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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/68470522562f44cf09b69ae5e361269ffaba0e94">68470522</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-13T14:32:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More yaml.load issues fixed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/0c6e72d195e43f8019b879d884d90eb308181406">0c6e72d1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-13T15:29:31Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix location of docs
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#6b4e31cdf8f9338db47a4fa236a08014b3851935">
debian/patches/yaml_load.patch
</a>
</li>
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<h4>Changes:</h4>
<li id="3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<a href="https://salsa.debian.org/med-team/spades/compare/639914be81dc5d563998c58ee9c98d64640d6369...0c6e72d195e43f8019b879d884d90eb308181406#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*manual.html</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">assembler/</span>*manual.html</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">README.md</span></pre>
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<li id="6b4e31cdf8f9338db47a4fa236a08014b3851935">
<a href="https://salsa.debian.org/med-team/spades/compare/639914be81dc5d563998c58ee9c98d64640d6369...0c6e72d195e43f8019b879d884d90eb308181406#6b4e31cdf8f9338db47a4fa236a08014b3851935"><strong>debian/patches/yaml_load.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,3 +14,23 @@ Description: Specify yaml loader</td>
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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>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/spades_pipeline/hammer_logic.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/spades_pipeline/hammer_logic.py</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="diff"><span class="p">@@ -94,7 +94,7 @@</span> def prepare_config_ih(filename, cfg, ext</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> elif sys.version.startswith('3.'):</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import pyyaml3 as pyyaml</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- data = pyyaml.load(open(filename, 'r'))</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;">+ data = pyyaml.load(open(filename, 'r'), Loader=pyyaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> data["dataset"] = cfg.dataset_yaml_filename</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> data["working_dir"] = cfg.tmp_dir</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> data["output_dir"] = cfg.output_dir</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -153,7 +153,7 @@</span> def run_hammer(corrected_dataset_yaml_fi</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> log.info("\n===== Skipping %s (already processed). \n" % "read error correction tool")</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> support.continue_from_here(log)</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- corrected_dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ corrected_dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> remove_not_corrected_reads(cfg.output_dir)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> is_changed = False</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> if cfg.gzip_output:</span></pre>
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