5.1) (2016-12-05)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.5.0...v2.5.1</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" 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="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown"><span class="p">-</span> Use flank length to choose best assembly <span class="p">[</span><span class="nv" style="color: teal;">\#150</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/150</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="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.5.0](https://github.com/sanger-pathogens/ariba/tree/v2.5.0) (2016-11-18)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.4.0...v2.5.0</span><span class="p">)</span></span>
</pre>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="markdown"><span class="p">-</span> broken link in the tarball hosted in pypi <span class="p">[</span><span class="nv" style="color: teal;">\#147</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/147</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="markdown"><span class="p">-</span> Ref seq choose use qry length <span class="p">[</span><span class="nv" style="color: teal;">\#149</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/149</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.4.0](https://github.com/sanger-pathogens/ariba/tree/v2.4.0) (2016-11-01)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.3.0...v2.4.0</span><span class="p">)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="markdown"><span class="p">-</span> Honour $TMPDIR for temporary files <span class="p">[</span><span class="nv" style="color: teal;">\#143</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/143</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="markdown"><span class="p">-</span> Report full codon change eg. AAT=<span class="se" style="color: #d14;">\></span>AGG <span class="p">[</span><span class="nv" style="color: teal;">\#142</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/142</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="markdown"><span class="p">-</span> Report "partial" when 1 contig but not full gene <span class="p">[</span><span class="nv" style="color: teal;">\#141</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/141</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="markdown"><span class="p">-</span> Add --force to allow overwriting of output<span class="se" style="color: #d14;">\_</span>dir <span class="p">[</span><span class="nv" style="color: teal;">\#138</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/138</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="markdown"><span class="p">-</span> Report original names from gene database <span class="p">[</span><span class="nv" style="color: teal;">\#136</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/136</span><span class="p">)</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="markdown"><span class="p">-</span> Cleanup after getref <span class="p">[</span><span class="nv" style="color: teal;">\#135</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/135</span><span class="p">)</span></span>
</pre>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC304" class="line" lang="markdown"><span class="p">-</span> Consecutive genes fix <span class="p">[</span><span class="nv" style="color: teal;">\#148</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/148</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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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC306" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.3.0](https://github.com/sanger-pathogens/ariba/tree/v2.3.0) (2016-10-12)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.2.5...v2.3.0</span><span class="p">)</span></span>
</pre>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC309" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown"><span class="p">-</span> Check minimap threads <span class="p">[</span><span class="nv" style="color: teal;">\#144</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/144</span><span class="p">)</span></span>
</pre>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="markdown"><span class="p">-</span> Torsten issues <span class="p">[</span><span class="nv" style="color: teal;">\#146</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/146</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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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="markdown"><span class="p">-</span> Report full codons and original sequence names <span class="p">[</span><span class="nv" style="color: teal;">\#145</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/145</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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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="markdown"><span class="p">-</span> Remove cdhit 2d <span class="p">[</span><span class="nv" style="color: teal;">\#140</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/140</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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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="markdown"><span class="p">-</span> Het snp bugs <span class="p">[</span><span class="nv" style="color: teal;">\#139</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/139</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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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown"><span class="p">-</span> Docker installation <span class="p">[</span><span class="nv" style="color: teal;">\#137</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/137</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="markdown"><span class="p">-</span> Fix for download changes to resfinder data <span class="p">[</span><span class="nv" style="color: teal;">\#134</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/134</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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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.5](https://github.com/sanger-pathogens/ariba/tree/v2.2.5) (2016-08-31)</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.2.4...v2.2.5</span><span class="p">)</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="markdown"><span class="p">-</span> Bcftools ploidy <span class="p">[</span><span class="nv" style="color: teal;">\#133</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/133</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="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="markdown"></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.4](https://github.com/sanger-pathogens/ariba/tree/v2.2.4) (2016-08-23)</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.2.3...v2.2.4</span><span class="p">)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="markdown"></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="markdown"></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="markdown"><span