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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/-/commit/bc06b1228af1ce5853eddfbcdd9773e3eab2e10a">bc06b122</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-07-28T12:17:59+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#4d68f969aad60c41a6adb3d49544ebb18af54229">
debian/patches/fix_binary_path.patch
</a>
</li>
<li class="file-stats">
<a href="#1810013904578e3ebd3a8479567f186a655fa4bf">
debian/patches/fix_temp_arrays.patch
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<li class="file-stats">
<a href="#9aeb3f33ba7407966ded6269d14de4bad9117663">
debian/patches/fix_test_path.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="4d68f969aad60c41a6adb3d49544ebb18af54229">
<a href="https://salsa.debian.org/med-team/simka/-/commit/bc06b1228af1ce5853eddfbcdd9773e3eab2e10a#4d68f969aad60c41a6adb3d49544ebb18af54229"><strong>debian/patches/fix_binary_path.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,10 +4,8 @@ Author: Shayan Doust <hello@shayandoust.me></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-09-13</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Index: simka/src/SimkaPotara.cpp</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- simka.orig/src/SimkaPotara.cpp 2019-09-13 08:44:18.831548830 +0100</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;">+++ simka/src/SimkaPotara.cpp 2019-09-13 08:44:18.831548830 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- simka.orig/src/SimkaPotara.cpp</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/src/SimkaPotara.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">@@ -28,7 +28,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> */</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> SimkaPotara::SimkaPotara(const string& execFilename) : Tool ("Simka")</span>
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<br>
</li>
<li id="1810013904578e3ebd3a8479567f186a655fa4bf">
<a href="https://salsa.debian.org/med-team/simka/-/commit/bc06b1228af1ce5853eddfbcdd9773e3eab2e10a#1810013904578e3ebd3a8479567f186a655fa4bf"><strong>debian/patches/fix_temp_arrays.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,24 +3,8 @@ Description: separate out array as a defined struct</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2019-09-16</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Index: simka/src/SimkaPotara.hpp</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/src/SimkaPotara.hpp 2019-09-16 15:21:36.549855248 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/src/SimkaPotara.hpp 2019-09-16 15:21:36.545855212 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -902,7 +902,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> else{</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> //sleep(1);</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nanosleep((const struct timespec[]){{0, 100000000L}}, NULL);</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ struct timespec ts = {0, 100000000L};</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;">+ nanosleep(&ts, NULL);</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> if(i >= this->_bankNames.size()) break;</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/src/minikc/SimkaCountProcess.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/src/minikc/SimkaCountProcess.cpp 2019-09-16 15:21:36.549855248 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/src/minikc/SimkaCountProcess.cpp 2019-09-16 15:21:36.545855212 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- simka.orig/src/minikc/SimkaCountProcess.cpp</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;">+++ simka/src/minikc/SimkaCountProcess.cpp</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -22,7 +22,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> int nbTries = 0;</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> while(ret != 0){</span>
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<li id="9aeb3f33ba7407966ded6269d14de4bad9117663">
<a href="https://salsa.debian.org/med-team/simka/-/commit/bc06b1228af1ce5853eddfbcdd9773e3eab2e10a#9aeb3f33ba7407966ded6269d14de4bad9117663"><strong>debian/patches/fix_test_path.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,16 +3,14 @@ Author: Shayan Doust <hello@shayandoust.me></td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2019-09-13</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">---</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Index: simka/tests/simkaMin/test_simkaMin.py</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-16 15:35:57.745165516 +0100</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-16 15:35:57.741165482 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- simka.orig/tests/simkaMin/test_simkaMin.py</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;">+++ simka/tests/simkaMin/test_simkaMin.py</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -16,28 +16,28 @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> def create_command(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "python " + scriptFilename</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command =scriptFilename</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command =<span class="idiff left right"> "python3 " + </span>scriptFilename</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> command += " -in " + input_filename</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> command += " -out " + outputPrefix + "/" + outputDir</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> command += " -nb-cores " + str(nb_cores)</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">@@ -28,9 +26,9 @@ Index: simka/tests/simkaMin/test_simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> def create_command_update(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)</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;">- command = "python " + scriptFilename</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = scriptFilename</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;">+ command = <span class="idiff left right">"python3 " + </span>scriptFilename</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> command += " -in " + input_filename</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> command += " -in-to-update " + outputPrefix + "/" + outputDir</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> command += " -in-to-update " + outputPrefix + "/" + outputDir<span class="idiff left right"> + "/simkamin"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> command += " -nb-cores " + str(nb_cores)</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> command += " -max-memory 100 "</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> #command += " -kmer-size " + str(k)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,8 +42,8 @@ Index: simka/tests/simkaMin/test_simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> for nb_reads in NB_READS:</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> for nb_kmers in NB_KMERS:</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> for nb_cores in NB_CORES:</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 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="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command("simkaMin<span class="idiff left right">", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ..