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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a">1d01bfcb</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-12-17T10:12:55Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 961</pre>

</li>

</ul>

<h4>27 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#57bf262130f956caf76c405086f0815caf4e0a89">

ChangeLog.txt

</a>

</li>

<li class="file-stats">

<a href="#d569d86e42565e3be7e6f2dd351c600fe0f19a6f">

doc/last-dotplot.html

</a>

</li>

<li class="file-stats">

<a href="#1b4eb23521879045d9184d50996b3aa277a711e9">

doc/last-dotplot.txt

</a>

</li>

<li class="file-stats">

<a href="#bf068196d49b041029d9a269a6e3d52acda15f9f">

doc/last-train.html

</a>

</li>

<li class="file-stats">

<a href="#03dd50d6a64beb7787e3bcc9eb6da79c482759d5">

doc/last-train.txt

</a>

</li>

<li class="file-stats">

<a href="#1d2db1d5c1263541e178e5c6d1a664dcaee43e97">

doc/lastal.html

</a>

</li>

<li class="file-stats">

<a href="#30d864ed8925787ee70643db49814772753a5f2c">

doc/lastal.txt

</a>

</li>

<li class="file-stats">

<a href="#0bf0c2b9afb77a75953faf3468b6707da7098872">

doc/lastdb.html

</a>

</li>

<li class="file-stats">

<a href="#485665224376f8470c80c62ef464a2a01e61c7e7">

doc/lastdb.txt

</a>

</li>

<li class="file-stats">

<a href="#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">

scripts/last-dotplot

</a>

</li>

<li class="file-stats">

<a href="#91df1cfad6631f83b9c232630119e09896361a09">

scripts/last-map-probs

</a>

</li>

<li class="file-stats">

<a href="#09de00a2f5fb0a5a61122f0d649401a900bbb57b">

scripts/last-postmask

</a>

</li>

<li class="file-stats">

<a href="#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">

scripts/last-train

</a>

</li>

<li class="file-stats">

<a href="#0c8579b85a61ba3e2feb036884e3e6d6da75cf0e">

scripts/maf-convert

</a>

</li>

<li class="file-stats">

<a href="#177815a02f622695617613b9dc8023a958d68f7b">

scripts/maf-cut

</a>

</li>

<li class="file-stats">

<a href="#350d50b528bcd24a057c181965b2a50120bca4c7">

scripts/maf-swap

</a>

</li>

<li class="file-stats">

<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">

src/LastalArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#54925a3b3158a751c06af7acce6d06070e5ac813">

src/LastdbArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#de5a928be30a99dcb150a5f687171caed2e9c00c">

src/MultiSequence.hh

</a>

</li>

<li class="file-stats">

<a href="#a06897230734e5ba8f58dabb84ae90af66f731e9">

src/MultiSequenceQual.cc

</a>

</li>

<li class="file-stats">

<a href="#39b07776472abcba47ba556e9f044177918c142c">

src/SequenceFormat.hh

</a>

</li>

<li class="file-stats">

<a href="#cbc8995f0e52a1d4b5b18e7df92014c01ec2dea1">

src/SubsetSuffixArray.cc

</a>

</li>

<li class="file-stats">

<a href="#6f06cc5de9b7ac057e2bab4944683b3802e6b62f">

src/last.hh

</a>

</li>

<li class="file-stats">

<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

src/lastal.cc

</a>

</li>

<li class="file-stats">

<a href="#de4252990d12a909e50ff0b994d1715eae0ea5fd">

src/lastdb.cc

</a>

</li>

<li class="file-stats">

<a href="#cff6a16c49a626871ebb6399a31650f25e4f5395">

src/split/last-split.cc

</a>

</li>

<li class="file-stats">

<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">

src/version.hh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="57bf262130f956caf76c405086f0815caf4e0a89">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2018-12-10  Martin C. Frith  <Martin C. Frith></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">      * doc/last-dotplot.txt, scripts/last-dotplot:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      Add last-dotplot --maxseqs option</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      [ed0fb9b1eb40] [tip]</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">      * src/split/last-split.cc:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      Make last-split -n keep E-values</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      [2063a5a7d7ac]</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">2018-10-30  Martin C. Frith  <Martin C. Frith></span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">     * doc/last-train.txt, doc/lastal.txt, doc/lastdb.txt, scripts/last-</span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">     train, src/LastalArguments.cc, src/LastdbArguments.cc,</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">     src/MultiSequence.hh, src/MultiSequenceQual.cc,</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">     src/SequenceFormat.hh, src/last.hh, test/last-test.out, test/last-</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">     test.sh:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" 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">

18

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     Add fastq-ignore option</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">     [c551d04a3928]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">2018-10-29  Martin C. Frith  <Martin C. Frith></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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="plaintext"></span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">     * src/LastalArguments.cc, src/SequenceFormat.hh,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">     src/SubsetSuffixArray.cc, src/lastal.cc, src/lastdb.cc:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="25" 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">

25

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">     Refactor</span>

</pre>

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26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">     [96b45da7bf0f]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="27" 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">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">     * scripts/last-dotplot, scripts/last-map-probs, scripts/last-postmask,</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">     scripts/last-train, scripts/maf-convert, scripts/maf-cut, scripts</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">     /maf-swap:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">

31

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">     Fix gz reading for Python3</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">     [c54672c8892e]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="33" 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">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="34" 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">

34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">2018-09-10  Martin C. Frith  <Martin C. Frith></span>

</pre>

</td>

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2

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<td class="diff-line-num new_line" data-linenumber="35" 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">

35

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="36" 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="LC36" class="line" lang="plaintext">     * scripts/last-map-probs:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">     Python3-ify last-map-probs</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">      [83191e47259e]<span class="idiff left right"> [tip]</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">     [83191e47259e]</span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">2018-09-07  Martin C. Frith  <Martin C. Frith></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>

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<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#d569d86e42565e3be7e6f2dd351c600fe0f19a6f"><strong>doc/last-dotplot.html</strong></a>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="html">set of sequences.  This document calls a <span class="ni" style="color: purple;">&quot;</span>set of sequences<span class="ni" style="color: purple;">&quot;</span> a</span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="html"><span class="ni" style="color: purple;">&quot;</span>genome<span class="ni" style="color: purple;">&quot;</span>, though it need not actually be a genome.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"choosing-sequences"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Choosing sequences<span class="nt" style="color: navy;"></h2></span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If there are too many sequences, the dotplot will be very cluttered,</span>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="html">or the script might give up with an error message.  You can exclude</span>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="html">sequences with names like <span class="ni" style="color: purple;">&quot;</span>chrUn_random522<span class="ni" style="color: purple;">&quot;</span> like this:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="html">last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png</span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Option <span class="ni" style="color: purple;">&quot;</span>-1<span class="ni" style="color: purple;">&quot;</span> selects sequences from the 1st (horizontal) genome, and</span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="html"><span class="ni" style="color: purple;">&quot;</span>-2<span class="ni" style="color: purple;">&quot;</span> selects sequences from the 2nd (vertical) genome.  'chr[!U]*' is</span>

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC348" class="line" lang="html">a <span class="nt" style="color: navy;"><em></span>pattern<span class="nt" style="color: navy;"></em></span> that specifies names starting with <span class="ni" style="color: purple;">&quot;</span>chr<span class="ni" style="color: purple;">&quot;</span>, followed by any</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="349" 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">

349

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<td class="diff-line-num new_line old" data-linenumber="338" 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="LC349" class="line" lang="html">character except U, followed by anything.<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="350" 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">

350

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC350" class="line" lang="html"><span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">border=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="351" 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">

351

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC351" class="line" lang="html"><span class="nt" style="color: navy;"><colgroup></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="352" 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">

