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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/f9e2c5013129921e1569e3ec6fdbea528335c3ea">f9e2c501</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-03-20T00:56:25+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install more test files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/fa43b96ec7d1ba23d7a401562f375f5d057ab25b">fa43b96e</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-03-20T01:15:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#66b39388abb4f33bf86cc794bd1090e0111ef566">
debian/kalign.examples
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</li>
<li class="file-stats">
<a href="#6cee11869b2606f322aad4595c1ddfbe768a71d2">
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debian/tests/data/BB11001.msf
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<li class="file-stats">
<a href="#798c05a0f6da7af4b54ef141e0897eabff71a88f">
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debian/tests/data/BB11001.tfa
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<li class="file-stats">
<a href="#577404c3daab2977706751498afd2306427a2a9e">
debian/tests.kalign/example.fa
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debian/tests/data/example.fa
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<li class="file-stats">
<a href="#fcfb6c2ee1e49f94d4db00229ce3e7999c746323">
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debian/tests/data/seqsA.fa
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debian/tests/data/seqsB.fa
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debian/tests/data/seqsC.fa
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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/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#66b39388abb4f33bf86cc794bd1090e0111ef566"><strong>debian/kalign.examples</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests<span class="idiff left right">.kalign</span>/*</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests<span class="idiff left right">/data</span>/*</span></pre>
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<td class="new_line diff-line-num" 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">\ No newline at end of file</td>
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<li id="6cee11869b2606f322aad4595c1ddfbe768a71d2">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#6cee11869b2606f322aad4595c1ddfbe768a71d2"><strong>debian/tests/data/BB11001.msf</strong></a>
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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="LC5" class="line" lang="plaintext"> MSF: 96 Type: P Check: 7038 .. </span>
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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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC12" 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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">1k99_A MKKLKKHPDF PKKPLTPYFR FFMEKRAKYA KLHP..EMSN LDLTKILSKK </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">2lef_A ........MH IKKPLNAFML YMKEMRANVV AEST..LKES AAINQILGRR </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">1aab_ WKTMSAKEKG KFEDMAKADK ARYEREMKTY IPPKGE.... ......</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">1j46_A WKMLTEAEKW PFFQEAQKLQ AMHREKYPNY KYRPRRKAKM LPK...</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">1k99_A YKELPEKKKM KYIQDFQREK QEFERNLARF REDHPDLIQN AKK...</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">2lef_A WHALSREEQA KYYELARKER QLHMQLYPGW SARDNYGKKK KRKREK</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#798c05a0f6da7af4b54ef141e0897eabff71a88f"><strong>debian/tests/data/BB11001.tfa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>1aab_</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">MSAKEKGKFEDMAKADKARYEREMKTYIPPKGE</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">>1j46_A</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAE</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">KWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>1k99_A</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYK</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">>2lef_A</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQA</span>
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12
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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/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#577404c3daab2977706751498afd2306427a2a9e"><strong>debian/tests.kalign/example.fa</strong>
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<strong>debian/tests/data/example.fa</strong>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#fcfb6c2ee1e49f94d4db00229ce3e7999c746323"><strong>debian/tests/data/seqsA.