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<h3>
Saira Hussain pushed to branch master
at <a href="https://salsa.debian.org/med-team/aevol">Debian Med / aevol</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/aevol/commit/ee794a137ac5c4c48255d5b3a18eec53c9a395f3">ee794a13</a></strong>
<div>
<span>by Saira Hussain</span>
<i>at 2019-07-24T07:44:12Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use the working script to debug
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">
debian/tests/run-unit-tests
</a>
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<h4>Changes:</h4>
<li id="b8880ead45e8d099a1552defb95ea70479f1572e">
<a href="https://salsa.debian.org/med-team/aevol/commit/ee794a137ac5c4c48255d5b3a18eec53c9a395f3#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" 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">@@ -19,12 +19,116 @@ gunzip -r *</td>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Just for debugging</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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21
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">Test 1</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">Run simulation</span></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>wild_type</span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">aevol_create</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">aevol_run <span class="nt" style="color: #000080;">-n</span> <span class="idiff left right">5</span>0 <span class="nt" style="color: #000080;">-p</span> <span class="nt" style="color: #000080;">-1</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">aevol_run <span class="nt" style="color: #000080;">-n</span> <span class="idiff left right">10</span>0 <span class="nt" style="color: #000080;">-p</span> <span class="nt" style="color: #000080;">-1</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test 2</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test setup</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">outdirsA</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"line01 line02 line03 line04 line05"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">outdirsB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"line06 line07 line08 line09 line10"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nv" style="color: #008080;">outdirsC</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"line11 line12 line13 line14 line15"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span> <span class="nv" style="color: #008080;">$outdirsB</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>aevol_propagate <span class="nt" style="color: #000080;">-o</span> ../<span class="nv" style="color: #008080;">$mydir</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For each experiment, create a file with the parameters to change</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# New environment</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.2 0.05</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.4 0.05</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.8 0.05</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_VARIATION none</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="s2" style="color: #d14;"># New rearrangement rates</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="s2" style="color: #d14;">DUPLICATION_RATE 1e-4</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="s2" style="color: #d14;">DELETION_RATE 1e-4</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="s2" style="color: #d14;">TRANSLOCATION_RATE 1e-4</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="s2" style="color: #d14;">INVERSION_RATE 1e-4"</span> <span class="o" style="font-weight: 600;">></span> newparam-groupA.in</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# New environment</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.2 0.05</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.4 0.05</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.8 0.05</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_VARIATION none</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="s2" style="color: #d14;"># New rearrangement rates</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="s2" style="color: #d14;">DUPLICATION_RATE 1e-6</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="s2" style="color: #d14;">DELETION_RATE 1e-6</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="s2" style="color: #d14;">TRANSLOCATION_RATE 1e-6</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="s2" style="color: #d14;">INVERSION_RATE 1e-6"</span> <span class="o" style="font-weight: 600;">></span> newparam-groupB.in</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# New environment</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.2 0.05</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.4 0.05</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_GAUSSIAN 0.5 0.8 0.05</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="s2" style="color: #d14;">ENV_VARIATION none"</span> <span class="o" style="font-weight: 600;">></span> newparam-groupC.in</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Apply these modifications</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"> aevol_modify <span class="nt" style="color: #000080;">-f</span> ../newparam-groupA.in</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsB</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"> aevol_modify <span class="nt" style="color: #000080;">-f</span> ../newparam-groupB.in</span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> aevol_modify <span class="nt" style="color: #000080;">-f</span> ../newparam-groupC.in</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run the simulations</span></span>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span> <span class="nv" style="color: #008080;">$outdirsB</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"> aevol_run <span class="nt" style="color: #000080;">-e</span> 200 <span class="nt" style="color: #000080;">-p</span> <span class="nt" style="color: #000080;">-1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># aevol_misc_create_eps </span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span> <span class="nv" style="color: #008080;">$outdirsB</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"> aevol_misc_create_eps &</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="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># aevol_misc_robustness </span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span> <span class="nv" style="color: #008080;">$outdirsB</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"> aevol_misc_robustness &</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># aevol_misc_lineage </span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span> <span class="nv" style="color: #008080;">$outdirsB</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"> aevol_misc_lineage</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># aevol_misc_ancstats </span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>mydir <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$outdirsA</span> <span class="nv" style="color: #008080;">$outdirsB</span> <span class="nv" style="color: #008080;">$outdirsC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$mydir</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"> aevol_misc_ancestor_stats lineage-<span class="k" style="font-weight: 600;">*</span>.ae <span class="nt" style="color: #000080;">-M</span> &</span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="29" 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">
29
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="shell"></span></pre>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test 3</span></span></pre>
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