class="p">-</span> Reportfilter bug <span class="p">[</span><span class="nv" style="color: teal;">\#132</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/132</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="LC335" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC336" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.3](https://github.com/sanger-pathogens/ariba/tree/v2.2.3) (2016-08-22)</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.2.2...v2.2.3</span><span class="p">)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="markdown"><span class="p">-</span> bug fix summary when no samtools alt <span class="p">[</span><span class="nv" style="color: teal;">\#131</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/131</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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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC343" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.2](https://github.com/sanger-pathogens/ariba/tree/v2.2.2) (2016-08-22)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.2.1...v2.2.2</span><span class="p">)</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="markdown"></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="markdown"></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="markdown"><span class="p">-</span> Contig renaming <span class="p">[</span><span class="nv" style="color: teal;">\#130</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/130</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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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.1](https://github.com/sanger-pathogens/ariba/tree/v2.2.1) (2016-08-18)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.2.0...v2.2.1</span><span class="p">)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="markdown"></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="markdown"><span class="p">-</span> Aln2meta fix <span class="p">[</span><span class="nv" style="color: teal;">\#129</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/129</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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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.0](https://github.com/sanger-pathogens/ariba/tree/v2.2.0) (2016-08-18)</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.1.0...v2.2.0</span><span class="p">)</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="markdown"><span class="p">-</span> Version bump 2.2.0 <span class="p">[</span><span class="nv" style="color: teal;">\#128</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/128</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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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="markdown"><span class="p">-</span> summary no/NA consistency, phandango NAs <span class="p">[</span><span class="nv" style="color: teal;">\#127</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/127</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="LC364" class="line" lang="markdown"><span class="p">-</span> Spaces in fasta headers <span class="p">[</span><span class="nv" style="color: teal;">\#126</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/126</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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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="markdown"><span class="p">-</span> Split show<span class="se" style="color: #d14;">\_</span>vars option into show<span class="se" style="color: #d14;">\_</span>known<span class="se" style="color: #d14;">\_</span>vars and show<span class="se" style="color: #d14;">\_</span>novel<span class="se" style="color: #d14;">\_</span>vars <span class="p">[</span><span class="nv" style="color: teal;">\#125</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/125</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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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="markdown"><span class="p">-</span> Bug fix reporting ref<span class="se" style="color: #d14;">\_</span>base<span class="se" style="color: #d14;">\_</span>assembled for a partial gene assembly <span class="p">[</span><span class="nv" style="color: teal;">\#124</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/124</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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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="markdown"><span class="p">-</span> When assembled is no, everything else should be no or NA <span class="p">[</span><span class="nv" style="color: teal;">\#123</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/123</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="LC368" class="line" lang="markdown"><span class="p">-</span> Vfdb get full and core <span class="p">[</span><span class="nv" style="color: teal;">\#122</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/122</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="LC369" class="line" lang="markdown"><span class="p">-</span> Add option to choose download version <span class="p">[</span><span class="nv" style="color: teal;">\#121</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/121</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="LC370" class="line" lang="markdown"><span class="p">-</span> Summary improvements <span class="p">[</span><span class="nv" style="color: teal;">\#120</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/120</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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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="markdown"><span class="p">-</span> Allow fasta only to prepareref <span class="p">[</span><span class="nv" style="color: teal;">\#119</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/119</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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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="markdown"><span class="p">-</span> Add srst2 argannot <span class="p">[</span><span class="nv" style="color: teal;">\#118</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/118</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="LC373" class="line" lang="markdown"><span class="p">-</span> Shorten filenames <span class="p">[</span><span class="nv" style="color: teal;">\#117</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/117</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="LC374" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.1.0](https://github.com/sanger-pathogens/ariba/tree/v2.1.0) (2016-08-03)</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.0.0...v2.1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="markdown"></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="markdown"><span class="p">-</span> V2.0.0 bug fixes/improvements <span class="p">[</span><span class="nv" style="color: teal;">\#116</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/116</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="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="markdown"><span