352

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<td class="diff-line-num new_line old" data-linenumber="338" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC352" class="line" lang="html"><span class="nt" style="color: navy;"><col</span> <span class="na" style="color: teal;">width=</span><span class="s" style="color: #d14;">"26%"</span> <span class="nt" style="color: navy;">/></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="353" 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">

353

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC353" class="line" lang="html"><span class="nt" style="color: navy;"><col</span> <span class="na" style="color: teal;">width=</span><span class="s" style="color: #d14;">"74%"</span> <span class="nt" style="color: navy;">/></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="354" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC354" class="line" lang="html"><span class="nt" style="color: navy;"></colgroup></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="355" 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">

355

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC355" class="line" lang="html"><span class="nt" style="color: navy;"><tbody</span> <span class="na" style="color: teal;">valign=</span><span class="s" style="color: #d14;">"top"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="356" 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">

356

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<td class="diff-line-num new_line old" data-linenumber="338" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC356" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>Pattern<span class="nt" style="color: navy;"></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="357" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC357" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Meaning<span class="nt" style="color: navy;"></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="358" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC358" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="359" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC359" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>*<span class="nt" style="color: navy;"></tt></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="360" 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">

360

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<td class="diff-line-num new_line old" data-linenumber="338" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC360" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>zero or more of any character<span class="nt" style="color: navy;"></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="361" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC361" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="362" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC362" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>?<span class="nt" style="color: navy;"></tt></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="363" 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">

363

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC363" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>any single character<span class="nt" style="color: navy;"></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="364" 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">

364

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<td class="diff-line-num new_line old" data-linenumber="338" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC364" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="365" 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">

365

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC365" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>[abc]<span class="nt" style="color: navy;"></tt></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="366" 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">

366

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<td class="diff-line-num new_line old" data-linenumber="338" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC366" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>any character in abc<span class="nt" style="color: navy;"></td></span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>[!abc]<span class="nt" style="color: navy;"></tt></td></span></span>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>any character not in abc<span class="nt" style="color: navy;"></td></span></span>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="html"><span class="nt" style="color: navy;"></tbody></span></span>

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<pre style="margin: 0;">-<span id="LC372" class="line" lang="html"><span class="nt" style="color: navy;"></table></span></span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If a sequence name has a dot (e.g. <span class="ni" style="color: purple;">&quot;</span>hg19.chr7<span class="ni" style="color: purple;">&quot;</span>), the pattern is</span>

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="html">compared to both the whole name and the part after the dot.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can specify more than one pattern, e.g. this gets sequences with</span>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="html">names starting in <span class="ni" style="color: purple;">&quot;</span>chr<span class="ni" style="color: purple;">&quot;</span> followed by one or two characters:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="html">last-dotplot -1 'chr?' -1 'chr??' alns alns.png</span>

</pre>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can also specify a sequence range; for example this gets the first</span>

</pre>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="html">1000 bases of chr9:<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="html">last-dotplot -1 chr9:0-1000 alns alns.png</span>

</pre>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"fonts"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Fonts<span class="nt" style="color: navy;"></h2></span></span>

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<td class="diff-line-num new_line old" data-linenumber="338" 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="LC388" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>last-dotplot tries to find a nice font on your computer, but may fail</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="338" 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="LC389" class="line" lang="html">and use an ugly font.  You can specify a font like this:<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="338" 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="LC391" class="line" lang="html">last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns.png</span>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"options"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Options<span class="nt" style="color: navy;"></h2></span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="html"><span class="nt" style="color: navy;"><blockquote></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="349" 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">@@ -405,18 +349,23 @@ last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns</td>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-v<span class="nt" style="color: navy;"></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--verbose<span class="nt" style="color: navy;"></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Show progress messages <span class="ni" style="color: purple;">&amp;</span> data about the plot.<span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-x <span class="nt" style="color: navy;"><var></span>INT<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--width=<span class="nt" style="color: navy;"><var></span>INT<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="353" 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="LC353" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum width in pixels.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-y <span class="nt" style="color: navy;"><var></span>INT<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--height=<span class="nt" style="color: navy;"><var></span>INT<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum height in pixels.<span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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357

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-m <span class="nt" style="color: navy;"><var></span>M<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--maxseqs=<span class="nt" style="color: navy;"><var></span>M<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum number of horizontal or vertical sequences.  If there</span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="html">are <span class="ni" style="color: purple;">&gt;</span>M sequences, the smallest ones (after cutting) will be</span>

</pre>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="html">discarded.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-1 <span class="nt" style="color: navy;"><var></span>PATTERN<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--seq1=<span class="nt" style="color: navy;"><var></span>PATTERN<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Which sequences to show from the 1st (horizontal) genome.<span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-2 <span class="nt" style="color: navy;"><var></span>PATTERN<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--seq2=<span class="nt" style="color: navy;"><var></span>PATTERN<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Which sequences to show from the 2nd (vertical) genome.<span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-x <span class="nt" style="color: navy;"><var></span>WIDTH<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--width=<span class="nt" style="color: navy;"><var></span>WIDTH<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum width in pixels.<span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-y <span class="nt" style="color: navy;"><var></span>HEIGHT<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--height=<span class="nt" style="color: navy;"><var></span>HEIGHT<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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418

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum height in pixels.<span class="nt" style="color: navy;"></td></tr></span></span>

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419

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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420

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-c <span class="nt" style="color: navy;"><var></span>COLOR<span class="nt" style="color: navy;"></var></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--forwardcolor=<span class="nt" style="color: navy;"><var></span>COLOR<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Color for forward alignments.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></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">@@ -602,6 +551,65 @@ of unknown sequence.</p></td>

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="html">pixel.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"choosing-sequences"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Choosing sequences<span class="nt" style="color: navy;"></h2></span></span>

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>For example, you can exclude sequences with names like</span>

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<pre style="margin: 0;">+<span id="LC557" class="line" lang="html"><span class="ni" style="color: purple;">&quot;</span>chrUn_random522<span class="ni" style="color: purple;">&quot;</span> like this:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<td class="diff-line-num new new_line" data-linenumber="559" 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="LC559" class="line" lang="html">last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png</span>

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Option <span class="ni" style="color: purple;">&quot;</span>-1<span class="ni" style="color: purple;">&quot;</span> selects sequences from the 1st (horizontal) genome, and</span>

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="html"><span class="ni" style="color: purple;">&quot;</span>-2<span class="ni" style="color: purple;">&quot;</span> selects sequences from the 2nd (vertical) genome.  'chr[!U]*' is</span>

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</td>

<td class="diff-line-num new new_line" data-linenumber="563" 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">

563

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC563" class="line" lang="html">a <span class="nt" style="color: navy;"><em></span>pattern<span class="nt" style="color: navy;"></em></span> that specifies names starting with <span class="ni" style="color: purple;">&quot;</span>chr<span class="ni" style="color: purple;">&quot;</span>, followed by any</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="564" 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">

564

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC564" class="line" lang="html">character except U, followed by anything.<span class="nt" style="color: navy;"></p></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="565" 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">

565

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC565" class="line" lang="html"><span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">border=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils"</span><span class="nt" style="color: navy;">></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="566" 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">

566

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC566" class="line" lang="html"><span class="nt" style="color: navy;"><colgroup></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="567" 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">

567

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC567" class="line" lang="html"><span class="nt" style="color: navy;"><col</span> <span class="na" style="color: teal;">width=</span><span class="s" style="color: #d14;">"26%"</span> <span class="nt" style="color: navy;">/></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="568" 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">

568

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC568" class="line" lang="html"><span class="nt" style="color: navy;"><col</span> <span class="na" style="color: teal;">width=</span><span class="s" style="color: #d14;">"74%"</span> <span class="nt" style="color: navy;">/></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="569" 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">

