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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pbcore">Debian Med / python-pbcore</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pbcore/commit/a5551c2f995d4170ddb7bfc1acadd1bfbd8e71c9">a5551c2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-25T08:19:17+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt to numpy 1.14 (thanks to Graham Inggs for cherry-picking from upstream)
</pre>
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<strong><a href="https://salsa.debian.org/med-team/python-pbcore/commit/9ce6ea2263880559e9778e7c824f5ec7dd35f8e2">9ce6ea22</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-25T08:55:37+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Relax test constraint which is rather a rounding issue
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#d65c59ab7e949c3fb5819665586833ba7c7bd830">
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+
debian/patches/numpy1.14.patch
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<li class="file-stats">
<a href="#58defd8f851480233cffd7df05280e7925b60cad">
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+
debian/patches/relax_test_constraint.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pbcore/compare/a60fd5be18191d305e1e3f04b855d63bd2481999...9ce6ea2263880559e9778e7c824f5ec7dd35f8e2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">python-pbcore (1.4.2+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Afif Elghraoui ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version (git f3bcf3a)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Updated patches</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Added tests dependency on python-coverage</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * d/control: use build profile declarations</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Adapt to numpy 1.14 (thanks to Graham Inggs for cherry-picking from</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> upstream)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Closes: #900485</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Relax test constraint which is rather a rounding issue</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> -- Afif Elghraoui <afif@debian.org> Sun, 07 Jan 2018 02:03:14 -0500</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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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">python-pbcore (1.2.11+dfsg-1) unstable; urgency=medium</span>
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<li id="d65c59ab7e949c3fb5819665586833ba7c7bd830">
<a href="https://salsa.debian.org/med-team/python-pbcore/compare/a60fd5be18191d305e1e3f04b855d63bd2481999...9ce6ea2263880559e9778e7c824f5ec7dd35f8e2#d65c59ab7e949c3fb5819665586833ba7c7bd830"><strong>debian/patches/numpy1.14.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix FTBFS with NumPy 1.14</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/900485</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Origin: upstream, https://github.com/PacificBiosciences/pbcore/commit/b7ef4238b6388f984a264b8a912450b652177dbf</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Author: David Seifert <dseifert@pacificbiosciences.com></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Last-Update: 2018-01-10</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_pbdataset.py</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_pbdataset.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1693,7 +1693,7 @@ class TestDataSet(unittest.TestCase):</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> self.assertEqual(len(readers[0].referenceInfoTable), 59)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> obstbl = [readers[0].referenceInfo('E.faecalis.1')]</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> exptbl = [(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482,</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'a1a59c267ac1341e5a12bce7a7d37bcb', 0L, 0L)]</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'a1a59c267ac1341e5a12bce7a7d37bcb', 0, 0)]</span></span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</span>
</pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # TODO: add a bam with a different referenceInfoTable to check merging</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> # and id remapping:</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2220,7 +2220,7 @@ class TestDataSet(unittest.TestCase):</span></span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> self.assertEqual(len3, 338114)</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> obstbl = aln.referenceInfoTable</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> exptbl = [(1, 1, 'lambda_NEB3011', 'lambda_NEB3011',</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 48502, 'a1319ff90e994c8190a4fe6569d0822a', 0L, 338113L)]</span></span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 48502, 'a1319ff90e994c8190a4fe6569d0822a', 0, 338113)]</span></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> self.assertEqual(set(aln.tId), {1})</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # + 1, because bounds are inclusive, rather than exclusive</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2247,9 +2247,9 @@ class TestDataSet(unittest.TestCase):</span></span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> self.assertEqual(len3, 57147)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> obstbl = aln.referenceInfoTable</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 57034L),</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 57034),</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'a1319ff90e994c8190a4fe6569d0822a', 57035L, 57146L)]</span></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'a1319ff90e994c8190a4fe6569d0822a', 57035, 57146)]</span></span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> self.assertEqual(set(aln.tId), {0, 1})</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> # + 1, because bounds are inclusive, rather than exclusive</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2282,7 +2282,7 @@ class TestDataSet(unittest.TestCase):</span></span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> self.assertEqual(len3, 65346)</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> obstbl = aln.referenceInfoTable</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]</span></span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]</span></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> self.assertEqual(set(aln.tId), {0})</span>
</pre>
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</tr>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2306,7 +2306,7 @@ class TestDataSet(unittest.TestCase):</span></span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> self.assertEqual(len1 + len2, len3)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> self.assertEqual(len3, 160264)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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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51
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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="LC51" class="line" lang="diff"> exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',</span>
</pre>
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</tr>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]</span></span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]</span></span>
</pre>
</td>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> obstbl = aln.referenceInfoTable</span>
</pre>
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55