class="p">-</span> Het snp reporting <span class="p">[</span><span class="nv" style="color: teal;">\#115</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/115</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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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="markdown"><span class="p">-</span> Minor fixes <span class="p">[</span><span class="nv" style="color: teal;">\#114</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/114</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[satta](https://github.com/satta</span><span class="p">)</span>)</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="markdown"><span class="p">-</span> Make sure c<span class="se" style="color: #d14;">\*</span>.h files included in distribution <span class="p">[</span><span class="nv" style="color: teal;">\#113</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/113</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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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.0.0](https://github.com/sanger-pathogens/ariba/tree/v2.0.0) (2016-07-29)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v1.0.1...v2.0.0</span><span class="p">)</span></span>
</pre>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="markdown"></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="markdown"></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="markdown"><span class="p">-</span> report.tsv empty <span class="p">[</span><span class="nv" style="color: teal;">\#96</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/96</span><span class="p">)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="markdown"></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="markdown"><span class="p">-</span> Update card version to 1.0.9 <span class="p">[</span><span class="nv" style="color: teal;">\#112</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/112</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="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="markdown"><span class="p">-</span> Tidy files <span class="p">[</span><span class="nv" style="color: teal;">\#111</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/111</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="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="markdown"><span class="p">-</span> Rename clusters <span class="p">[</span><span class="nv" style="color: teal;">\#110</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/110</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="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="markdown"><span class="p">-</span> End extend assemble flag bug <span class="p">[</span><span class="nv" style="color: teal;">\#109</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/109</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="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="markdown"><span class="p">-</span> Use fermilite <span class="p">[</span><span class="nv" style="color: teal;">\#108</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/108</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="LC399" class="line" lang="markdown"><span class="p">-</span> General tidying <span class="p">[</span><span class="nv" style="color: teal;">\#107</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/107</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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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="markdown"><span class="p">-</span> Put -h option back for older python versions <span class="p">[</span><span class="nv" style="color: teal;">\#106</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/106</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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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="markdown"><span class="p">-</span> Use subcommands <span class="p">[</span><span class="nv" style="color: teal;">\#105</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/105</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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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="markdown"><span class="p">-</span> Check dendropy found and version ok <span class="p">[</span><span class="nv" style="color: teal;">\#104</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/104</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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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="markdown"><span class="p">-</span> Dendropy <span class="p">[</span><span class="nv" style="color: teal;">\#103</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/103</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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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="markdown"><span class="p">-</span> Minimap remove noise <span class="p">[</span><span class="nv" style="color: teal;">\#102</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/102</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="LC405" class="line" lang="markdown"><span class="p">-</span> Use minimap <span class="p">[</span><span class="nv" style="color: teal;">\#101</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/101</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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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="markdown"><span class="p">-</span> allow full VFDB to be downloaded <span class="p">[</span><span class="nv" style="color: teal;">\#99</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/99</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.1](https://github.com/sanger-pathogens/ariba/tree/v1.0.1) (2016-06-28)</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v1.0.0...v1.0.1</span><span class="p">)</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="markdown"><span class="p">-</span> Error running --test with CD-HIT and SPAdes <span class="p">[</span><span class="nv" style="color: teal;">\#95</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/95</span><span class="p">)</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="markdown"><span class="p">-</span> Spades not untrusted <span class="p">[</span><span class="nv" style="color: teal;">\#98</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/98</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="LC418" class="line" lang="markdown"><span class="p">-</span> add disclaimer to readme <span class="p">[</span><span class="nv" style="color: teal;">\#97</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/97</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="LC419" class="line" lang="markdown"><span class="p">-</span> Add tmp dir description <span class="p">[</span><span class="nv" style="color: teal;">\#94</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/94</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="LC420" class="line" lang="markdown"><span