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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbalign">Debian Med / pbalign</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/-/commit/d7bd68f14e78f6fc660f6916b920d14498df6fed">d7bd68f1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-02-27T15:26:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try to get rid of pbh5tools
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/-/commit/86f2ff100e4700f0f52cde0817e7cf4ab22cc25b">86f2ff10</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-02-27T15:29:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mention issues with pbcore and pbcommand -> seems not to be maintaineable any more thus asking for removal
</pre>
</li>
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<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="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#bbd1d9117fbc420c013c25eff71e2c97f4880fae">
<span class="new-file">
+
debian/patches/no_pbh5tools.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/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b#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">@@ -9,9 +9,49 @@ pbalign (0.3.2-2) 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">
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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"> * Remove trailing whitespace in debian/rules</span>
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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">
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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"> * Trim trailing whitespace.</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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<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"> * Set upstream metadata fields: Repository, Repository-Browse.</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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<td class="diff-line-num new_line old" 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"> TODO: python3-pbh5tools not yet available</span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> pbh5tools is waiting for</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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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<td class="diff-line-num new_line old" 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="LC14" class="line" lang="plaintext"> https://github.com/PacificBiosciences/pbh5tools/issues/37</span>
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<td class="diff-line-num new old_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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<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="plaintext"> * Drop pbh5tools from Recommends since its not available any more</span>
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<td class="diff-line-num new old_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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<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="plaintext"></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="plaintext">Not supported by latest pbcore and pbcommand any more:</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="plaintext"></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="plaintext">pylint --errors-only pbalign</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="plaintext">************* Module pbalign.pbalignrunner</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="plaintext">pbalign/pbalignrunner.py:50:0: E0611: No name 'pbparser_runner' in module 'pbcommand.cli' (no-name-in-module)</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="plaintext">************* Module pbalign.options</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="plaintext">pbalign/options.py:40:0: E0611: No name 'get_pbparser' in module 'pbcommand.models' (no-name-in-module)</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="plaintext">************* Module pbalign.alignservice.gmap</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">pbalign/alignservice/gmap.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">pbalign/alignservice/gmap.py:40:0: E0401: Unable to import 'pbcore.util.Process' (import-error)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">************* Module pbalign.alignservice.bowtie</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">pbalign/alignservice/bowtie.py:39:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)</span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">pbalign/alignservice/bowtie.py:39:0: E0401: Unable to import 'pbcore.util.Process' (import-error)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">************* Module pbalign.alignservice.fastabasedalign</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">pbalign/alignservice/fastabasedalign.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">pbalign/alignservice/fastabasedalign.py:40:0: E0401: Unable to import 'pbcore.util.Process' (import-error)</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">************* Module pbalign.tasks.align_minorvariants</span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">pbalign/tasks/align_minorvariants.py:9:0: E0611: No name 'get_pbparser' in module 'pbcommand.models' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(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="LC32" class="line" lang="plaintext">pbalign/tasks/align_minorvariants.py:10:0: E0611: No name 'pbparser_runner' in module 'pbcommand.cli' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">************* Module pbalign.utils.RgnH5IO</span>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">pbalign/utils/RgnH5IO.py:13:0: E0611: No name 'BasH5IO' in module 'pbcore.io' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">pbalign/utils/RgnH5IO.py:13:0: E0401: Unable to import 'pbcore.io.BasH5IO' (import-error)</span>
</pre>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">pbalign/utils/RgnH5IO.py:56:0: E1126: Sequence index is not an int, slice, or instance with __index__ (invalid-sequence-index)</span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">************* Module pbalign.utils.fileutil</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">pbalign/utils/fileutil.py:42:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">pbalign/utils/fileutil.py:42:0: E0401: Unable to import 'pbcore.util.Process' (import-error)</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">************* Module pbalign.utils.progutil</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">pbalign/utils/progutil.py:37:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">pbalign/utils/progutil.py:37:0: E0401: Unable to import 'pbcore.util.Process' (import-error)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">************* Module pbalign.tools.createChemistryHeader</span>