569

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC569" class="line" lang="html"><span class="nt" style="color: navy;"></colgroup></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="570" 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">

570

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC570" class="line" lang="html"><span class="nt" style="color: navy;"><tbody</span> <span class="na" style="color: teal;">valign=</span><span class="s" style="color: #d14;">"top"</span><span class="nt" style="color: navy;">></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="571" 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">

571

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC571" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>Pattern<span class="nt" style="color: navy;"></td></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="572" 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">

572

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC572" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Meaning<span class="nt" style="color: navy;"></td></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="573" 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">

573

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC573" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="574" 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">

574

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC574" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>*<span class="nt" style="color: navy;"></tt></td></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="575" 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">

575

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC575" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>zero or more of any character<span class="nt" style="color: navy;"></td></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="576" 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">

576

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC576" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="577" 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">

577

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC577" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>?<span class="nt" style="color: navy;"></tt></td></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="578" 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">

578

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC578" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>any single character<span class="nt" style="color: navy;"></td></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="579" 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">

579

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC579" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="580" 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">

580

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC580" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>[abc]<span class="nt" style="color: navy;"></tt></td></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="605" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="581" 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">

581

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC581" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>any character in abc<span class="nt" style="color: navy;"></td></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

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583

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>[!abc]<span class="nt" style="color: navy;"></tt></td></span></span>

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584

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>any character not in abc<span class="nt" style="color: navy;"></td></span></span>

</pre>

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585

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="html"><span class="nt" style="color: navy;"></tbody></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC587" class="line" lang="html"><span class="nt" style="color: navy;"></table></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If a sequence name has a dot (e.g. <span class="ni" style="color: purple;">&quot;</span>hg19.chr7<span class="ni" style="color: purple;">&quot;</span>), the pattern is</span>

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589

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="html">compared to both the whole name and the part after the dot.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can specify more than one pattern, e.g. this gets sequences with</span>

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="html">names starting in <span class="ni" style="color: purple;">&quot;</span>chr<span class="ni" style="color: purple;">&quot;</span> followed by one or two characters:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="html">last-dotplot -1 'chr?' -1 'chr??' alns alns.png</span>

</pre>

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can also specify a sequence range; for example this gets the first</span>

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="html">1000 bases of chr9:<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC597" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="598" 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="LC598" class="line" lang="html">last-dotplot -1 chr9:0-1000 alns alns.png</span>

</pre>

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

</pre>

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600

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"text-font"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Text font<span class="nt" style="color: navy;"></h2></span></span>

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<pre style="margin: 0;">+<span id="LC603" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can improve the font quality by increasing its size, e.g. to 20</span>

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<pre style="margin: 0;">+<span id="LC604" class="line" lang="html">points:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC605" class="line" lang="html"><span class="nt" style="color: navy;"><blockquote></span></span>

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="html">last-dotplot -s20 my-alignments my-plot.png<span class="nt" style="color: navy;"></blockquote></span></span>

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<pre style="margin: 0;">+<span id="LC607" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>last-dotplot tries to find a nice font on your computer, but may fail</span>

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<pre style="margin: 0;">+<span id="LC608" class="line" lang="html">and use an ugly font.  You can specify a font like this:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC610" class="line" lang="html">last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns.png</span>

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<pre style="margin: 0;">+<span id="LC611" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;">+<span id="LC612" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"colors"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC614" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Colors<span class="nt" style="color: navy;"></h2></span></span>

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<pre style="margin: 0;"> <span id="LC615" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Colors can be specified in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://effbot.org/imagingbook/imagecolor.htm"</span><span class="nt" style="color: navy;">></span>various ways described here<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>

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<br>

</li>

<li id="1b4eb23521879045d9184d50996b3aa277a711e9">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#1b4eb23521879045d9184d50996b3aa277a711e9"><strong>doc/last-dotplot.txt</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">@@ -19,50 +19,6 @@ last-dotplot shows alignments of one set of sequences against another</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">set of sequences.  This document calls a "set of sequences" a</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">"genome", though it need not actually be a genome.</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Choosing sequences</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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">

23

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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="LC23" class="line" lang="plaintext">------------------</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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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="LC24" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

</td>

<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="LC25" class="line" lang="plaintext">If there are too many sequences, the dotplot will be very cluttered,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

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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="LC26" class="line" lang="plaintext">or the script might give up with an error message.  You can exclude</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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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="LC27" class="line" lang="plaintext">sequences with names like "chrUn_random522" like this::</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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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="LC28" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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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="LC29" class="line" lang="plaintext">  last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

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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="LC30" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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">

31

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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="LC31" class="line" lang="plaintext">Option "-1" selects sequences from the 1st (horizontal) genome, and</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" 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">

32

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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="LC32" class="line" lang="plaintext">"-2" selects sequences from the 2nd (vertical) genome.  'chr[!U]*' is</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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">

33

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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="LC33" class="line" lang="plaintext">a *pattern* that specifies names starting with "chr", followed by any</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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">

34

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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="LC34" class="line" lang="plaintext">character except U, followed by anything.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" 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">

35

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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">

</td>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

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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="LC36" class="line" lang="plaintext">==========  =============================</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

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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="LC37" class="line" lang="plaintext">Pattern     Meaning</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

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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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">----------  -----------------------------</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

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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">

</td>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">``*``       zero or more of any character</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

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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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">``?``       any single character</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

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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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">``[abc]``   any character in abc</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="42" 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">

42

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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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">``[!abc]``  any character not in abc</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" 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">

43

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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">

</td>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">==========  =============================</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="44" 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">

44

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">If a sequence name has a dot (e.g. "hg19.chr7"), the pattern is</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="46" 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">

46

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">compared to both the whole name and the part after the dot.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">You can specify more than one pattern, e.g. this gets sequences with</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">names starting in "chr" followed by one or two characters::</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="50" 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">

50

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="51" 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">

51

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">  last-dotplot -1 'chr?' -1 'chr??' alns alns.png</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="52" 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">

52

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="53" 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">

53

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">You can also specify a sequence range; for example this gets the first</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="54" 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">

54

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">1000 bases of chr9::</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="55" 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">

55

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="56" 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">

56

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">  last-dotplot -1 chr9:0-1000 alns alns.png</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="57" 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">

57

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="58" 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">

58

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">Fonts</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="59" 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">

59

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">-----</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="60" 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">

60

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="61" 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">

61

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">last-dotplot tries to find a nice font on your computer, but may fail</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="62" 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">

62

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">and use an ugly font.  You can specify a font like this::</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="63" 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">

63

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="64" 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">

64

</td>

<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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">  last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns.png</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="65" 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">

65

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"></span>

</pre>

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66

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Options</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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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<td class="diff-line-num new_line" data-linenumber="23" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">-------</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" 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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<td class="diff-line-num new_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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" 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">@@ -70,14 +26,18 @@ Options</td>

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<td class="diff-line-num old_line" data-linenumber="70" 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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<td class="diff-line-num new_line" data-linenumber="26" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">      Show a help message, with default option values, and exit.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" 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">

71

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<td class="diff-line-num new_line" data-linenumber="27" 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">

27

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">  -v, --verbose</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" 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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<td class="diff-line-num new_line" data-linenumber="28" 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">

28

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">      Show progress messages & data about the plot.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" 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="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">

29

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">  -x INT, --width=INT</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" 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="30" 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">

30

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">      Maximum width in pixels.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" 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="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">

31

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">  -y INT, --height=INT</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" 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">

</td>

<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">

32

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">      Maximum height in pixels.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="73" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">  -m M, --maxseqs=M</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">      Maximum number of horizontal or vertical sequences.  If there</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="73" 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="35" 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">

