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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/smalt">Debian Med / smalt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/7c08f2535baafe78a35342d08724fdb64e1f9533">7c08f253</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T17:02:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/1f0ab66571f176ef9b7ec1f2fc9087ad461c3c4f">1f0ab665</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T17:03:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/6e66f8ebd8689f24558644a187e06a1e7327d59d">6e66f8eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T17:52:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try to fix some tests or at least make these more verbose but failed.
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/smalt/compare/13e417919ba28b0a287b4dc3d962f7196c6cc2fe...6e66f8ebd8689f24558644a187e06a1e7327d59d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,12 +3,41 @@ smalt (0.7.6-9) UNRELEASED; urgency=medium</td>
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3
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Closes: #938501</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7" 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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" 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="7" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Use secure URI in debian/watch.</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Set upstream metadata fields: Archive, Bug-Submit.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> TODO: Fix some Python3 issues in test scripts</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> make check-TESTS</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> make[4]: Entering directory '/build/smalt-0.7.6/test'</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> PASS: splitReads_test.py</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> PASS: results_split_test.py</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> PASS: ouform_cigar_test.py</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> mappings don't match for read 'SIM_000000000_MAL11_001337747_10_F_75m/1'</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> FAIL: sample_test.py</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> PASS: cigar_test.py</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Discrepancy:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> cigA1.mapq=60 > MAPQ_THRESH=6 and cigB1.mapq=60 > MAPQ_THRESH=6</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> FAIL: mthread_test.py</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> PASS: ioform_test.py</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> PASS: xali_test.py</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Traceback (most recent call last):</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> File "./bam_cigar_test.py", line 254, in <module></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> isOK = testSAMfilesAreIdentical(sambamnam, samoufilnam)</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> File "./bam_cigar_test.py", line 149, in testSAMfilesAreIdentical</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> linA = infilA.readline()</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> File "/usr/lib/python3.7/codecs.py", line 322, in decode</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> (result, consumed) = self._buffer_decode(data, self.errors, final)</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 366: invalid start byte</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> FAIL: bam_cigar_test.py</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> =================================</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> 3 of 9 tests failed</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> Please report to hp3@sanger.ac.uk</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> =================================</span>
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12
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 05 Sep 2019 15:07:37 +0200</span>
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14
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> samtools,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbambamc-dev</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/smalt</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/smalt.git</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://www.sanger.ac.uk/science/tools/smalt-0</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/smalt/compare/13e417919ba28b0a287b4dc3d962f7196c6cc2fe...6e66f8ebd8689f24558644a187e06a1e7327d59d#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -225,7 +225,8 @@ Last-Update: Thu, 05 Sep 2019 15:07:37 +0200</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin)</span></span>
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin))</span></span>
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="diff"> if cigA1.mapq > MAPQ_THRESH and cigB1.mapq > MAPQ_THRESH:</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"> exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit("Discrepancy:\n%s\n%s\ncigA1.mapq=%i > MAPQ_THRESH=%i and cigB1.mapq=%i > MAPQ_THRESH=%i" % (cigA1.lin, cigB1.lin, cigA1.mapq, MAPQ_THRESH, cigB1.mapq, MAPQ_THRESH))</span></span>
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229
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="diff"> if cigA2 != cigB2:</span>
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="diff"> if is_verbose:</span>
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231
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin) </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" 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="284" 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">@@ -283,6 +284,15 @@ Last-Update: Thu, 05 Sep 2019 15:07:37 +0200</td>
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283
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="diff"> if not allok:</span>
</pre>
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284
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/testdata.py</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/testdata.py</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -62,7 +62,7 @@</span> class DataFiles:</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> if len(filnam) < 4 or filnam[-3:] != '.gz': fn_from = fn_from + '.gz'</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> fn_to = path.join(DataFiles.WORKDIR, filnam)</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> infil = openFile(fn_from, 'r')</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- oufil = openFile(fn_to, 'w')</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oufil = openFile(fn_to, 'wb')</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> self.logfil_out.write("unpacking '%s' -> '%s'\n" % (fn_from, fn_to))</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> while 1:</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> lin = infil.readline()</span>
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286
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="diff"><span class="p">@@ -139,9 +139,9 @@</span> class DataFiles:</span>
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287
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="diff"> for filnam in (self.datafiles + self.tmpfiles):</span>
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288
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="diff"> if access(filnam, F_OK):</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" 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="314" 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">@@ -304,3 +314,26 @@ Last-Update: Thu, 05 Sep 2019 15:07:37 +0200</td>
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304
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="diff"> exit(1)</span>
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="diff"> </span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="diff"> return oufil</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/sample_test.py</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/sample_test.py</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="p">@@ -1,5 +1,7 @@</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> # test sampling of insert lengths</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from operator import ne</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> PROGNAM = "../src/smalt"</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> REF_FASTA_NAME = "genome_1.fa.gz"</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> READ_PREFIX = "gen1l75i300e0"</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="p">@@ -105,10 +107,10 @@</span> def compare_mapping(oufilnam1, oufilnam2</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> break</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> ctr2 = ctr2 + 1</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if cmp(cig1.qnam, cig2.qnam):</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ne(cig1.qnam, cig2.qnam):</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> exit("readnames don't match: '%s' vs '%s'" % \</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> (cig1.qnam, cig2.qnam))</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if cmp(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ne(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> exit("mappings don't match for read '%s'" % \</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> cig1.qnam)</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> infil2.close()</span></pre>
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<a href="https://salsa.debian.org/med-team/smalt/compare/13e417919ba28b0a287b4dc3d962f7196c6cc2fe...6e66f8ebd8689f24558644a187e06a1e7327d59d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,11 +2,11 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#debug=1</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/smalt-test.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/smalt-test.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/smalt/test/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/smalt/test/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="k" style="font-weight: 600;">*</span>.py.gz data/<span class="k" style="font-weight: 600;">*</span>.bam.gz</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">TESTS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"splitReads_test.py</span></span>
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