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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/simka">Debian Med / simka</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/3bd0ff7d817f43e92e84cb9f119cd75c88f936c4">3bd0ff7d</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-12T05:17:16Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify 2to3 patch to fix writing str / byte complaint
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/110103a80b7587f42fa69c4cf3a921a912150851">110103a8</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-12T05:18:08Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix test paths
Tests referred to binaries within the working project directory and not the system
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#9aeb3f33ba7407966ded6269d14de4bad9117663">
<span class="new-file">
+
debian/patches/fix_test_path.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/simka/compare/54405f07fed643180d6d169755d68ebcf2d0868b...110103a80b7587f42fa69c4cf3a921a912150851#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/simkaMin/simkaMin.py</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/simkaMin/simkaMin.py 2019-09-12 0<span class="idiff left right">4:15:09.951278183</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/simkaMin/simkaMin.py 2019-09-12 0<span class="idiff left right">4:15:39.035180723</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/simkaMin/simkaMin.py 2019-09-12 0<span class="idiff left right">6:14:44.083241551</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/simkaMin/simkaMin.py 2019-09-12 0<span class="idiff left right">6:14:44.075241578</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></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">@@ -25,8 +25,8 @@ Index: simka/simkaMin/simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(("Result dir: " + args.out))</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/simkaMin/simkaMin_update.py</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/simkaMin/simkaMin_update.py 2019-09-12 0<span class="idiff left right">4:15:09.951278183</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/simkaMin/simkaMin_update.py 2019-09-12 0<span class="idiff left right">4:15:49.975144063</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/simkaMin/simkaMin_update.py 2019-09-12 0<span class="idiff left right">6:14:44.083241551</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/simkaMin/simkaMin_update.py 2019-09-12 0<span class="idiff left right">6:14:44.079241565</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></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">@@ -48,3 +48,16 @@ Index: simka/simkaMin/simkaMin_update.py</td>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> print("\n\n")</span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("Result dir: " + existingDir)</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(("Result dir: " + existingDir))</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/tests/simple_test.py</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py 2019-09-12 06:14:44.039241699 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py 2019-09-12 06:15:23.251110325 +0100</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> for filename_gz in result_filenames:</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #filename_gz = result_dir + "/" + filename</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> with gzip.open(filename_gz, 'rb') as f:</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outFile = open(filename_gz[:-3], "w")</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outFile = open(filename_gz[:-3], "wb")</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> outFile.write(f.read())</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> outFile.close()</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> os.remove(filename_gz)</span></pre>
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<li id="9aeb3f33ba7407966ded6269d14de4bad9117663">
<a href="https://salsa.debian.org/med-team/simka/compare/54405f07fed643180d6d169755d68ebcf2d0868b...110103a80b7587f42fa69c4cf3a921a912150851#9aeb3f33ba7407966ded6269d14de4bad9117663"><strong>debian/patches/fix_test_path.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/tests/simkaMin/test_simkaMin.py</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-11 23:39:55.656682381 +0100</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-12 06:10:03.252182437 +0100</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> for nb_reads in NB_READS:</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> for nb_kmers in NB_KMERS:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> for nb_cores in NB_CORES:</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command, outputDir = create_command("../../simkaMin/simkaMin.py", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")</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;">+ command, outputDir = create_command("simkaMin", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> print (command)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ret = os.system(command)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -146,7 +146,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> for nb_reads in NB_READS:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> for nb_kmers in NB_KMERS:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> for nb_cores in NB_CORES:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command, outputDir = create_command("../../simkaMin/simkaMin.py", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command("simkaMin", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> print (command)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -179,14 +179,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> f.close()</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> sketch_filename = os.path.join(out_dir, "sketch.bin")</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "../../build/bin/simkaMinCore sketch -in " + filename_temp + " -out " + sketch_filename + " -nb-kmers 100 -kmer-size 21 -nb-cores 4"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "simkaMinCore sketch -in " + filename_temp + " -out " + sketch_filename + " -nb-kmers 100 -kmer-size 21 -nb-cores 4"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> if os.path.exists(merged_sketch_filename):</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "../../build/bin/simkaMinCore append -in1 " + merged_sketch_filename + " -in2 " + sketch_filename</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "simkaMinCore append -in1 " + merged_sketch_filename + " -in2 " + sketch_filename</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> print(command)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if ret != 0: exit(1)</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -196,12 +196,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> os.remove(filename_temp)</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "../../build/bin/simkaMinCore distance -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir + " -nb-cores 4 "</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "simkaMinCore distance -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir + " -nb-cores 4 "</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> if ret != 0: exit(1)</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "../../build/bin/simkaMinCore export -in " + dir + " -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "simkaMinCore export -in " + dir + " -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -237,12 +237,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> f.close()</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> if init:</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command, outputDir = create_command_update("../../simkaMin/simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command_update("simkaMin_update", out_dir, 21, "", 0, 100, 4, filename_temp)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> if ret != 0: exit(1)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> else:</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command, outputDir = create_command("../../simkaMin/simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command("simkaMin", out_dir, 21, "", 0, 100, 4, filename_temp)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> print(command)</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> if ret != 0: exit(1)</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/tests/simple_test.py</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py 2019-09-11 23:39:55.668682342 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py 2019-09-12 06:14:31.939282238 +0100</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -91,7 +91,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> #test k=31 t=0</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> clear()</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> print("TESTING k=31 t=0")</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "/usr/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> print(command)</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> os.system(command + suffix)</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> test_dists("results_k31_t0")</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -99,7 +99,7 @@</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> #test k=21 t=0</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> clear()</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> print("TESTING k=21 t=0")</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "/usr/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> print(command)</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> os.system(command + suffix)</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> test_dists("results_k21_t0")</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -107,7 +107,7 @@</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> #test k=31 t=2</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> clear()</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> print("TESTING k=31 t=2")</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "/usr/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> print(command)</span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> os.system(command + suffix)</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> test_dists("results_k31_t2")</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -115,7 +115,7 @@</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> #test k=21 t=2</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> clear()</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> print("TESTING k=21 t=2")</span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "/usr/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> print(command)</span>
</pre>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> test_dists("results_k21_t2")</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -123,9 +123,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> #test resources 1</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> clear()</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> print("TESTING parallelization")</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "/usr/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "/usr/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> os.system(command + suffix)</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> test_parallelization()</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_test_path.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">2to3.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_debian_packaged_libraries.patch</span></pre>
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