35

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">      are >M sequences, the smallest ones (after cutting) will be</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">      discarded.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" 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">

73

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<td class="diff-line-num new_line" data-linenumber="37" 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">

37

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">  -1 PATTERN, --seq1=PATTERN</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" 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">

74

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<td class="diff-line-num new_line" data-linenumber="38" 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">

38

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">      Which sequences to show from the 1st (horizontal) genome.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="75" 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">

75

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<td class="diff-line-num new_line" data-linenumber="39" 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">

39

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">  -2 PATTERN, --seq2=PATTERN</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="76" 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">

76

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<td class="diff-line-num new_line" data-linenumber="40" 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">

40

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">      Which sequences to show from the 2nd (vertical) genome.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="77" 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">

77

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<td class="diff-line-num new_line old" data-linenumber="41" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">  -x WIDTH, --width=WIDTH</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="78" 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">

78

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<td class="diff-line-num new_line old" data-linenumber="41" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">      Maximum width in pixels.</span>

</pre>

</td>

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<td class="diff-line-num new_line old" data-linenumber="41" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">  -y HEIGHT, --height=HEIGHT</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" 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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<td class="diff-line-num new_line old" data-linenumber="41" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">      Maximum height in pixels.</span>

</pre>

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41

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">  -c COLOR, --forwardcolor=COLOR</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" 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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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">      Color for forward alignments.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" 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">

83

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<td class="diff-line-num new_line" data-linenumber="43" 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">

43

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">  -r COLOR, --reversecolor=COLOR</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" 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">@@ -207,6 +167,54 @@ of unknown sequence.</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">An unsequenced gap will be shown only if it covers at least one whole</span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">pixel.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="170" 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="LC170" class="line" lang="plaintext">Choosing sequences</span>

</pre>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">------------------</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="172" 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="LC172" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="173" 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="LC173" class="line" lang="plaintext">For example, you can exclude sequences with names like</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="174" 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="LC174" class="line" lang="plaintext">"chrUn_random522" like this::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="175" 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="LC175" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="176" 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="LC176" class="line" lang="plaintext">  last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" 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="LC177" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="178" 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="LC178" class="line" lang="plaintext">Option "-1" selects sequences from the 1st (horizontal) genome, and</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="179" 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="LC179" class="line" lang="plaintext">"-2" selects sequences from the 2nd (vertical) genome.  'chr[!U]*' is</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="180" 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="LC180" class="line" lang="plaintext">a *pattern* that specifies names starting with "chr", followed by any</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="181" 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="LC181" class="line" lang="plaintext">character except U, followed by anything.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="183" 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">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">==========  =============================</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="184" 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">

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">Pattern     Meaning</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="185" 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">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">----------  -----------------------------</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="186" 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">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">``*``       zero or more of any character</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="187" 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">

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">``?``       any single character</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="188" 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">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">``[abc]``   any character in abc</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="189" 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">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">``[!abc]``  any character not in abc</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="190" 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">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">==========  =============================</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="191" 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">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="192" 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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">If a sequence name has a dot (e.g. "hg19.chr7"), the pattern is</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="193" 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">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">compared to both the whole name and the part after the dot.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="194" 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">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="195" 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">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">You can specify more than one pattern, e.g. this gets sequences with</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="196" 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">

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">names starting in "chr" followed by one or two characters::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="197" 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">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="198" 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">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">  last-dotplot -1 'chr?' -1 'chr??' alns alns.png</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="199" 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">

199

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="200" 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">

200

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">You can also specify a sequence range; for example this gets the first</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="201" 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">

201

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">1000 bases of chr9::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="202" 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">

202

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="203" 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="LC203" class="line" lang="plaintext">  last-dotplot -1 chr9:0-1000 alns alns.png</span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="205" 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="LC205" class="line" lang="plaintext">Text font</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="206" 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="LC206" class="line" lang="plaintext">---------</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="207" 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">

207

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="208" 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="LC208" class="line" lang="plaintext">You can improve the font quality by increasing its size, e.g. to 20</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="209" 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">

209

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">points:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="210" 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="LC210" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="211" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">  last-dotplot -s20 my-alignments my-plot.png</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="212" 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">

212

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="213" 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="LC213" class="line" lang="plaintext">last-dotplot tries to find a nice font on your computer, but may fail</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="214" 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="LC214" class="line" lang="plaintext">and use an ugly font.  You can specify a font like this::</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="215" 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="LC215" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="216" 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="LC216" class="line" lang="plaintext">  last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns.png</span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">Colors</span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">------</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="220" 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="LC220" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="bf068196d49b041029d9a269a6e3d52acda15f9f">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#bf068196d49b041029d9a269a6e3d52acda15f9f"><strong>doc/last-train.html</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">@@ -333,7 +333,7 @@ last-train mydb queries.fasta</td>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>last-train prints a summary of each alignment step, followed by the</span>

</pre>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="html">final score parameters, in a format that can be read by <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"lastal.html#score-options"</span><span class="nt" style="color: navy;">></span>lastal's -p</span>

</pre>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="html">option<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="html"><span class="nt" style="color: navy;"><p></span><span class="idiff left right">You can also pipe sequences into last-train, for example</span>:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="html"><span class="nt" style="color: navy;"><p></span><span class="idiff left right">last-train can read .gz files, or from pipes</span>:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="html">bzcat queries.fasta.bz2 | last-train mydb</span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="html"><span class="nt" style="color: navy;"></pre></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">@@ -479,15 +479,21 @@ position in each query.</td></tr></td>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Number of parallel threads.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-Q <span class="nt" style="color: navy;"><var></span>NUMBER<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>Query sequence format: 0=fasta, 1=fastq-sanger.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>last-train assumes that fastq quality codes indicate</span>

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<pre style="margin: 0;">-<span id="LC484" class="line" lang="html">substitution error probabilities, <span class="nt" style="color: navy;"><em></span>not<span class="nt" style="color: navy;"></em></span> insertion or</span>

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="html">deletion error probabilities.  If this assumption is</span>

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<pre style="margin: 0;">-<span id="LC486" class="line" lang="html">dubious (e.g. for data with many insertion or deletion</span>

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<pre style="margin: 0;">-<span id="LC487" class="line" lang="html">errors), it may be better to use fasta.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC488" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>For fastq, last-train finds the rates of substitutions</span>

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="html">not explained by the quality data (ideally, real</span>

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="html">substitutions as opposed to errors).<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>How to read the query sequences.  By default, they must</span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="html">be in <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>fasta<span class="nt" style="color: navy;"></tt></span> format.  <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>-Q0<span class="nt" style="color: navy;"></span></tt></span> means <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>fasta<span class="nt" style="color: navy;"></tt></span> or</span>

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<td class="diff-line-num new new_line" data-linenumber="484" 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="LC484" class="line" lang="html"><span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>fastq-ignore<span class="nt" style="color: navy;"></span></tt></span>.  <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>-Q1<span class="nt" style="color: navy;"></span></tt></span> means <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>fastq-sanger<span class="nt" style="color: navy;"></span></tt></span>.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>fastq<span class="nt" style="color: navy;"></tt></span> formats are described here:</span>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="html"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: navy;">></span>lastal.html<span class="nt" style="color: navy;"></a></span>.  <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>fastq-ignore<span class="nt" style="color: navy;"></span></tt></span> means that the</span>

</pre>

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487

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="html">quality data is ignored, so the results will be the same</span>