</pre>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">pbalign/tools/createChemistryHeader.py:14:0: E0611: No name 'BasH5IO' in module 'pbcore.io' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">************* Module pbalign.tools.loadChemistry</span>
</pre>
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<td class="diff-line-num new old_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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<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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">pbalign/tools/loadChemistry.py:71:14: E0602: Undefined variable 'BasH5Reader' (undefined-variable)</span>
</pre>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">************* Module pbalign.tools.mask_aligned_reads</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">pbalign/tools/mask_aligned_reads.py:12:0: E0611: No name 'CmpH5Reader' in module 'pbcore.io' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">pbalign/tools/mask_aligned_reads.py:12:0: E0611: No name 'EmptyCmpH5Error' in module 'pbcore.io' (no-name-in-module)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">pbalign/tools/mask_aligned_reads.py:124:13: E1123: Unexpected keyword argument 'version' in constructor call (unexpected-keyword-arg)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">make: *** [Makefile:19: pylint] Fehler 2</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Issue tracker for https://github.com/PacificBiosciences/pbalign/ is disabled - so no idea how to ask for updates</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 13 Dec 2019 10:59:33 +0100</span>
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17
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b#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">@@ -24,8 +24,7 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> python3-pbalign (= ${source:Version}),</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> python3-pkg-resources,</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> blasr</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Recommends: python3-pbh5tools,</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> hdf5-tools</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Recommends: hdf5-tools</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Suggests: bowtie2,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> gmap,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> pbalign-doc</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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="41" 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">@@ -42,8 +41,7 @@ Architecture: all</td>
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42
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> blasr</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">Recommends: python3-pbh5tools,</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> hdf5-tools</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Recommends: hdf5-tools</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Suggests: bowtie2,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> gmap,</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> pbalign-doc</span>
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<a href="https://salsa.debian.org/med-team/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</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">@@ -5,7 +5,7 @@ Last-Update: Fri, 13 Dec 2019 10:59:33 +0100</td>
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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/Makefile</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/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -3,<span class="idiff left right">25 +3,25</span> @@</span> SHELL = /bin/bash -e</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -3,<span class="idiff left right">17 +3,17</span> @@</span> SHELL = /bin/bash -e</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> all: build install</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"> build:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,9 +27,8 @@ Last-Update: Fri, 13 Dec 2019 10:59:33 +0100</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py develop</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> pylint:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pylint --errors-only pbalign</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pylint3 --errors-only pbalign</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> pylint --errors-only pbalign</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span> pylint:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> test: pylint</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> # Unit tests</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> #find tests/unit -name "*.py" | xargs nosetests</span>
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<li id="bbd1d9117fbc420c013c25eff71e2c97f4880fae">
<a href="https://salsa.debian.org/med-team/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b#bbd1d9117fbc420c013c25eff71e2c97f4880fae"><strong>debian/patches/no_pbh5tools.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Drop pbh5tools from Recommends since its not available any more</span></span>
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<pre style="margin: 0;">+<span id="LC2" 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="LC3" class="line" lang="diff"><span class="p">Last-Update: Thu, 27 Feb 2020 15:10:44 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/tests/cram_h5/ccs.t</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram_h5/ccs.t</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -39,8 +39,6 @@</span> Set up</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> $ rm -f $BAS_CMPOUT</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> $ pbalign $Q $T $BAS_CMPOUT --useccs=useccsdenovo 2>/dev/null</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $ /mnt/secondary/Smrtanalysis/smrtcmds/bin/smrtwrap cmph5tools.py sort $BAS_CMPOUT --deep --inPlace</span></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;">- $ /mnt/secondary/Smrtanalysis/smrtcmds/bin/smrtwrap cmph5tools.py sort $CCS_CMPOUT --deep --inPlace</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> $ h5diff $CCS_CMPOUT $BAS_CMPOUT /AlnGroup /AlnGroup</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> $ h5diff $CCS_CMPOUT $BAS_CMPOUT /AlnInfo /AlnInfo</span></pre>
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<a href="https://salsa.debian.org/med-team/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">find_definitions_from_pbcore.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">no_pbh5tools.patch</span></pre>
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