class="p">-</span> Make clearer that the env vars are exectuables, not dirs <span class="p">[</span><span class="nv" style="color: teal;">\#93</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/93</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="LC421" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.0](https://github.com/sanger-pathogens/ariba/tree/v1.0.0) (2016-05-27)</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/wip...v1.0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC425" 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="LC427" class="line" lang="markdown"><span class="p">-</span> Readme for 1.0.0 <span class="p">[</span><span class="nv" style="color: teal;">\#92</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/92</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="LC428" class="line" lang="markdown"><span class="p">-</span> Phandango colours <span class="p">[</span><span class="nv" style="color: teal;">\#91</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/91</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="LC429" class="line" lang="markdown"><span class="p">-</span> Group snps <span class="p">[</span><span class="nv" style="color: teal;">\#90</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/90</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="LC430" class="line" lang="markdown"><span class="p">-</span> Only calculate half the matrix <span class="se" style="color: #d14;">\(</span>it's symmetric<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: teal;">\#89</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/89</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="LC431" class="line" lang="markdown"><span class="p">-</span> No attr assembly compare bug <span class="p">[</span><span class="nv" style="color: teal;">\#88</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/88</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="LC432" class="line" lang="markdown"><span class="p">-</span> Vfdb names <span class="p">[</span><span class="nv" style="color: teal;">\#87</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/87</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="LC433" class="line" lang="markdown"><span class="p">-</span> Say type is INT in the help <span class="p">[</span><span class="nv" style="color: teal;">\#86</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/86</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="LC434" class="line" lang="markdown"><span class="p">-</span> Match gene ends <span class="p">[</span><span class="nv" style="color: teal;">\#85</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/85</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="LC435" class="line" lang="markdown"><span class="p">-</span> Always report presabs vars <span class="p">[</span><span class="nv" style="color: teal;">\#84</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/84</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="LC436" class="line" lang="markdown"><span class="p">-</span> Stop returning error when all clusters successful <span class="p">[</span><span class="nv" style="color: teal;">\#83</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/83</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="LC437" class="line" lang="markdown"><span class="p">-</span> Tmp dir cleaning <span class="p">[</span><span class="nv" style="color: teal;">\#82</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/82</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="LC438" class="line" lang="markdown"><span class="p">-</span> Die if spades error code is -7 <span class="p">[</span><span class="nv" style="color: teal;">\#81</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/81</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="LC439" class="line" lang="markdown"><span class="p">-</span> Specify cdhit clusters <span class="p">[</span><span class="nv" style="color: teal;">\#80</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/80</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="LC440" class="line" lang="markdown"><span class="p">-</span> Tmp dir option <span class="p">[</span><span class="nv" style="color: teal;">\#79</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/79</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="LC441" class="line" lang="markdown"><span class="p">-</span> Bug fix with presets. Should be y/n not yes/no <span class="p">[</span><span class="nv" style="color: teal;">\#78</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/78</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="LC442" class="line" lang="markdown"><span class="p">-</span> Update card from 1.0.5 to 1.0.6 <span class="p">[</span><span class="nv" style="color: teal;">\#77</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/77</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="LC443" class="line" lang="markdown"><span class="p">-</span> Summary fixes <span class="p">[</span><span class="nv" style="color: teal;">\#76</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/76</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="LC444" class="line" lang="markdown"><span class="p">-</span> Summary column control <span class="p">[</span><span class="nv" style="color: teal;">\#75</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/75</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="LC445" class="line" lang="markdown"><span class="p">-</span> Minimise files <span class="p">[</span><span class="nv" style="color: teal;">\#74</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/74</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="LC446" class="line" lang="markdown"><span class="p">-</span> Summary inconsistent bug <span class="p">[</span><span class="nv" style="color: teal;">\#73</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/73</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="LC447" class="line" lang="markdown"><span class="p">-</span> bug fix, files were not being deleted <span class="p">[</span><span class="nv" style="color: teal;">\#72</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/72</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="LC448" class="line" lang="markdown"><span class="p">-</span> Bug fix, now it actually deletes files as it goes <span class="p">[</span><span class="nv" style="color: teal;">\#71</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/71</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="LC449" class="line" lang="markdown"><span class="p">-</span> Various fixes <span class="p">[</span><span class="nv" style="color: teal;">\#70</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/70</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="LC450" class="line" lang="markdown"><span class="p">-</span> Various fixes <span class="p">[</span><span class="nv" style="color: teal;">\#69</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/69</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="LC451" class="line" lang="markdown"><span