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<td class="diff-line-num new new_line" data-linenumber="488" 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="LC488" class="line" lang="html">as for <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">></span>fasta<span class="nt" style="color: navy;"></tt></span>.<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="489" 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="LC489" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>For <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>fastq-sanger<span class="nt" style="color: navy;"></span></tt></span>, last-train assumes the quality</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="490" 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="LC490" class="line" lang="html">codes indicate substitution error probabilities, <span class="nt" style="color: navy;"><em></span>not<span class="nt" style="color: navy;"></em></span></span>

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<td class="diff-line-num new new_line" data-linenumber="491" 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="LC491" class="line" lang="html">insertion or deletion error probabilities.  If this</span>

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<td class="diff-line-num new new_line" data-linenumber="492" 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="LC492" class="line" lang="html">assumption is dubious (e.g. for data with many insertion</span>

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<td class="diff-line-num new new_line" data-linenumber="493" 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="LC493" class="line" lang="html">or deletion errors), it may be better to use</span>

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<td class="diff-line-num new new_line" data-linenumber="494" 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="LC494" class="line" lang="html"><span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>fastq-ignore<span class="nt" style="color: navy;"></span></tt></span>.  For <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>fastq-sanger<span class="nt" style="color: navy;"></span></tt></span>, last-train finds</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="495" 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">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="html">the rates of substitutions not explained by the quality</span>

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="html">data (ideally, real substitutions as opposed to errors).<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="html"><span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: navy;">></span>If specified, this parameter is written in last-train's</span>

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="html">output, so it will override lastal's default.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>

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<br>

</li>

<li id="03dd50d6a64beb7787e3bcc9eb6da79c482759d5">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#03dd50d6a64beb7787e3bcc9eb6da79c482759d5"><strong>doc/last-train.txt</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">@@ -19,7 +19,7 @@ last-train prints a summary of each alignment step, followed by the</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">final score parameters, in a format that can be read by `lastal's -p</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">option <lastal.html#score-options>`_.</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"><span class="idiff left right">You can also pipe sequences into last-train, for example</span>::</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><span class="idiff left right">last-train can read .gz files, or from pipes</span>::</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">  bzcat queries.fasta.bz2 | last-train mydb</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></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">@@ -102,17 +102,23 @@ Alignment options</td>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">  -k STEP    Look for initial matches starting only at every STEP-th</span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">             position in each query.</span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">  -P COUNT   Number of parallel threads.</span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">  -Q NUMBER  Query sequence format: 0=fasta, 1=fastq-sanger.</span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">             last-train assumes that fastq quality codes indicate</span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">             substitution error probabilities, *not* insertion or</span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">             deletion error probabilities.  If this assumption is</span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">             dubious (e.g. for data with many insertion or deletion</span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">             errors), it may be better to use fasta.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" 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">

112

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" 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">

113

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">             For fastq, last-train finds the rates of substitutions</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" 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">

114

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">             not explained by the quality data (ideally, real</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="115" 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">

115

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">             substitutions as opposed to errors).</span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">  -Q NUMBER  How to read the query sequences.  By default, they must</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">             be in ``fasta`` format.  ``-Q0`` means ``fasta`` or</span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">             ``fastq-ignore``.  ``-Q1`` means ``fastq-sanger``.</span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">             The ``fastq`` formats are described here:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="plaintext">             `<lastal.html>`_.  ``fastq-ignore`` means that the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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="LC111" class="line" lang="plaintext">             quality data is ignored, so the results will be the same</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">             as for ``fasta``.</span>

</pre>

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<td class="diff-line-num new old_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">

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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="plaintext"></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="114" 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">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">             For ``fastq-sanger``, last-train assumes the quality</span>

</pre>

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<td class="diff-line-num new old_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">

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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="plaintext">             codes indicate substitution error probabilities, *not*</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">             insertion or deletion error probabilities.  If this</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">             assumption is dubious (e.g. for data with many insertion</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">             or deletion errors), it may be better to use</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">             ``fastq-ignore``.  For ``fastq-sanger``, last-train finds</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" 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="LC120" class="line" lang="plaintext">             the rates of substitutions not explained by the quality</span>

</pre>

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121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">             data (ideally, real substitutions as opposed to errors).</span>

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116

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"></span>

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117

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">             If specified, this parameter is written in last-train's</span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext">             output, so it will override lastal's default.</span>

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<br>

</li>

<li id="1d2db1d5c1263541e178e5c6d1a664dcaee43e97">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#1d2db1d5c1263541e178e5c6d1a664dcaee43e97"><strong>doc/lastal.html</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">@@ -849,13 +849,18 @@ generalized affine gap costs.  They are:</p></td>

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<pre style="margin: 0;"> <span id="LC849" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC850" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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851

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<pre style="margin: 0;"> <span id="LC851" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-Q <span class="nt" style="color: navy;"><var></span>NUMBER<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC852" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>This option allows lastal to use sequence quality scores, or</span>

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853

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC853" class="line" lang="html">PSSMs, for the queries.  0 means read queries in fasta format</span>

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854

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC854" class="line" lang="html">(without quality scores); 1 means fastq-sanger format; 2 means</span>

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<td class="diff-line-num old old_line" data-linenumber="855" 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">

855

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC855" class="line" lang="html">fastq-solexa format; 3 means fastq-illumina format; 4 means prb</span>

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<td class="diff-line-num old old_line" data-linenumber="856" 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">

856

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC856" class="line" lang="html">format; 5 means read PSSMs.  (<span class="nt" style="color: navy;"><em></span>Warning<span class="nt" style="color: navy;"></em></span>: Illumina data is not</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC857" class="line" lang="html">necessarily in fastq-illumina format; it is often in</span>

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<td class="diff-line-num old old_line" data-linenumber="858" 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">

858

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<td class="diff-line-num new_line old" data-linenumber="852" 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="LC858" class="line" lang="html">fastq-sanger format.)<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>Specify how to read the query sequences:<span class="nt" style="color: navy;"></p></span></span>

</pre>

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853

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="html">Default    fasta</span>

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<pre style="margin: 0;">+<span id="LC855" class="line" lang="html">   0       fasta or fastq-ignore</span>

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856

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="html">   1       fastq-sanger</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="857" 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">

857

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="html">   2       fastq-solexa</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" 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="858" 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">

858

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<pre style="margin: 0;">+<span id="LC858" class="line" lang="html">   3       fastq-illumina</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="859" 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">

859

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<pre style="margin: 0;">+<span id="LC859" class="line" lang="html">   4       prb</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="860" 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">

860

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<pre style="margin: 0;">+<span id="LC860" class="line" lang="html">   5       PSSM</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="861" 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">

861

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<pre style="margin: 0;">+<span id="LC861" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="862" 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">

862

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<pre style="margin: 0;">+<span id="LC862" class="line" lang="html"><span class="nt" style="color: navy;"><p><em></span>Warning<span class="nt" style="color: navy;"></em></span>: Illumina data is not necessarily in fastq-illumina</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="863" 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">

863

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<pre style="margin: 0;">+<span id="LC863" class="line" lang="html">format; it is often in fastq-sanger format.<span class="nt" style="color: navy;"></p></span></span>

</pre>

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859

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<td class="diff-line-num new_line" data-linenumber="864" 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">

864

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<pre style="margin: 0;"> <span id="LC864" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The fastq formats look like this:<span class="nt" style="color: navy;"></p></span></span>

</pre>

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860

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<td class="diff-line-num new_line" data-linenumber="865" 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">

865

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC865" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="861" 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">

861

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<td class="diff-line-num new_line" data-linenumber="866" 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">

866

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC866" class="line" lang="html"><span class="ni" style="color: purple;">&#64;</span>mySequenceName</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="868" 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">@@ -863,12 +868,18 @@ TTTTTTTTGCCTCGGGCCTGAGTTCTTAGCCGCG</td>

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863

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868

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<pre style="margin: 0;"> <span id="LC868" class="line" lang="html">+</span>