</span>/simka_input.txt ")</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command, outputDir = create_command("../../simkaMin/simkaMin.py", "truth_simkaMin<span class="idiff left right">_symetrical</span>", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command("simkaMin<span class="idiff left right">.py", "truth_simkaMin_symetrical", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example</span>/simka_input.txt ")</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> print (command)</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> ret = os.system(command)</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> if ret != 0: exit(1)</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">@@ -58,7 +56,7 @@ Index: simka/tests/simkaMin/test_simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> print (command)</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="p">@@ -16<span class="idiff left right">8,25 +168</span>,25 @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -16<span class="idiff left right">6,25 +166</span>,25 @@</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> os.mkdir(out_dir)</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> merged_sketch_filename = os.path.join(out_dir, "merged_sketch.bin")</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">@@ -88,7 +86,7 @@ Index: simka/tests/simkaMin/test_simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="p">@@ -19<span class="idiff left right">6,12 +196</span>,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="p">@@ -19<span class="idiff left right">4,12 +194</span>,12 @@</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> os.remove(filename_temp)</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,38 +101,38 @@ Index: simka/tests/simkaMin/test_simkaMin.py</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="p">@@ -226,23 +226,23 @@</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -223,10 +223,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> clear(out_dir)</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> os.mkdir(out_dir)</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"> init = False</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filename = "../../example/simka_input.txt"</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filename_temp1 = os.path.join("../../example/test_simkaMin_input_temp1.txt")</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filename = "../simka_input.txt"</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"> for line in open(filename):</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"> line = line.strip()</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"> if len(line) == 0: continue</span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filename_temp = os.path.join("../../example/test_simkaMin_input_temp.txt")</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filename_temp = os.path.join("../test_simkaMin_input_temp.txt")</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"> f = open(filename_temp, "w")</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"> f.write(line)</span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"> f.close()</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filename_temp1 = os.path.join("../test_simkaiMin_input_temp1.txt")</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> f1 = open(filename_temp1, "w")</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filename_temp2 = os.path.join("../../example/test_simkaMin_input_temp2.txt")</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filename_temp2 = os.path.join("../test_simkaMin_input_temp2.txt")</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> f2 = open(filename_temp2, "w")</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> N=2 #where to split the file</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> i=0</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="p">@@ -241,13 +241,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> f2.close()</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> # init</span>
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<pre style="margin: 0;">+<span id="LC122" 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_temp1)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command("simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp1)</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> if ret != 0: exit(1)</span>
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121
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"> if init:</span>
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123
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<pre style="margin: 0;">-<span id="LC123" 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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124
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<pre style="margin: 0;">-<span id="LC124" 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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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"> print(command)</span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"> if ret != 0: exit(1)</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"> else:</span>
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129
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<pre style="margin: 0;">-<span id="LC129" 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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130
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<pre style="margin: 0;">-<span id="LC130" 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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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/tests/simple_test.py</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py 2019-09-16 15:35:57.745165516 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py 2019-09-16 15:35:57.741165482 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> # update</span>
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<pre style="margin: 0;">+<span id="LC129" 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_temp2)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command, outputDir = create_command_update("simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp2)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> print(command)</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> ret = os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> if ret != 0: exit(1)</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"><span class="p">@@ -91,7 +91,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> #test k=31 t=0</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"> clear()</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,10 +181,8 @@ Index: simka/tests/simple_test.py</td>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="diff"> os.system(command + suffix)</span>
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184
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="diff"> test_parallelization()</span>
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185
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="diff"> </span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gh" style="color: #999;">Index: simka/example/simple_test.sh</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/example/simple_test.sh 2019-09-16 15:35:57.745165516 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/example/simple_test.sh 2019-09-16 15:36:47.117582577 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/example/simple_test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/example/simple_test.sh</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="diff"><span class="p">@@ -3,23 +3,23 @@</span></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="diff"> # look for simka binary. In devel mode, it's in ../build/bin directory.</span>
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