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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/filtlong">Debian Med / filtlong</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/filtlong/-/commit/ff0db5ecd8372e3ce40f691ebdabb69561199359">ff0db5ec</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-05-14T22:55:17+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix patch for unittests
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<h4>1 changed file:</h4>
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<a href="#81753ead8ca1835e4e8a8723ea6671c520f57629">
debian/patches/ignore_locales_in_test_output.patch
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<h4>Changes:</h4>
<li id="81753ead8ca1835e4e8a8723ea6671c520f57629">
<a href="https://salsa.debian.org/med-team/filtlong/-/commit/ff0db5ecd8372e3ce40f691ebdabb69561199359#81753ead8ca1835e4e8a8723ea6671c520f57629"><strong>debian/patches/ignore_locales_in_test_output.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Ignore commas in numbers in test output</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> filtlong prints numbers with commas according to the locale</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> while unittests expect output in one particular format</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> This patch makes unittests ignore commas, so tests pass irrespective of locale.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Pranav Ballaney <ballaneypranav@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Bug: https://github.com/rrwick/Filtlong/issues/15</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-05-14 </span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_sort.py</span></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;">+++ b/test/test_sort.py</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="p">@@ -90,7 +90,7 @@</span> class TestSort(unittest.TestCase):</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> output_reads = load_fasta(self.output_file)</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> read_names = [x[0].decode() for x in output_reads]</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])</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;">- self.assertTrue('target: 100000 bp' in console_out)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('target: 100<span class="idiff left right">,</span>000 bp' in console_out)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> self.assertTrue('not enough reads to reach target' in console_out)</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </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">@@ -294,3 +303,118 @@</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="diff"> self.assertTrue('target: 1 bp' in console_out)</span>
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('keeping 5,000 bp' in console_out)</span></span>
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296
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_split.py</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_split.py</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span> class TestSplit(unittest.TestCase):</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> When splitting is off, the reads aren't split.</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> """</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> console_out = self.run_command('filtlong --min_length 1 -a ASSEMBLY INPUT > OUTPUT.fastq')</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('4 reads (11,600 bp)' in console_out)</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('4 reads (11600 bp)' in console_out.replace(',', ''))</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> self.assertTrue('after splitting' not in console_out)</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> self.assertEqual(len(split_reads), 4)</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="p">@@ -86,7 +86,7 @@</span> class TestSplit(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> When the split threshold is over 200, no reads are split.</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> """</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 250 INPUT > OUTPUT.fastq')</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 4 reads (11,600 bp)' in console_out)</span></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;">+ self.assertTrue('after splitting: 4 reads (11600 bp)' in console_out.replace(',', ''))</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> self.assertEqual(len(split_reads), 4)</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> for i in range(0, 4):</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="p">@@ -97,7 +97,7 @@</span> class TestSplit(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> When the split threshold is over 200, no reads are split.</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> """</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 201 INPUT > OUTPUT.fastq')</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 4 reads (11,600 bp)' in console_out)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 4 reads (11600 bp)' in console_out.replace(',', ''))</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> self.assertEqual(len(split_reads), 4)</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> for i in range(0, 4):</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="p">@@ -108,7 +108,7 @@</span> class TestSplit(unittest.TestCase):</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> When the split threshold is exactly 200, only the last read is split.</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> """</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 200 INPUT > OUTPUT.fastq')</span>
</pre>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 5 reads (11,400 bp)' in console_out)</span></span>
</pre>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 5 reads (11400 bp)' in console_out.replace(',', ''))</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> self.assertEqual(len(split_reads), 5)</span>
</pre>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> for i in range(0, 3):</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -121,7 +121,7 @@</span> class TestSplit(unittest.TestCase):</span>
</pre>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> When the split threshold is between 150 and 200, only the last read is split.</span>
</pre>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> """</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 175 INPUT > OUTPUT.fastq')</span>
</pre>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 5 reads (11,400 bp)' in console_out)</span></span>
