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<h3>
Afif Elghraoui pushed to branch master
at <a href="https://salsa.debian.org/med-team/nanopolish">Debian Med / nanopolish</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/commit/cccda95767831a76187a9cd96bbc76c67fdd2ff3">cccda957</a></strong>
<div>
<span>by Afif Elghraoui</span>
<i>at 2018-02-17T20:46:45-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump minimum required fast5 version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/commit/5844c0608db4dee311152925db6e921254ddbcbc">5844c060</a></strong>
<div>
<span>by Afif Elghraoui</span>
<i>at 2018-02-17T22:01:39-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include upstream patch to fix HDF5 errors appearing in autopkgtest

See https://github.com/jts/nanopolish/issues/335
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/commit/34ec40c2564b5e7fa2abeb244259b52bb47d8b00">34ec40c2</a></strong>
<div>
<span>by Afif Elghraoui</span>
<i>at 2018-02-17T22:02:38-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">releasing package nanopolish version 0.9.0-1
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ceda9c89e9ce1eb1cd91cabdbc995cf525eddb63">
<span class="new-file">
+
debian/patches/hdf5-groupcheck.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/nanopolish/compare/326887cec4e0a418b5b9089c13910c75334d181b...34ec40c2564b5e7fa2abeb244259b52bb47d8b00#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">nanopolish (0.9.0-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">nanopolish (0.9.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  * New upstream version<span class="idiff left right"> 0.9.0</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>
</pre>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * Refresh patches</span>
</pre>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * Bump upstream copyright year</span>
</pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Bump minimum required fast5 version</span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Include upstream patch to fix HDF5 errors appearing in autopkgtest</span>
</pre>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Afif Elghraoui <afif@debian.org>  Sat, 17 Feb 2018 <span class="idiff left right">18:06:03</span> -0500</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Afif Elghraoui <afif@debian.org>  Sat, 17 Feb 2018 <span class="idiff left right">22:02:10</span> -0500</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">nanopolish (0.8.5-2) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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</table>
<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/nanopolish/compare/326887cec4e0a418b5b9089c13910c75334d181b...34ec40c2564b5e7fa2abeb244259b52bb47d8b00#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@ Uploaders: Afif Elghraoui <afif@debian.org></td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends:</span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">      debhelper (>= 10),</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">      zlib1g-dev,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">      libfast5-dev (>= 0.6.<span class="idiff left right">4</span>),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      libfast5-dev (>= 0.6.<span class="idiff left right">5</span>),</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">     libhts-dev,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">     libeigen3-dev,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.1.3</span>
</pre>
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</table>
<br>
</li>
<li id="ceda9c89e9ce1eb1cd91cabdbc995cf525eddb63">
<a href="https://salsa.debian.org/med-team/nanopolish/compare/326887cec4e0a418b5b9089c13910c75334d181b...34ec40c2564b5e7fa2abeb244259b52bb47d8b00#ceda9c89e9ce1eb1cd91cabdbc995cf525eddb63"><strong>debian/patches/hdf5-groupcheck.patch</strong></a>
<hr>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From 303971c245d507988132ad8404f840461ff4d87d Mon Sep 17 00:00:00 2001</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Jared Simpson <jared.simpson@gmail.com></span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Sat, 17 Feb 2018 21:48:45 -0500</span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Subject: [PATCH] check for existence of group before opening it (#335)</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">---</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> src/common/nanopolish_fast5_io.cpp | 7 +++++++</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 1 file changed, 7 insertions(+)</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/common/nanopolish_fast5_io.cpp b/src/common/nanopolish_fast5_io.cpp</span></span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index 0144062..7f38719 100644</span></span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/common/nanopolish_fast5_io.cpp</span></span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/common/nanopolish_fast5_io.cpp</span></span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -208,6 +208,13 @@ std::string fast5_get_fixed_string_attribute(hid_t hdf5_file, const std::string&</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">     int ret;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">     std::string out;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    // according to http://hdf-forum.184993.n3.nabble.com/check-if-dataset-exists-td194725.html</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    // we should use H5Lexists to check for the existence of a group/dataset using an arbitrary path</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    ret = H5Lexists(hdf5_file, group_name.c_str(), H5P_DEFAULT);</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if(ret <= 0) {</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return "";</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    }</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">     // Open the group /Raw/Reads/Read_nnn</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff">     group = H5Gopen(hdf5_file, group_name.c_str(), H5P_DEFAULT);</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff">     if(group < 0) {</span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/compare/326887cec4e0a418b5b9089c13910c75334d181b...34ec40c2564b5e7fa2abeb244259b52bb47d8b00#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">add-shebang-to-script.patch</span>
</pre>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">reproducible.patch</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">hdf5-groupcheck.patch</span></pre>
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