</pre>

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864

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<td class="diff-line-num new_line" data-linenumber="869" 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">

869

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<pre style="margin: 0;"> <span id="LC869" class="line" lang="html">55555555*<span class="ni" style="color: purple;">&amp;</span>5-/55*5//5(55,5#<span class="ni" style="color: purple;">&amp;</span>$)$)*+$</span>

</pre>

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865

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<td class="diff-line-num new_line" data-linenumber="870" 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">

870

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC870" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

</pre>

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866

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<td class="diff-line-num new_line old" data-linenumber="871" 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="LC866" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The <span class="ni" style="color: purple;">&quot;</span>+<span class="ni" style="color: purple;">&quot;</span> may optionally be followed by a name (ignored), and the</span>

</pre>

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867

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<td class="diff-line-num new_line old" data-linenumber="871" 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="LC867" class="line" lang="html">sequence and quality codes are allowed to wrap onto more than</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="868" 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">

868

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<td class="diff-line-num new_line old" data-linenumber="871" 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="LC868" class="line" lang="html">one line.  For fastq-sanger, the quality scores are obtained by</span>

</pre>

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869

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<td class="diff-line-num new_line old" data-linenumber="871" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC869" class="line" lang="html">subtracting 33 from the ASCII values of the characters below the</span>

</pre>

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870

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<td class="diff-line-num new_line old" data-linenumber="871" 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="LC870" class="line" lang="html"><span class="ni" style="color: purple;">&quot;</span>+<span class="ni" style="color: purple;">&quot;</span>.  For fastq-solexa and fastq-illumina, they are obtained by</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="871" 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">

871

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<td class="diff-line-num new_line old" data-linenumber="871" 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="LC871" class="line" lang="html">subtracting 64.<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC871" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The <span class="ni" style="color: purple;">&quot;</span>+<span class="ni" style="color: purple;">&quot;</span> may be followed by text (ignored).  The symbols below</span>

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<pre style="margin: 0;">+<span id="LC872" class="line" lang="html">the <span class="ni" style="color: purple;">&quot;</span>+<span class="ni" style="color: purple;">&quot;</span> are quality codes, one per sequence letter.  The</span>

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<pre style="margin: 0;">+<span id="LC873" class="line" lang="html">sequence and quality codes may wrap onto more than one line.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>fastq-ignore means that the quality codes are ignored.  For the</span>

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="html">other fastq variants, lastal assumes the quality codes indicate</span>

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<pre style="margin: 0;">+<span id="LC876" class="line" lang="html">substitution error probabilities, <span class="nt" style="color: navy;"><em></span>not<span class="nt" style="color: navy;"></em></span> insertion or deletion</span>

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<pre style="margin: 0;">+<span id="LC877" class="line" lang="html">error probabilities.  If this assumption is dubious (e.g. for</span>

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<pre style="margin: 0;">+<span id="LC878" class="line" lang="html">data with many insertion or deletion errors), it may be better</span>

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<pre style="margin: 0;">+<span id="LC879" class="line" lang="html">to use fastq-ignore.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC880" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>For fastq-sanger, quality scores are obtained by subtracting 33</span>

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<pre style="margin: 0;">+<span id="LC881" class="line" lang="html">from the ASCII values of the quality codes.  For fastq-solexa</span>

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<pre style="margin: 0;">+<span id="LC882" class="line" lang="html">and fastq-illumina, they are obtained by subtracting 64.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC883" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>prb format stores four quality scores (A, C, G, T) per position,</span>

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<pre style="margin: 0;"> <span id="LC884" class="line" lang="html">with one sequence per line, like this:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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</li>

<li id="30d864ed8925787ee70643db49814772753a5f2c">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#30d864ed8925787ee70643db49814772753a5f2c"><strong>doc/lastal.txt</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">@@ -474,13 +474,18 @@ Miscellaneous options</td>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="plaintext">      * The count of adjacent pairs of insertions and unaligned letter pairs.</span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="plaintext">  -Q NUMBER</span>

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<pre style="margin: 0;">-<span id="LC477" class="line" lang="plaintext">      This option allows lastal to use sequence quality scores, or</span>

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<pre style="margin: 0;">-<span id="LC478" class="line" lang="plaintext">      PSSMs, for the queries.  0 means read queries in fasta format</span>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="plaintext">      (without quality scores); 1 means fastq-sanger format; 2 means</span>

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<pre style="margin: 0;">-<span id="LC480" class="line" lang="plaintext">      fastq-solexa format; 3 means fastq-illumina format; 4 means prb</span>

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<pre style="margin: 0;">-<span id="LC481" class="line" lang="plaintext">      format; 5 means read PSSMs.  (*Warning*: Illumina data is not</span>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="plaintext">      necessarily in fastq-illumina format; it is often in</span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="plaintext">      fastq-sanger format.)</span>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">      Specify how to read the query sequences::</span>

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext">        Default    fasta</span>

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext">           0       fasta or fastq-ignore</span>

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">           1       fastq-sanger</span>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">           2       fastq-solexa</span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">           3       fastq-illumina</span>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">           4       prb</span>

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">           5       PSSM</span>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"></span>

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<td class="diff-line-num new new_line" data-linenumber="487" 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="LC487" class="line" lang="plaintext">      *Warning*: Illumina data is not necessarily in fastq-illumina</span>

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<td class="diff-line-num new new_line" data-linenumber="488" 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="LC488" class="line" lang="plaintext">      format; it is often in fastq-sanger format.</span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line" data-linenumber="490" 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="LC490" class="line" lang="plaintext">      The fastq formats look like this::</span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="plaintext"></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">@@ -489,12 +494,20 @@ Miscellaneous options</td>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="plaintext">        +</span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="plaintext">        55555555*&5-/55*5//5(55,5#&$)$)*+$</span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line old" data-linenumber="497" 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="LC492" class="line" lang="plaintext">      The "+" may optionally be followed by a name (ignored), and the</span>

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<td class="diff-line-num new_line old" data-linenumber="497" 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="LC493" class="line" lang="plaintext">      sequence and quality codes are allowed to wrap onto more than</span>

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<pre style="margin: 0;">-<span id="LC494" class="line" lang="plaintext">      one line.  For fastq-sanger, the quality scores are obtained by</span>

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<td class="diff-line-num new_line old" data-linenumber="497" 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="LC495" class="line" lang="plaintext">      subtracting 33 from the ASCII values of the characters below the</span>

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="plaintext">      "+".  For fastq-solexa and fastq-illumina, they are obtained by</span>

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<pre style="margin: 0;">-<span id="LC497" class="line" lang="plaintext">      subtracting 64.</span>

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">      The "+" may be followed by text (ignored).  The symbols below</span>

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<td class="diff-line-num new new_line" data-linenumber="498" 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="LC498" class="line" lang="plaintext">      the "+" are quality codes, one per sequence letter.  The</span>

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<td class="diff-line-num new new_line" data-linenumber="499" 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="LC499" class="line" lang="plaintext">      sequence and quality codes may wrap onto more than one line.</span>

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<td class="diff-line-num new new_line" data-linenumber="500" 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="LC500" class="line" lang="plaintext"></span>

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<td class="diff-line-num new new_line" data-linenumber="501" 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="LC501" class="line" lang="plaintext">      fastq-ignore means that the quality codes are ignored.  For the</span>

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<td class="diff-line-num new new_line" data-linenumber="502" 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="LC502" class="line" lang="plaintext">      other fastq variants, lastal assumes the quality codes indicate</span>

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<td class="diff-line-num new new_line" data-linenumber="503" 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="LC503" class="line" lang="plaintext">      substitution error probabilities, *not* insertion or deletion</span>