class="p">-</span> Various fixes <span class="p">[</span><span class="nv" style="color: teal;">\#68</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/68</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="LC452" class="line" lang="markdown"><span class="p">-</span> VFDB downloader <span class="p">[</span><span class="nv" style="color: teal;">\#67</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/67</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="markdown"><span class="p">-</span> Rename sequences <span class="p">[</span><span class="nv" style="color: teal;">\#66</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/66</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="LC455" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [wip](https://github.com/sanger-pathogens/ariba/tree/wip) (2016-04-27)</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.6.0...wip</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Implemented enhancements:**</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="markdown"><span class="p">-</span> Tests assume installed version of SPAdes <span class="p">[</span><span class="nv" style="color: teal;">\#40</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/40</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC462" 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="LC463" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="markdown"><span class="p">-</span> Catch when no coverage from samtools <span class="p">[</span><span class="nv" style="color: teal;">\#65</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/65</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="LC465" class="line" lang="markdown"><span class="p">-</span> Summary improvements <span class="p">[</span><span class="nv" style="color: teal;">\#64</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/64</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="LC466" class="line" lang="markdown"><span class="p">-</span> Card rename <span class="p">[</span><span class="nv" style="color: teal;">\#63</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/63</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="LC467" class="line" lang="markdown"><span class="p">-</span> Better cluster naming <span class="p">[</span><span class="nv" style="color: teal;">\#62</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/62</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="LC468" class="line" lang="markdown"><span class="p">-</span> contig cov col report <span class="p">[</span><span class="nv" style="color: teal;">\#61</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/61</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="LC469" class="line" lang="markdown"><span class="p">-</span> Catch when cannot determine insert size data <span class="p">[</span><span class="nv" style="color: teal;">\#60</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/60</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="LC470" class="line" lang="markdown"><span class="p">-</span> Report all versions <span class="p">[</span><span class="nv" style="color: teal;">\#59</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/59</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="LC471" class="line" lang="markdown"><span class="p">-</span> Bug fix with free text being put into more than one column <span class="p">[</span><span class="nv" style="color: teal;">\#58</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/58</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="LC472" class="line" lang="markdown"><span class="p">-</span> Set nucmer opts to match nucmers defaults, but add --maxmatch <span class="p">[</span><span class="nv" style="color: teal;">\#57</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/57</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="LC473" class="line" lang="markdown"><span class="p">-</span> New task prepareref <span class="p">[</span><span class="nv" style="color: teal;">\#56</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/56</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="LC474" class="line" lang="markdown"><span class="p">-</span> Do not assume cluster representative comes first <span class="p">[</span><span class="nv" style="color: teal;">\#55</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/55</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="LC475" class="line" lang="markdown"><span class="p">-</span> Card update use json <span class="p">[</span><span class="nv" style="color: teal;">\#54</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/54</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="LC476" class="line" lang="markdown"><span class="p">-</span> Add files for TravisCI <span class="p">[</span><span class="nv" style="color: teal;">\#53</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/53</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="LC477" class="line" lang="markdown"><span class="p">-</span> Phandango r bug <span class="p">[</span><span class="nv" style="color: teal;">\#52</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/52</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="LC478" class="line" lang="markdown"><span class="p">-</span> Check all input files exist <span class="p">[</span><span class="nv" style="color: teal;">\#51</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/51</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="LC479" class="line" lang="markdown"><span class="p">-</span> Bug in get one variant for one contig coding <span class="p">[</span><span class="nv" style="color: teal;">\#50</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/50</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="LC480" class="line" lang="markdown"><span class="p">-</span> Check reads files exists before running pipeline <span class="p">[</span><span class="nv" style="color: teal;">\#49</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/49</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="LC481" class="line" lang="markdown"><span class="p">-</span> Provide getref prefix to run <span class="p">[</span><span class="nv" style="color: teal;">\#48</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/48</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="LC482" class="line" lang="markdown"><span class="p">-</span> Phandango fix <span class="p">[</span><span class="nv" style="color: teal;">\#47</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/47</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="LC483" class="line" lang="markdown"><span class="p">-</span> Sample reads <span class="p">[</span><span class="nv" style="color: teal;">\#46</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/46</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="LC484" class="line" lang="markdown"><span class="p">-</span> One thread not use multithreaded <span class="p">[</span><span class="nv" style="color: teal;">\#45</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/45</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="LC485" class="line" lang="markdown"><span class="p">-</span> Make