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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/python-pysam">Debian Med / python-pysam</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/043a6b0c683e98ce0de512ecb61b8c771dc37df5">043a6b0c</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-12T12:36:24Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Please do not silently ignore changes from unreleased changelog paragraphs

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/cb0b80a614589723637b21b0bbb7b9b2038f9769">cb0b80a6</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-12T12:37:34Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove ancient fields X-Python*-Version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/84eb0baf30ce2db15c457d6582da213ec69e1abe">84eb0baf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-12T14:53:40Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust patches for failed tests

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/fb52fc1745b89c1c9ecff51e76bcb08ea6e167a3">fb52fc17</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-12T14:54:46Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust versioned Dependencies

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/0004b93eb49ac7a146b7f8012fe0d395a31c9a0a">0004b93e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-12T14:57:44Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1

</pre>

</li>

</ul>

<h4>7 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="#c0968845ef64303d5ddb227b9b727137bee71a01">

<span class="deleted-file">

−

debian/patches/execute-linking-tests-only-when-explicitely-reque.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#82c051b99c070fc2f1f308116da2fe94cf1e6e15">

<span class="new-file">

+

debian/patches/skip_test_remote.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#593d6e450afb14d1b3a401061fd48026b2b58f95">

<span class="deleted-file">

−

debian/patches/xfail.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.0.1+ds-2) UNRELEASED; urgency=medium</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="2" 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">

2

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="3" 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">

3

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Remove ancient fields X-Python*-Version</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="4" 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">

4

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Adjust patches for build time test suite</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.2.1</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="6" 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">

6

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Wed, 12 Sep 2018 14:37:26 +0200</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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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">

9

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">python-pysam (0.15.0.1+ds-1) experimental; urgency=medium</span>

</pre>

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2

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="5" 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">

13

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  [ Steffen Moeller ]</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num 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">

14

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">  * New upstream version.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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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">

15

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line old" 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="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org>  Sun, 29 Jul 2018 00:51:38 +0200</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" 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="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="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="LC9" class="line" lang="plaintext">python-pysam (0.14.1+ds-1) UNRELEASED; urgency=medium</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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="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="LC10" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext">  [ Afif Elghraoui ]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">  * New upstream version 0.14.1+ds</span>

</pre>

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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">

13

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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext">  * Update patches</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="22" 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">@@ -17,7 +22,7 @@ python-pysam (0.14.1+ds-1) UNRELEASED; urgency=medium</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">  * Rename d/tests/control to d/tests/control.autodep8</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">  * Standards-Version: 4.1.4</span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

</pre>

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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="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="LC20" class="line" lang="plaintext"> -- <span class="idiff left right">Afif Elghraoui <afif@debian.org>  Sun, 22 Apr 2018 19:02:41 -04</span>00</span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext"> -- <span class="idiff left right">Steffen Moeller <moeller@debian.org>  Sun, 29 Jul 2018 00:51:38 +02</span>00</span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">python-pysam (0.14+ds-2) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,16 +18,14 @@ Build-Depends: debhelper (>= 11~),</td>

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<td class="diff-line-num old_line" data-linenumber="18" 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="18" 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="LC18" class="line" lang="plaintext">               python3-setuptools,</span>

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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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">               cython3 (>= 0.23),</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">               tabix <!nocheck>,</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">

21

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<td class="diff-line-num new_line old" 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">               samtools (>= 1.<span class="idiff left right">7</span>) <!nocheck>,</span>

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<td class="diff-line-num new_line old" 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="LC22" class="line" lang="plaintext">               bcftools (>= 1.<span class="idiff left right">7</span>) <!nocheck>,</span>

</pre>

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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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">               samtools (>= 1.<span class="idiff left right">9</span>) <!nocheck>,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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="22" 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">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">               bcftools (>= 1.<span class="idiff left right">9</span>) <!nocheck>,</span>

</pre>

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23

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23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">               python-pytest <!nocheck>,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">               python3-pytest <!nocheck></span>

</pre>

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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">

25

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<td class="diff-line-num new_line old" 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">Standards-Version: 4.<span class="idiff left right">1.4</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-pysam</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git</span>

</pre>

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28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Homepage: http://pysam.readthedocs.org/en/latest</span>

</pre>

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29

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">X-Python-Version: >= 2.7</span>

</pre>

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30

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">X-Python3-Version: >= 3.2</span>

</pre>

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31

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29

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Package: python-pysam</span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Architecture: any</span>

</pre>

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<br>

</li>

<li id="c0968845ef64303d5ddb227b9b727137bee71a01">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#c0968845ef64303d5ddb227b9b727137bee71a01"><strong>debian/patches/execute-linking-tests-only-when-explicitely-reque.patch</strong>

deleted

</a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC1" class="line" lang="diff">From: Andreas Heger <andreas.heger@gmail.com></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Date: Mon, 18 Sep 2017 11:19:28 +0100</span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/871083</span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Subject: execute linking tests only when explicitly</span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> requested via PYSAM_LINKING_TESTS env var. Keep on travis. Fixes #534</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">---</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> .travis.yml           |  2 ++</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> tests/TestUtils.py    |  1 +</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> tests/linking_test.py | 10 ++++++++++</span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> 3 files changed, 13 insertions(+)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/.travis.yml</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/.travis.yml</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,8 +11,6 @@ env:</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff">     - CONDA_PY=3.4</span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">     - CONDA_PY=3.5</span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">     - CONDA_PY=3.6</span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  global:</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    - PYSAM_LINKING_TEST=1</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> addons:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff">   apt:</span></pre>