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<td class="diff-line-num new new_line" data-linenumber="504" 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="LC504" class="line" lang="plaintext">      error probabilities.  If this assumption is dubious (e.g. for</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="505" 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="LC505" class="line" lang="plaintext">      data with many insertion or deletion errors), it may be better</span>

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<td class="diff-line-num new new_line" data-linenumber="506" 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="LC506" class="line" lang="plaintext">      to use fastq-ignore.</span>

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<td class="diff-line-num new new_line" data-linenumber="507" 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="LC507" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext">      For fastq-sanger, quality scores are obtained by subtracting 33</span>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext">      from the ASCII values of the quality codes.  For fastq-solexa</span>

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext">      and fastq-illumina, they are obtained by subtracting 64.</span>

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="plaintext">      prb format stores four quality scores (A, C, G, T) per position,</span>

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="plaintext">      with one sequence per line, like this::</span>

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<li id="0bf0c2b9afb77a75953faf3468b6707da7098872">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#0bf0c2b9afb77a75953faf3468b6707da7098872"><strong>doc/lastdb.html</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">@@ -457,11 +457,10 @@ about 4 billion.</p></td>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-Q <span class="nt" style="color: navy;"><var></span>NUMBER<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Specify the input format.  0 means fasta, 1 means fastq-sanger,</span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="html">2 means fastq-solexa, and 3 means fastq-illumina.  The fastq</span>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="html">formats provide sequence quality data, which will be stored by</span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="html">lastdb and then used by lastal.  These formats are described in</span>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="html"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: navy;">></span>lastal.html<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Specify how to read the sequences.  The default is fasta, 0</span>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="html">means fasta or fastq-ignore, 1 means fastq-sanger, 2 means</span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="html">fastq-solexa, and 3 means fastq-illumina.  The fastq formats are</span>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="html">described in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: navy;">></span>lastal.html<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-P <span class="nt" style="color: navy;"><var></span>THREADS<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Divide the work between this number of threads running in</span>

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<br>

</li>

<li id="485665224376f8470c80c62ef464a2a01e61c7e7">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#485665224376f8470c80c62ef464a2a01e61c7e7"><strong>doc/lastdb.txt</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">@@ -125,11 +125,10 @@ Advanced Options</td>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">      about 4 billion.</span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext">  -Q NUMBER</span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">      Specify the input format.  0 means fasta, 1 means fastq-sanger,</span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">      2 means fastq-solexa, and 3 means fastq-illumina.  The fastq</span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">      formats provide sequence quality data, which will be stored by</span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">      lastdb and then used by lastal.  These formats are described in</span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">      `<lastal.html>`_.</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">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">      Specify how to read the sequences.  The default is fasta, 0</span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">      means fasta or fastq-ignore, 1 means fastq-sanger, 2 means</span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">      fastq-solexa, and 3 means fastq-illumina.  The fastq formats are</span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">      described in `<lastal.html>`_.</span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">  -P THREADS</span>

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<td class="diff-line-num old_line" data-linenumber="135" 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="LC134" class="line" lang="plaintext">      Divide the work between this number of threads running in</span>

</pre>

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<br>

</li>

<li id="d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8"><strong>scripts/last-dotplot</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" 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">@@ -13,6 +13,7 @@ import collections</td>

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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">functools</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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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<td class="diff-line-num new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" 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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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">fnmatch</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fnmatchcase</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="16" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">operator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">itemgetter</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span><span class="p">,</span> <span class="n" style="color: #333;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" 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">@@ -34,14 +35,9 @@ def myOpen(fileName):  # faster than fileinput</td>

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<td class="diff-line-num old_line" data-linenumber="34" 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="LC35" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="35" 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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<td class="diff-line-num new_line" data-linenumber="36" 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="LC36" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>

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<td class="diff-line-num old_line" data-linenumber="36" 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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<td class="diff-line-num new_line" data-linenumber="37" 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="LC37" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" 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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<td class="diff-line-num new_line old" data-linenumber="38" 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="LC37" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" 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="38" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rt"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx dubious for Python2</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" 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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<td class="diff-line-num new_line" data-linenumber="39" 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="LC39" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" 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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<td class="diff-line-num new_line" data-linenumber="40" 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="LC40" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" 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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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">warn</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" 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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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC41" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="42" 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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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC42" class="line" lang="python">        <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">groupByFirstItem</span><span class="p">(</span><span class="n" style="color: #333;">things</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">things</span><span class="p">,</span> <span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)):</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">]</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">@@ -414,8 +410,8 @@ def dataFromRanges(sortedRanges, font, fontSize, imageMode, labelOpt, textRot):</td>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python">        <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">rangeBeg</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">rangeEnd</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strandNum</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python">            <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">".+-"</span><span class="p">[</span><span class="n" style="color: #333;">strandNum</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python">    <span class="n" style="color: #333;">rangeSizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sortedRanges</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python">    <span class="n" style="color: #333;">labs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rangeLabels</span><span class="p">(</span><span class="n" style="color: #333;">sortedRanges</span><span class="p">,</span> <span class="n" style="color: #333;">labelOpt</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">fontSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python">                            <span class="n" style="color: #333;">imageMode</span><span class="p">,</span> <span class="n" style="color: #333;">textRot</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="426" 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">@@ -430,7 +426,7 @@ def div_ceil(x, y):</td>

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<td class="diff-line-num new_line" data-linenumber="426" 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="LC426" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="431" 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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<td class="diff-line-num new_line" data-linenumber="427" 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="LC427" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_bp_per_pix</span><span class="p">(</span><span class="n" style="color: #333;">rangeSizes</span><span class="p">,</span> <span class="n" style="color: #333;">pixTweenRanges</span><span class="p">,</span> <span class="n" style="color: #333;">maxPixels</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="428" 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="LC428" class="line" lang="python">    <span class="s" style="color: #d14;">'''Get the minimum bp-per-pixel that fits in the size limit.'''</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="433" 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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<td class="diff-line-num new_line old" data-linenumber="429" 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="LC433" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"choosing bp per pixel..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="434" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="429" 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="LC429" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"choosing bp per pixel..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="434" 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">

434

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<td class="diff-line-num new_line" data-linenumber="430" 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="LC430" class="line" lang="python">    <span class="n" style="color: #333;">numOfRanges</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rangeSizes</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="435" 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">

435

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<td class="diff-line-num new_line" data-linenumber="431" 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">

431

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">    <span class="n" style="color: #333;">maxPixelsInRanges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxPixels</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pixTweenRanges</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">numOfRanges</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="436" 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">

436

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<td class="diff-line-num new_line" data-linenumber="432" 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">

432

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">maxPixelsInRanges</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfRanges</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="714" 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">@@ -718,18 +714,37 @@ def getFont(opts):</td>

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<td class="diff-line-num old_line" data-linenumber="718" 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">

718

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<td class="diff-line-num new_line" data-linenumber="714" 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="LC714" class="line" lang="python">        <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="719" 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">

719

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<td class="diff-line-num new_line" data-linenumber="715" 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">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python">        <span class="n" style="color: #333;">fileNames</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="720" 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">

720

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<td class="diff-line-num new_line" data-linenumber="716" 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">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="721" 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">

721

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<td class="diff-line-num new_line old" data-linenumber="717" 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="LC721" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"fc-match error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="722" 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="717" 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">

717

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"fc-match error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="722" 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">

722

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<td class="diff-line-num new_line" data-linenumber="718" 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">

718

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python">    <span class="n" style="color: #333;">fileNames</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"/Library/Fonts/Arial.ttf"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># for Mac</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="723" 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">

723

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<td class="diff-line-num new_line" data-linenumber="719" 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">

719

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fileNames</span><span class="p">:</span></span>