filtered report <span class="p">[</span><span class="nv" style="color: teal;">\#44</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/44</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="LC486" class="line" lang="markdown"><span class="p">-</span> New task reportfilter <span class="p">[</span><span class="nv" style="color: teal;">\#43</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/43</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="LC487" class="line" lang="markdown"><span class="p">-</span> Bux fix filtering rows <span class="p">[</span><span class="nv" style="color: teal;">\#42</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/42</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="LC488" class="line" lang="markdown"><span class="p">-</span> Auto get ref genes, variant handling <span class="p">[</span><span class="nv" style="color: teal;">\#41</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/41</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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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="markdown"><span class="p">-</span> fix typo <span class="p">[</span><span class="nv" style="color: teal;">\#39</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/39</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[satta](https://github.com/satta</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="markdown"><span class="p">-</span> Implement multithreading <span class="p">[</span><span class="nv" style="color: teal;">\#38</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/38</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="LC491" class="line" lang="markdown"><span class="p">-</span> Always run refcheck; Add JS candy output <span class="p">[</span><span class="nv" style="color: teal;">\#37</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/37</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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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.0](https://github.com/sanger-pathogens/ariba/tree/v0.6.0) (2015-10-28)</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.5.0...v0.6.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC496" 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="LC497" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="markdown"><span class="p">-</span> Improvements to summary output; new flag for non-synonymous variants <span class="p">[</span><span class="nv" style="color: teal;">\#36</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/36</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="LC499" class="line" lang="markdown"><span class="p">-</span> Clarify usage: input must be tsv, not xls <span class="p">[</span><span class="nv" style="color: teal;">\#35</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/35</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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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC501" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.0](https://github.com/sanger-pathogens/ariba/tree/v0.5.0) (2015-09-10)</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.4.1...v0.5.0</span><span class="p">)</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="markdown"></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="markdown"><span class="p">-</span> Various improvements <span class="p">[</span><span class="nv" style="color: teal;">\#34</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/34</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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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="markdown"><span class="p">-</span> Bug fix: refcheck now dies if spaces in sequence names <span class="p">[</span><span class="nv" style="color: teal;">\#33</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/33</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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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="markdown"><span class="p">-</span> Added AUTHORS with mh12 as author <span class="p">[</span><span class="nv" style="color: teal;">\#32</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/32</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[aslett1](https://github.com/aslett1</span><span class="p">)</span>)</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC510" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4.1](https://github.com/sanger-pathogens/ariba/tree/v0.4.1) (2015-07-14)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.4.0...v0.4.1</span><span class="p">)</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="markdown"><span class="p">-</span> Spades use untrusted-contigs <span class="p">[</span><span class="nv" style="color: teal;">\#31</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/31</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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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC517" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4.0](https://github.com/sanger-pathogens/ariba/tree/v0.4.0) (2015-06-10)</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.3.2...v0.4.0</span><span class="p">)</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="markdown"><span class="p">-</span> Flag hit both strands <span class="p">[</span><span class="nv" style="color: teal;">\#30</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/30</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="LC523" class="line" lang="markdown"><span class="p">-</span> Make cdhit optional <span class="p">[</span><span class="nv" style="color: teal;">\#29</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/29</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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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC525" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3.2](https://github.com/sanger-pathogens/ariba/tree/v0.3.2) (2015-05-12)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.3.1...v0.3.2</span><span class="p">)</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="markdown"></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="markdown"><span class="p">-</span> Bug when samtools zero depth <span class="p">[</span><span class="nv" style="color: teal;">\#28</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/28</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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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3.1](https://github.com/sanger-pathogens/ariba/tree/v0.3.1) (2015-04-20)</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.3.0...v0.3.1</span><span class="p">)</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="markdown"></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="markdown"><span class="p">-</span> Bug fix aln score zero <span class="p">[</span><span class="nv" style="color: teal;">\#27</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/27</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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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="markdown"><span class="p">-</span> Bug fix getting read depth when there is an indel <span class="p">[</span><span class="nv" style="color: teal;">\#26</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="markdown"><span class="p">-</span> SSAPCE sd cannot exceed 1 <span class="p">[</span><span class="nv" style="color: teal;">\#25</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC541" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3.0](https://github.com/sanger-pathogens/ariba/tree/v0.3.0) (2015-04-07)</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.2.0...v0.3.0</span><span class="p">)</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC544" 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="LC545" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="markdown"><span class="p">-</span> Add test log file and do not gitignore .log files <span class="p">[</span><span class="nv" style="color: teal;">\#24</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="markdown"><span class="p">-</span> add option bowtie2<span class="se" style="color: #d14;">\_</span>preset; version bump <span class="p">[</span><span class="nv" style="color: teal;">\#23</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC548" class="line" lang="markdown"><span class="p">-</span> Convert to uppercase <span class="p">[</span><span class="nv" style="color: teal;">\#22</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC549" class="line" lang="markdown"><span class="p">-</span> Use bowtie2 <span class="p">[</span><span class="nv" style="color: teal;">\#21</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/21</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="LC550" class="line" lang="markdown"><span class="p">-</span> Add ref alt read depth <span class="p">[</span><span class="nv" style="color: teal;">\#20</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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="LC551" class="line" lang="markdown"><span class="p">-</span> Report read counts <span class="p">[</span><span class="nv" style="color: teal;">\#19</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC552" class="line" lang="markdown"><span class="p">-</span> Refcheck max length <span class="p">[</span><span class="nv" style="color: teal;">\#18</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC553" class="line" lang="markdown"><span class="p">-</span> Make sspace and gapfiller optional <span class="p">[</span><span class="nv" style="color: teal;">\#17</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC554" class="line" lang="markdown"><span class="p">-</span> write bad checked ref seqs to file; fix genetic<span class="se" style="color: #d14;">\_</span>code options <span class="p">[</span><span class="nv" style="color: teal;">\#16</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC555" class="line" lang="markdown"><span class="p">-</span> Add summary task <span class="p">[</span><span class="nv" style="color: teal;">\#15</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/15</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="LC556" class="line" lang="markdown"><span class="p">-</span> Check res genes <span class="p">[</span><span class="nv" style="color: teal;">\#14</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<pre style="margin: 0;">+<span id="LC557" class="line" lang="markdown"><span class="p">-</span> Report percent identity and number bases assembled <span class="p">[</span><span class="nv" style="color: teal;">\#13</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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="LC558" class="line" lang="markdown"><span class="p">-</span> Use cd-hit-est <span class="p">[</span><span class="nv" style="color: teal;">\#12</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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="LC559" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.2.0](https://github.com/sanger-pathogens/ariba/tree/v0.2.0) (2015-02-20)</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.1.2...v0.2.0</span><span class="p">)</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="markdown"><span class="p">-</span> Version 0.1.2 -<span class="se" style="color: #d14;">\></span> 0.2.0 <span class="p">[</span><span class="nv" style="color: teal;">\#11</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="markdown"><span class="p">-</span> Use cdhit <span class="p">[</span><span class="nv" style="color: teal;">\#10</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/10</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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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.1.2](https://github.com/sanger-pathogens/ariba/tree/v0.1.2) (2015-02-18)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.1.1...v0.1.2</span><span class="p">)</span></span>
</pre>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="markdown"></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="markdown"></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="markdown"><span class="p">-</span> Bux fixes velvet path <span class="p">[</span><span class="nv" style="color: teal;">\#9</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/9</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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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.1.1](https://github.com/sanger-pathogens/ariba/tree/v0.1.1) (2015-02-18)</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.1.0...v0.1.1</span><span class="p">)</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="markdown"></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="markdown"><span class="p">-</span> Update version to 0.1.1 <span class="p">[</span><span class="nv" style="color: teal;">\#8</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="markdown"><span class="p">-</span> Remove debugging sys.exit <span class="p">[</span><span class="nv" style="color: teal;">\#7</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.1.0](https://github.com/sanger-pathogens/ariba/tree/v0.1.0) (2015-02-18)</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v0.0.1...v0.1.0</span><span class="p">)</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="markdown"><span class="p">-</span> Move usage info to wiki <span class="p">[</span><span class="nv" style="color: teal;">\#6</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="markdown"><span class="p">-</span> fix executables and paths <span class="p">[</span><span class="nv" style="color: teal;">\#5</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/5</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="LC590" class="line" lang="markdown"><span class="p">-</span> Fix bugs finding paths of dependencies <span class="p">[</span><span class="nv" style="color: teal;">\#4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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="LC591" class="line" lang="markdown"><span