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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/spades">Debian Med / spades</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/2a1a3c6d49d64565cb581136e266ccb3f8a98941">2a1a3c6d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-12T17:57:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Specify yaml loader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/54bc9d00e8638f0ab350c620e9b5446f776340e7">54bc9d00</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-12T18:12:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hopefully fix
File "/build/spades-3.13.1/install_spades/../../share/spades/spades_pipeline/spades_logic.
for src, target in replacements.iteritems():
AttributeError: 'dict' object has no attribute 'iteritems'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/9207cab94da2e59b88cc9a282b48efa7b0233e84">9207cab9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-12T18:13:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: s/python-all-dev/python3-dev/
</pre>
</li>
</ul>
<h4>5 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="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#6b4e31cdf8f9338db47a4fa236a08014b3851935">
<span class="new-file">
+
debian/patches/yaml_load.patch
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@ spades (3.13.1-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Move source package lintian overrides to debian/source.</span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Set upstream metadata fields: Repository.</span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Make sure Python3 interpreter is used in scripts</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Specify yaml loader</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 08 Oct 2019 18:17:07 +0200</span>
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
</pre>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh-python,</span>
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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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> cmake,</span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="plaintext"> python<span class="idiff left right">-all</span>-dev,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libbz2-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libboost-dev,</span>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,6 +115,24 @@ Description: Make sure Python3 interpreter is used in scripts</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</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="diff"><span class="p">@@ -214,7 +214,7 @@</span> def run_iteration(configs_dir, execution</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> lines = []</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> with open(cfg_file) as infile:</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> for line in infile:</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for src, target in replacements.iteritems():</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for src, target in list(replacements.iteritems()):</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> line = line.replace(src, target)</span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> lines.append(line)</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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> with open(cfg_file, 'w') as outfile:</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="diff"><span class="p">@@ -275,7 +275,7 @@</span> def run_scaffold_correction(configs_dir,</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> lines = []</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> with open(cfg_file) as infile:</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> for line in infile:</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for src, target in replacements.iteritems():</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for src, target in list(replacements.iteritems()):</span></span>
</pre>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> line = line.replace(src, target)</span>
</pre>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> lines.append(line)</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> with open(cfg_file, 'w') as outfile:</span>
</pre>
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118
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/spades_pipeline/truspades/reference_construction.py</span></span>
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119
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/spades_pipeline/truspades/reference_construction.py</span></span>
</pre>
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120
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
</pre>
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<br>
</li>
<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,3 +19,4 @@ fix-bool-cast</td>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">spelling</span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">gcc7.patch</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">yaml_load.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84#6b4e31cdf8f9338db47a4fa236a08014b3851935"><strong>debian/patches/yaml_load.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 12 Nov 2019 17:11:17 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Specify yaml loader</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/assembler/spades.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/spades.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -107,7 +107,7 @@</span> def print_used_values(cfg, log):</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> " or --meta flag if processing metagenomic dataset)")</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> log.info(" Reads:")</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'), Loader=yaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> support.pretty_print_reads(dataset_data, log)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span></pre>
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