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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="LC55" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> self.assertEqual(set(aln.tId), {0})</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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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="LC57" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2338,9 +2338,9 @@ class TestDataSet(unittest.TestCase):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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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="LC58" class="line" lang="diff"> # and endrow fields for bams someday...</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="59" 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">
59
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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="LC59" class="line" lang="diff"> obstbl = aln.referenceInfoTable</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="60" 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">
60
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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="LC60" class="line" lang="diff"> exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L),</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
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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="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0),</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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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="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]</span></span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]</span></span>
</pre>
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</tr>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</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="0" 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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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> self.assertEqual(set(aln.tId), {0, 1})</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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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68
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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="LC68" class="line" lang="diff"> self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="69" 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">
69
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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="LC69" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2372,9 +2372,9 @@ class TestDataSet(unittest.TestCase):</span></span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> self.assertEqual(len4, 160376)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="71" 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">
71
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> obstbl = aln.referenceInfoTable</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="72" 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">
72
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="73" 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">
73
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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="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L),</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0),</span></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="0" 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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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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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="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="77" 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">
77
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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="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]</span></span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> self.assertListOfTuplesEqual(obstbl, exptbl)</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> self.assertEqual(set(aln.tId), {0, 1})</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),</span></pre>
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<li id="58defd8f851480233cffd7df05280e7925b60cad">
<a href="https://salsa.debian.org/med-team/python-pbcore/compare/a60fd5be18191d305e1e3f04b855d63bd2481999...9ce6ea2263880559e9778e7c824f5ec7dd35f8e2#58defd8f851480233cffd7df05280e7925b60cad"><strong>debian/patches/relax_test_constraint.patch</strong></a>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 25 Jun 2018 08:54:11 +0200</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Relax test constraint which is rather a rounding issue</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Traceback (most recent call last):</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> File "/build/python-pbcore-1.4.2+dfsg/tests/test_pbdataset.py", line 2125, in test_stats_metadata</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> 2322.16060475)</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> AssertionError: 2322.1606047549185 != 2322.16060475</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_pbdataset.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_pbdataset.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2121,7 +2121,7 @@ class TestDataSet(unittest.TestCase):</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 2322.805559802698)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> self.assertEqual(ds2.metadata.summaryStats.readLenDist.sampleStd,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 2322.805559802698)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(ds3.metadata.summaryStats.readLenDist.sampleStd,</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;">+ self.assertAlmostEqual(ds3.metadata.summaryStats.readLenDist.sampleStd,</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> 2322.16060475)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> # uses the bins, not the previous values for mean, std, etc.:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> self.assertEqual(ds3.metadata.summaryStats.readLenDist.sampleMed, 45)</span></pre>
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<br>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-pbcore/compare/a60fd5be18191d305e1e3f04b855d63bd2481999...9ce6ea2263880559e9778e7c824f5ec7dd35f8e2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,3 +2,5 @@ doc-theme.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">enable-build-time-testing.patch</span>
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<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="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">remove-unnecessary-cython-dep.patch</span>
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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="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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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">ignore-pyxb.patch</span>
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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="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">numpy1.14.patch</span>
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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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">relax_test_constraint.patch</span></pre>
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