</td>

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</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#execute-linking-tests-only-when-explicitely-reque.patch</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">#xfail.patch</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">#skip_test_needing_missing_data.patch</span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">skip_test_needing_missing_data.patch</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">skip_test_remote.patch</span></pre>

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</li>

<li id="82c051b99c070fc2f1f308116da2fe94cf1e6e15">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#82c051b99c070fc2f1f308116da2fe94cf1e6e15"><strong>debian/patches/skip_test_remote.patch</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Tue, 11 Sep 2018 14:12:55 +0200</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Skip tests trying to access remote site</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/AlignmentFile_test.py</span></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/AlignmentFile_test.py</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1596,6 +1596,7 @@ class TestDoubleFetchCRAMWithReference(T</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">     reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </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"><span class="gi" style="color: #000; background-color: #dfd;">+@unittest.skip</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> class TestRemoteFileFTP(unittest.TestCase):</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">     '''test remote access.</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/tabix_test.py</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/tabix_test.py</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1039,6 +1039,7 @@ for vcf_file in vcf_files:</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">     globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+@unittest.skip</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> class TestRemoteFileHTTP(unittest.TestCase):</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1078,25 +1079,28 @@ class TestRemoteFileHTTP(unittest.TestCa</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff">         self.assertEqual(list(self.local_file.header), [])</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </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"><span class="gd" style="color: #000; background-color: #fdd;">-class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):</span></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;">-</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"</span></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;">-    region = "chr1:1-1000"</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def setUp(self):</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if not pysam.config.HAVE_LIBCURL or not check_url(self.url):</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            self.remote_file = None</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        else:</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            self.remote_file = pysam.TabixFile(self.url, "r")</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.local_file = pysam.TabixFile(self.local, "r")</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def testHeader(self):</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if self.remote_file is None:</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            return</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(list(self.local_file.header), ["# comment at start"])</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(list(self.local_file.header), self.remote_file.header)</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#@unittest.skip  #  this leads to</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 #  E   TypeError: Error when calling the metaclass bases</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 #  E       function() argument 1 must be code, not str</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    region = "chr1:1-1000"</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def setUp(self):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        if not pysam.config.HAVE_LIBCURL or not check_url(self.url):</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#            self.remote_file = None</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        else:</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#            self.remote_file = pysam.TabixFile(self.url, "r")</span></span>

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62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.local_file = pysam.TabixFile(self.local, "r")</span></span>

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63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def testHeader(self):</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        if self.remote_file is None:</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#            return</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

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68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(list(self.local_file.header), ["# comment at start"])</span></span>

</pre>

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69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(list(self.local_file.header), self.remote_file.header)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> class TestIndexArgument(unittest.TestCase):</span></pre>

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<br>

</li>

<li id="593d6e450afb14d1b3a401061fd48026b2b58f95">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#593d6e450afb14d1b3a401061fd48026b2b58f95"><strong>debian/patches/xfail.patch</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: temporarily skip failing test</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> See https://github.com/pysam-developers/pysam/issues/542</span>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Author: Afif Elghraoui <afif@debian.org></span>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Forwarded: not-needed</span>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Last-Update: 2017-10-01</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">Index: python-pysam/tests/AlignmentFile_test.py</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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8

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/tests/AlignmentFile_test.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/tests/AlignmentFile_test.py</span></span>

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10

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -472,6 +472,7 @@ class TestIO(unittest.TestCase):</span></span>

</pre>

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11

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC11" class="line" lang="diff">                        "tmp_ex2.bam",</span>

</pre>

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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">

12

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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff">                        "rb", "wb")</span>

</pre>

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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">

13

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>

</pre>

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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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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    @unittest.skip</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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="0" 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="LC15" class="line" lang="diff">     def testCRAM2CRAM(self):</span>

</pre>

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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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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff">         # in some systems different reference sequence paths might be</span>

</pre>

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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">

17

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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff">         # embedded in the CRAM files which will result in different headers</span></pre>

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</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,10 +15,6 @@ HTSLIBDIR  := /usr/lib/$(DEB_HOST_MULTIARCH)</td>

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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">

15

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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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">export HTSLIB_INCLUDE_DIR=/usr/include</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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="17" 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="LC17" class="line" lang="plaintext"></span>

</pre>

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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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<td class="diff-line-num new_line old" 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"># unfortunately this does not work - any hint to fix this would be really welcome</span>

</pre>

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19

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<td class="diff-line-num new_line old" 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="LC19" class="line" lang="plaintext">#export PYBUILD_TEST_ARGS_python2=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader</span>

</pre>

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<td class="diff-line-num new_line old" 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="LC20" class="line" lang="plaintext">#export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader</span>

</pre>

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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">

21

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<td class="diff-line-num new_line old" 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="LC21" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line" data-linenumber="18" 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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">clean: clean-tests</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num 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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">%:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">     dh $@ --with python2,python3 --buildsystem=pybuild</span>

</pre>

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