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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/6619322cfadbaa61ce0561b4a0dbdc7cb726537b">6619322c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-12T15:25:57+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog - valid syntax to reduce noise in metadata gatherer even if package is removed</pre>
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<h4>1 changed file:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbalign/-/commit/6619322cfadbaa61ce0561b4a0dbdc7cb726537b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,47 +11,8 @@ pbalign (0.3.2-2) UNRELEASED; urgency=medium</td>
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11
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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_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="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 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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<td class="diff-line-num new_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="LC13" class="line" lang="plaintext"></span>
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14
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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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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext">pylint --errors-only pbalign</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext">************* Module pbalign.pbalignrunner</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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="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 old old_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext">************* Module pbalign.options</span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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="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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<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 old old_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">************* Module pbalign.alignservice.gmap</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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="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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<td class="diff-line-num old old_line" data-linenumber="23" 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="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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<td class="diff-line-num old old_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext">************* Module pbalign.alignservice.bowtie</span>
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<td class="diff-line-num old old_line" data-linenumber="25" 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="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 old old_line" data-linenumber="26" 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="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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<td class="diff-line-num old old_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">************* Module pbalign.alignservice.fastabasedalign</span>
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<td class="diff-line-num old old_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext">pbalign/alignservice/fastabasedalign.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)</span>
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<td class="diff-line-num old old_line" data-linenumber="29" 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="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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<td class="diff-line-num old old_line" data-linenumber="30" 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="LC30" class="line" lang="plaintext">************* Module pbalign.tasks.align_minorvariants</span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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="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>
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<td class="diff-line-num old old_line" data-linenumber="32" 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="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>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">************* Module pbalign.utils.RgnH5IO</span>
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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>
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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>
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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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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>
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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>
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<td class="diff-line-num old old_line" data-linenumber="42" 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">
42
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<td class="diff-line-num new_line old" 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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<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>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">************* Module pbalign.tools.createChemistryHeader</span>
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<td class="diff-line-num old old_line" data-linenumber="44" 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">
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>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">************* Module pbalign.tools.loadChemistry</span>
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<td class="diff-line-num old old_line" data-linenumber="46" 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">
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>
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<td class="diff-line-num old old_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">************* Module pbalign.tools.mask_aligned_reads</span>
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<td class="diff-line-num old old_line" data-linenumber="48" 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">
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>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
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>
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<td class="diff-line-num old old_line" data-linenumber="50" 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">
50
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<td class="diff-line-num new_line old" 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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<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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<td class="diff-line-num old old_line" data-linenumber="51" 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">
51
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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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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="54" 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">
54
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<td class="diff-line-num new_line old" 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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<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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<td class="diff-line-num new old_line" data-linenumber="55" 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="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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Removed since 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">
15
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<pre style="margin: 0;">+<span id="LC15" 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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55
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 13 Dec 2019 10:59:33 +0100</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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