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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/kalign">Debian Med / kalign</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/79ce77e9d2b9b76c6f97ae3cd7175ae427fc54a6">79ce77e9</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-03-21T01:13:38+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reinstall examples properly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/aed1399182de322bcfb255e946ef845390188a79">aed13991</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-03-21T01:13:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add more autopkgtests
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#66b39388abb4f33bf86cc794bd1090e0111ef566">
debian/kalign.examples
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<li class="file-stats">
<a href="#6cee11869b2606f322aad4595c1ddfbe768a71d2">
<span class="deleted-file">
−
debian/tests/data/BB11001.msf
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<a href="#798c05a0f6da7af4b54ef141e0897eabff71a88f">
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−
debian/tests/data/BB11001.tfa
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="66b39388abb4f33bf86cc794bd1090e0111ef566">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/fa43b96ec7d1ba23d7a401562f375f5d057ab25b...aed1399182de322bcfb255e946ef845390188a79#66b39388abb4f33bf86cc794bd1090e0111ef566"><strong>debian/kalign.examples</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">dev/data/B*</span></pre>
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<li id="6cee11869b2606f322aad4595c1ddfbe768a71d2">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/fa43b96ec7d1ba23d7a401562f375f5d057ab25b...aed1399182de322bcfb255e946ef845390188a79#6cee11869b2606f322aad4595c1ddfbe768a71d2"><strong>debian/tests/data/BB11001.msf</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">PileUp</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> MSF: 96 Type: P Check: 7038 .. </span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Name: 1aab_ oo Len: 96 Check: 4681 Weight: 10.0</span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Name: 1j46_A oo Len: 96 Check: 1914 Weight: 10.0</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Name: 1k99_A oo Len: 96 Check: 8221 Weight: 10.0</span>
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<td class="diff-line-num old old_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Name: 2lef_A oo Len: 96 Check: 2222 Weight: 10.0</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">//</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">1aab_ ...GKGDPKK PRGKMSSYAF FVQTSREEHK KKHPDASVNF SEFSKKCSER </span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">1j46_A ......MQDR VKRPMNAFIV WSRDQRRKMA LENP..RMRN SEISKQLGYQ </span>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/fa43b96ec7d1ba23d7a401562f375f5d057ab25b...aed1399182de322bcfb255e946ef845390188a79#798c05a0f6da7af4b54ef141e0897eabff71a88f"><strong>debian/tests/data/BB11001.tfa</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">>1aab_</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">>1j46_A</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAE</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">KWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">>1k99_A</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYK</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">ELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">>2lef_A</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQA</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/fa43b96ec7d1ba23d7a401562f375f5d057ab25b...aed1399182de322bcfb255e946ef845390188a79#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -14,6 +14,8 @@ cd $AUTOPKGTEST_TMP</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Passing input files via -i never works for some reason inside the testing chroot</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># LOG : kalign -i BB11001.tfa -f msf -o out.msf </span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ERROR : Input alignment format could not be detected. (rwalign.c line 314)</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">@@ -37,17 +39,25 @@ cat seqsA.fa seqsB.fa seqsC.fa | kalign -f fasta > combined.afa</td>
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37
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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>TEST 4: Align sequences and output the alignment <span class="k" style="font-weight: 600;">in </span>MSF format</span>
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38
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kalign -i BB11001.tfa -f msf -o out.msf</span></span>
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39
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB11001.tfa | kalign <span class="nt" style="color: #000080;">-f</span> msf <span class="nt" style="color: #000080;">-o</span> out.msf</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB12006.tfa | kalign <span class="nt" style="color: #000080;">-f</span> msf <span class="nt" style="color: #000080;">-o</span> out.msf</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB30014.tfa | kalign <span class="nt" style="color: #000080;">-f</span> msf <span class="nt" style="color: #000080;">-o</span> out.msf</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>TEST 5: Align sequences and output the alignment <span class="k" style="font-weight: 600;">in </span>clustal format</span>
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42
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kalign -i BB11001.tfa -f clu -o out.clu</span></span>
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43
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB11001.tfa | kalign <span class="nt" style="color: #000080;">-f</span> clu <span class="nt" style="color: #000080;">-o</span> out.clu</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB12006.tfa | kalign <span class="nt" style="color: #000080;">-f</span> clu <span class="nt" style="color: #000080;">-o</span> out.clu</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB30014.tfa | kalign <span class="nt" style="color: #000080;">-f</span> clu <span class="nt" style="color: #000080;">-o</span> out.clu</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>TEST 6: Re-align sequences <span class="k" style="font-weight: 600;">in </span>an existing alignment</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kalign -i BB11001.msf -o out.afa</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB11001.msf | kalign <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB12006.msf | kalign <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB30014.msf | kalign <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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<td class="diff-line-num old_line" data-linenumber="48" 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">
48
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>TEST 7: Reformat existing alignment</span>
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50
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kalign -i BB11001.msf -r afa -o out.afa</span></span>
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<td class="diff-line-num old_line" data-linenumber="51" 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">
51
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB11001.msf | kalign <span class="nt" style="color: #000080;">-r</span> afa <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB12006.msf | kalign <span class="nt" style="color: #000080;">-r</span> afa <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>BB30014.msf | kalign <span class="nt" style="color: #000080;">-r</span> afa <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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52
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"></span>
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53
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span></pre>
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