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>random sequence 1 consisting of 500 residues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">QWKPFLTTAQSKLFEMIQHAEMDCPASDYKYPAHESVRVSYCFGCFGHQSTLFAQCQAKL</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">SNIESSIEGYAFPSVYWYNNHKHPTNNDHIGPACAVTQGKCDYNPANPFSWLVNIPEYQG</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">TFVPNTNLNWKIGNIMGWFYTVVMADYCDQWYEDVFTISWCPRAFKLEDRWDRVTDANTK</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">PSKLWFNNRQEPAYQWMDSPDHKVRRIVLTPRNMFTETKSCYAVETRNCDGLHVVVHETM</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">TAKREDNIGEWHILKTHQNKGWVKQKMHAEMSALEFDAYLLVGMARMQCRVYQHNAKIRN</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">TDSPVVFCKWYGTATHKQPSSCMCEDEVSDGKMWYGWNHYQYLAEFDDGAPHHLECTWAM</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">DYNPDAAQPMPYDCNNCAFQNQVHFTIDRGFQHGTRNQVHNRVDQDENYMGISEFTNYFL</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">DQCDFIQEQIDSDTESNHQCYTWAKLTRYVQVTNPRSDMGAVIENREMENCVEQGAHSDN</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">HSPVNMEKWYCECESPPKNV</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>random sequence 2 consisting of 500 residues</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">PDGNKPKEPWKGPKMGQDMVTNSIVNTPGDDTKGFDEMIWLMDKRTRLVVKACMWPMILA</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">LNTYQNKNDNEMPWPHWGMRMHGHDLLQRRKPIFQQYTIVAMFNMGSSDQQEFLMIKPPI</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">QATCSSGLDPHRLMRCYKWDTKKTQKGDHKGQEKCQSEAVYDKCIIKQVVFHSMYCYWTY</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">WCICYLPTAEMGDDYQPECWHVWYIMDYVVKFKMLYNNRLWYSHMNQMWINHHIHVYYRC</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">GDQYLADHPYRMGIVDAYWFISFGHRIRQRMCVQLKVWGWVFLNAAGSPVHRFKSAHHVG</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">GGADGRMPRTCRDDPRMYEAKWSYAPPYVITCALRPGMFANYHPRSFVRPCQQPMYWMRN</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">MLSDQSEAYGGNVDMGWLARDNISSQCYHSDIQWPGIQMILHSPAANPGHHQIACVKRSH</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">TEALELFQAVTASNVAIGCFIQTACPIDMSIEKPDDAIMEWPGYTFGYDRTRCKWTRAND</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">IPHPDKNKSSGLRCYHTVNL</span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#2396d4931d4c97028c482cb04b1b5c3f86dd5998"><strong>debian/tests/data/seqsB.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>random sequence 3 consisting of 500 residues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">PTANCDANENICAHSYFKLLMIFDFWYDYFVLCRATIHHMHYWRPCFEPPYHIVWKYKDM</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">HRCLANYWTHQMKTVSVRRINNNEARWMIREWHGSSWGIMLMVKKLVTTQWHPYNFREEE</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">PWYMNIPPWEVGQEIKAFVCLECAGPEMWPNCQDKNSPYMTGSLLVGGDVRYTIMQWDLE</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">APKIKRETPGESWAPLLIFCRMKAMQQDGVAGLEKTGGHLMQCRHLGHAVHRRHNNMHTC</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">YVQCQVFPYNEMIHSPCMPYLSCHQRLKLHDGEYKTHTGLIYDMEAKCQLSEAMRHTSMR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ESACGQHYNYAKQSDHRFKLDAFTHYDFDFDRLKSGNCCSTISACICYAKPVAWRMRCMM</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">IWTTGKCTKNCFDGCSYICPTIQNTQCLWEMSQYWADLDPKKKFWFWPSATIYWTEGIVQ</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">EHSLTIWTLDTGVVIGLADP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>random sequence 4 consisting of 500 residues</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">NQLFCNMDIYHRGVREQKMFHNCESICQKHKAIAVRMANKTPRQSLMMTCSALQHSNPTT</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">NEYLQDTKVWYFMQALRVSRSWGWRASYFYRPMDYKRNWHEPVRHPATWCFPIWCFNIPM</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">WHGHDYQMHTLRLLSMKCNCYDWRDNFDEYFTDPSAQSKHNHMADYVLLMIQLLKIARYR</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">INVWDTHLMWRNLSQQVPYIMHPYSDHLREWTNANFKFIWQQGMCQHEMTYGKIWDVMGG</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">EYCTTVMKHHWAVAKHHPALPHQERRIIGLVWKMSNKWAANFGSCNWELYIGLHQQASKG</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">PSAWGLMCMCYHTRYHRALQRLSDAHCNWDDDKYHWGKKESAEVNTSDSHFRHCTRWEMV</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">AIALCWWEHHTHNYRTIDWF</span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#ba4540ceb6d11012bfd9f5484edd3bc57a1304f1"><strong>debian/tests/data/seqsC.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>random sequence 5 consisting of 500 residues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RNLELKAMVFEFPHAWAIKHAWLAFLNHGSTLRRMRIFCHHYRALHTSLIFIWISMNWYF</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">NIQNMSAMTNDTLCLCGNTTNLQHTGIPAWYDKCNHPRIDDMVEVQDWKERWQHHGHYEG</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">VHNIGTMMSKDSFHNKEGKGERWPEWDYRITIMLSYHCEEQHPKCTWKMKAGCMGAVLWD</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">MEFCFRGPQNSGPHWCQMEQYLGPNGRNMGEDINHMAFNTHWDITLQDLTDAPYREPHDK</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">QYACLPMKPHIPFMFVGDADSDFGWDQPDTDGNMMRPLHPWGEIQIHKCNCFCHPCDQEV</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">MNWLLCMWEEVPDWLTNKGARTNARCPYGHPICMIEERNALPSSQHKIVLTSLKWMNRIE</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">DDGMGLNYNYQCDASLWCGVIRWPYIHHWEETGCLDYGQTKELRYCMIRFFGKRIDHNSL</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">SLGKDIACAQQHTHMWTSAVPCARHEVDQATLKHCDAFPRGPQTSYQMKLYRCSNPETYW</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">PRQCHQSVIQNLMRNKWDST</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>random sequence 6 consisting of 500 residues</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">RKPARRCVCSKNMNHYDNEQCGWEQPWLEISFMMSWGVHPEANHIKPVEGLSWVEHVSEF</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">IIRYYDWSNSSFQHYKPEVEWMPSAREDEHFKETRQPTPNAYNIGERWKWSYWLGNEKEY</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">SNWQMTCDYLDFQKIQDMPRSGPGQLCGSPLYMEISPIWWKGLGCVAHLWMKFPWKIQHI</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">SACHHSTGDDQMKTGSDDDGAEDNAINIGKTWQGYDKERCTWLHIMMTGYIRWCCSKDRM</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">PSKPFIHNHYIILRKSMWLTDKSKDGDCWVLIANSRGDPCAGNAAHIYPKQMCHRPSLQV</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">FEWMFCCPLHDRQGWLKDWNSRSNGTSPKPTLRAEKMFMFHTFLPCFPVHYLMHTRMDHM</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">FMMMTTEDKSDKKKDDAEGRMILDYRCKRCPIVCWGVNDHKYSHGHHDMNGAEAEKYYKM</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">DMSALRTFPGCCSDNESDGNDRGYDDQGLKRFIFFCKQKAYYICYCRVRSMWHVSRKHNC</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">MNTKQCEMESIWGFIIFNSN</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b#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">@@ -12,11 +12,42 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"---test1---"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">/usr/bin/kalign < example.fa <span class="o" style="font-weight: 600;">></span> output1</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;">cat </span>output1</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"---test2---"</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell">/usr/bin/kalign <span class="nt" style="color: #000080;">-gpo</span> 60 <span class="nt" style="color: #000080;">-gpe</span> 9 <span class="nt" style="color: #000080;">-tgpe</span> 0 <span class="nt" style="color: #000080;">-bonus</span> 0 < example.fa <span class="o" style="font-weight: 600;">></span> output2</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;">cat </span>output2</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="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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18
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<pre style="margin: 0;">+<span id="LC18" 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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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;"># ERROR : Input alignment format could not be detected. (rwalign.c line 314)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187)</span></span>
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21
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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 : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383)</span></span>
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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;"># ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># However, input through stdin works</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Input via -i also works outside the chroot, just not inside it</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="nb" style="color: #0086b3;">echo </span>TEST 1: Passing sequences via stdin</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>example.fa | kalign <span class="nt" style="color: #000080;">-f</span> fasta <span class="o" style="font-weight: 600;">></span> out.afa</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo TEST 2: Passing sequences via flags</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kalign -f fasta -i example.fa -o out.afa</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>TEST 3: Combining multiple input files</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kalign -i seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa </span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>seqsA.fa seqsB.fa seqsC.fa | kalign <span class="nt" style="color: #000080;">-f</span> fasta <span class="o" style="font-weight: 600;">></span> combined.afa </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC37" 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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<pre style="margin: 0;">+<span id="LC38" 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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<pre style="margin: 0;">+<span id="LC39" 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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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"></span>
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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;">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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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" 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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<pre style="margin: 0;">+<span id="LC43" 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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" 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="LC46" 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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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.msf | kalign <span class="nt" style="color: #000080;">-o</span> out.afa</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></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;">echo </span>TEST 7: Reformat existing alignment</span>
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50
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<pre style="margin: 0;">+<span id="LC50" 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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51
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<pre style="margin: 0;">+<span id="LC51" 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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21
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC53" 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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