class="p">-</span> Use spades <span class="p">[</span><span class="nv" style="color: teal;">\#3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/3</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="LC592" class="line" lang="markdown"><span class="p">-</span> Add velvet to dependencies <span class="p">[</span><span class="nv" style="color: teal;">\#2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.0.1](https://github.com/sanger-pathogens/ariba/tree/v0.0.1) (2015-02-12)</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="markdown"><span class="p">-</span> Initial working version <span class="p">[</span><span class="nv" style="color: teal;">\#1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/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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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="markdown"></span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(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">@@ -60,7 +60,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions.</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown">If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug please log it <span class="p">[</span><span class="nv" style="color: teal;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues</span><span class="p">)</span> or email us at ariba-help@sanger.ac.uk.</span>
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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"><span class="gu" style="color: #800080; font-weight: 600;">### Required dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Python3</span><span class="p">][</span><span class="ss" style="color: #990073;">python</span><span class="p">]</span> version >= 3.<span class="idiff left right">3.2</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Python3</span><span class="p">][</span><span class="ss" style="color: #990073;">python</span><span class="p">]</span> version >= 3.<span class="idiff left right">4.0</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Bowtie2</span><span class="p">][</span><span class="ss" style="color: #990073;">bowtie2</span><span class="p">]</span> version >= 2.1.0</span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">CD-HIT</span><span class="p">][</span><span class="ss" style="color: #990073;">cdhit</span><span class="p">]</span> version >= 4.6</span>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">MUMmer</span><span class="p">][</span><span class="ss" style="color: #990073;">mummer</span><span class="p">]</span> version >= 3.23</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(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="73" style="width: 35px; color: rgba(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">@@ -73,6 +73,7 @@ are not already installed:</td>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="p"> *</span> pyfastaq >= 3.12.0</span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="p"> *</span> pysam >= 0.9.1</span>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"><span class="p"> *</span> pymummer >= 0.10.1</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="p"> *</span> biopython</span>
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76
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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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77
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using pip3</span></span>
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78
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown">Install ARIBA using pip:</span>
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<li id="2a1e1b6414ed603b06fec0cdbe3def87a6de5920">
<a href="https://salsa.debian.org/med-team/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4#2a1e1b6414ed603b06fec0cdbe3def87a6de5920"><strong>ariba/tb.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">@@ -212,8 +212,8 @@ def write_prepareref_metadata_file(mutations, outfile):</td>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_prepareref_files</span><span class="p">(</span><span class="n" style="color: #333;">outprefix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">genbank_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'NC_000962.3.gb'</span><span class="p">)</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">mut_to_drug_json</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.20181<span class="idiff left right">115</span>.json'</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">panel_txt_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.20181<span class="idiff left right">115</span>.txt'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">mut_to_drug_json</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.20181<span class="idiff left right">221</span>.json'</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">panel_txt_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.20181<span class="idiff left right">221</span>.txt'</span><span class="p">)</span></span>
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.fa'</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">tsv_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tsv'</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4#4b78fa5767d377d1fc130725caf805bf47f3e4c4"><strong>ariba/tb_data/panel.20181221.json</strong></a>
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<a href="https://salsa.debian.org/med-team/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4#a2f1073cafb9afe39c2031034fa8f513ace067ba"><strong>ariba/tb_data/panel.20181221.txt</strong></a>
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<a href="https://salsa.debian.org/med-team/ariba/commit/897a8148f5427713eb4fd74a68db139264fe50b4#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -55,7 +55,7 @@ vcfcall_mod = Extension(</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">minimap_mod</span><span class="p">,</span> <span class="n" style="color: #333;">fermilite_mod</span><span class="p">,</span> <span class="n" style="color: #333;">vcfcall_mod</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC57" 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;">'ariba'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC58" 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;">'2.13.<span class="idiff left right">1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" 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;">'2.13.<span class="idiff left right">2</span>'</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" 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;">'ARIBA: Antibiotic Resistance Identification By Assembly'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" 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="LC61" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'test_run_data/*'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tb_data/*'</span><span class="p">]},</span></span>
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