</pre>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 5 reads (11400 bp)' in console_out.replace(',', ''))</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> self.assertEqual(len(split_reads), 5)</span>
</pre>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> for i in range(0, 3):</span>
</pre>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="p">@@ -134,7 +134,7 @@</span> class TestSplit(unittest.TestCase):</span>
</pre>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> When the split threshold is between 50 and 100, tbe last two reads are split.</span>
</pre>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> """</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 75 INPUT > OUTPUT.fastq')</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 6 reads (11,300 bp)' in console_out)</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 6 reads (11300 bp)' in console_out.replace(',', ''))</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> self.assertEqual(len(split_reads), 6)</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> for i in range(0, 2):</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="p">@@ -149,7 +149,7 @@</span> class TestSplit(unittest.TestCase):</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> When the split threshold is between 50 and 100, tbe last two reads are split.</span>
</pre>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> """</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 51 INPUT > OUTPUT.fastq')</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 6 reads (11,300 bp)' in console_out)</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 6 reads (11300 bp)' in console_out.replace(',', ''))</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> self.assertEqual(len(split_reads), 6)</span>
</pre>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> for i in range(0, 2):</span>
</pre>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="p">@@ -164,7 +164,7 @@</span> class TestSplit(unittest.TestCase):</span>
</pre>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> When the split threshold is exactly 50, tbe last three reads are split.</span>
</pre>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> """</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 50 INPUT > OUTPUT.fastq')</span>
</pre>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 7 reads (11,250 bp)' in console_out)</span></span>
</pre>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 7 reads (11250 bp)' in console_out.replace(',', ''))</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> self.assertEqual(len(split_reads), 7)</span>
</pre>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> self.check_one_read(split_reads[0], 2900, b'TCATTACG', b'AAAAGGAC')</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="p">@@ -180,7 +180,7 @@</span> class TestSplit(unittest.TestCase):</span>
</pre>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> When the split threshold is less than 50, tbe last three reads are split.</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> """</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --split 25 INPUT > OUTPUT.fastq')</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 7 reads (11,250 bp)' in console_out)</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 7 reads (11250 bp)' in console_out.replace(',', ''))</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> self.assertEqual(len(split_reads), 7)</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> self.check_one_read(split_reads[0], 2900, b'TCATTACG', b'AAAAGGAC')</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="p">@@ -196,7 +196,7 @@</span> class TestSplit(unittest.TestCase):</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> Same as the previous test, but using reads as a reference.</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> """</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --split 25 INPUT > OUTPUT.fastq')</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after splitting: 7 reads (11,250 bp)' in console_out)</span></span>
</pre>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after splitting: 7 reads (11250 bp)' in console_out.replace(',', ''))</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> split_reads = load_fastq(self.output_file)</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> self.assertEqual(len(split_reads), 7)</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> self.check_one_read(split_reads[0], 2900, b'TCATTACG', b'AAAAGGAC')</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_trim.py</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_trim.py</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="p">@@ -76,16 +76,16 @@</span> class TestTrim(unittest.TestCase):</span>
</pre>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> Tests read trimming console output using an assembly reference.</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> """</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> console_out = self.run_command('filtlong -a ASSEMBLY --trim INPUT > OUTPUT.fastq')</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('4 reads (4,901 bp)' in console_out)</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after trimming: 4 reads (4,824 bp)' in console_out)</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('4 reads (4901 bp)' in console_out.replace(',', ''))</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after trimming: 4 reads (4824 bp)' in console_out.replace(',', ''))</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> </span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> def test_trim_2(self):</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> """</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> Tests read trimming console output using Illumina read references.</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --trim INPUT > OUTPUT.fastq')</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('4 reads (4,901 bp)' in console_out)</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('after trimming: 4 reads (4,824 bp)' in console_out)</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('4 reads (4901 bp)' in console_out.replace(',', ''))</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue('after trimming: 4 reads (4824 bp)' in console_out.replace(',', ''))</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> </span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> def test_trim_3(self):</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> """</span></pre>
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