</pre>

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724

</td>

<td class="diff-line-num new_line" data-linenumber="720" 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">

720

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC720" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="725" 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">

725

</td>

<td class="diff-line-num new_line" data-linenumber="721" 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">

721

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC721" class="line" lang="python">            <span class="n" style="color: #333;">font</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ImageFont</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">truetype</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fontsize</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="726" 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">

726

</td>

<td class="diff-line-num new_line old" data-linenumber="722" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC726" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"font: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="727" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="722" 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">

722

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC722" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"font: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="727" 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">

727

</td>

<td class="diff-line-num new_line" data-linenumber="723" 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">

723

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC723" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">font</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="728" 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">

728

</td>

<td class="diff-line-num new_line" data-linenumber="724" 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">

724

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC724" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="729" 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">

729

</td>

<td class="diff-line-num new_line old" data-linenumber="725" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC729" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"font load error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="730" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="725" 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">

725

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC725" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"font load error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="730" 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">

730

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<td class="diff-line-num new_line" data-linenumber="726" 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">

726

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ImageFont</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_default</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="731" 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">

731

</td>

<td class="diff-line-num new_line" data-linenumber="727" 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">

727

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="728" 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">

728

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC728" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sequenceSizesAndNames</span><span class="p">(</span><span class="n" style="color: #333;">seqRanges</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="729" 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">

729

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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">ranges</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">seqRanges</span><span class="p">,</span> <span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="730" 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">

730

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">        <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ranges</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="731" 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">

731

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC731" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="732" 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">

732

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC732" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="733" 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">

733

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">biggestSequences</span><span class="p">(</span><span class="n" style="color: #333;">seqRanges</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumOfSequences</span><span class="p">):</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="734" 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">

734

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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python">    <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">sequenceSizesAndNames</span><span class="p">(</span><span class="n" style="color: #333;">seqRanges</span><span class="p">),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="735" 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">

735

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC735" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxNumOfSequences</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="736" 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">

736

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC736" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"too many sequences - discarding the smallest ones"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="737" 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">

737

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC737" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">[:</span><span class="n" style="color: #333;">maxNumOfSequences</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="738" 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">

738

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC738" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="739" 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">

739

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC739" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="740" 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">

740

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remainingSequenceRanges</span><span class="p">(</span><span class="n" style="color: #333;">seqRanges</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">seqIndex</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="741" 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">

741

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC741" class="line" lang="python">    <span class="n" style="color: #333;">remainingSequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="n" style="color: #333;">seqIndex</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignments</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="742" 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">

742

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC742" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqRanges</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">remainingSequences</span><span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="732" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="743" 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">

743

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="732" 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">

732

</td>

<td class="diff-line-num new_line" data-linenumber="744" 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">

744

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC744" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lastDotplot</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="733" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" 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">

745

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC745" class="line" lang="python">    <span class="n" style="color: #333;">logLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WARNING</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="733" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="746" 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">

746

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC746" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%(filename)</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%(message)</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logLevel</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="733" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="747" 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">

747

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC747" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="733" 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">

733

</td>

<td class="diff-line-num new_line" data-linenumber="748" 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">

748

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC748" class="line" lang="python">    <span class="n" style="color: #333;">font</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getFont</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="734" 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">

734

</td>

<td class="diff-line-num new_line" data-linenumber="749" 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">

749

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC749" class="line" lang="python">    <span class="n" style="color: #333;">image_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'RGB'</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="735" 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">

735

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<td class="diff-line-num new_line" data-linenumber="750" 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="LC750" class="line" lang="python">    <span class="n" style="color: #333;">forward_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ImageColor</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcolor</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">forwardcolor</span><span class="p">,</span> <span class="n" style="color: #333;">image_mode</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="755" 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">@@ -740,11 +755,11 @@ def lastDotplot(opts, args):</td>

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<td class="diff-line-num old_line" data-linenumber="740" 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">

740

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<td class="diff-line-num new_line" data-linenumber="755" 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">

755

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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python">    <span class="n" style="color: #333;">maxGap1</span><span class="p">,</span> <span class="n" style="color: #333;">maxGapB1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">twoValuesFromOption</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_gap1</span><span class="p">,</span> <span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="741" 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">

741

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<td class="diff-line-num new_line" data-linenumber="756" 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="LC756" class="line" lang="python">    <span class="n" style="color: #333;">maxGap2</span><span class="p">,</span> <span class="n" style="color: #333;">maxGapB2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">twoValuesFromOption</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_gap2</span><span class="p">,</span> <span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="742" 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">

742

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<td class="diff-line-num new_line" data-linenumber="757" 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">

757

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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="743" 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">

743

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<td class="diff-line-num new_line old" data-linenumber="758" 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="LC743" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"reading alignments..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="744" 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="758" 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="LC758" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"reading alignments..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="744" 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">

744

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<td class="diff-line-num new_line" data-linenumber="759" 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">

759

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<pre style="margin: 0;"> <span id="LC759" class="line" lang="python">    <span class="n" style="color: #333;">alnData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readAlignments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="745" 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">

745

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<td class="diff-line-num new_line" data-linenumber="760" 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">

760

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<pre style="margin: 0;"> <span id="LC760" class="line" lang="python">    <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">seqRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">coverDict1</span><span class="p">,</span> <span class="n" style="color: #333;">seqRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">coverDict2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnData</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="746" 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">

746

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<td class="diff-line-num new_line" data-linenumber="761" 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">

761

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<pre style="margin: 0;"> <span id="LC761" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignments</span><span class="p">:</span> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"there are no alignments"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="747" 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">

747

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<td class="diff-line-num new_line old" data-linenumber="762" 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="LC747" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"cutting..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="748" 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="762" 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">

762

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<pre style="margin: 0;">+<span id="LC762" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"cutting..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="748" 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">

748

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<td class="diff-line-num new_line" data-linenumber="763" 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">

763

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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python">    <span class="n" style="color: #333;">coverDict1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">mergedRangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">coverDict1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="749" 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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<td class="diff-line-num new_line" data-linenumber="764" 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="LC764" class="line" lang="python">    <span class="n" style="color: #333;">coverDict2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">mergedRangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">coverDict2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="750" 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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<td class="diff-line-num new_line" data-linenumber="765" 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="LC765" class="line" lang="python">    <span class="n" style="color: #333;">minAlignedBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">coveredLength</span><span class="p">(</span><span class="n" style="color: #333;">coverDict1</span><span class="p">),</span> <span class="n" style="color: #333;">coveredLength</span><span class="p">(</span><span class="n" style="color: #333;">coverDict2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="769" 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">@@ -754,10 +769,20 @@ def lastDotplot(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python">    <span class="n" style="color: #333;">cutRanges2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">trimmed</span><span class="p">(</span><span class="n" style="color: #333;">seqRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">coverDict2</span><span class="p">,</span> <span class="n" style="color: #333;">minAlignedBases</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="755" 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">

755

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<td class="diff-line-num new_line" data-linenumber="770" 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">

770

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python">                              <span class="n" style="color: #333;">maxGap2</span><span class="p">,</span> <span class="n" style="color: #333;">pad</span><span class="p">,</span> <span class="n" style="color: #333;">pad</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="756" 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">

756

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<td class="diff-line-num new_line" data-linenumber="771" 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">

771

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="757" 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">

757

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<td class="diff-line-num new_line old" data-linenumber="772" 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="LC757" class="line" lang="python">    <span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"reading secondary alignments..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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="772" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC772" class="line" lang="python">    <span class="n" style="color: #333;">biggestSeqs1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biggestSequences</span><span class="p">(</span><span class="n" style="color: #333;">cutRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maxseqs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="773" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">    <span class="n" style="color: #333;">cutRanges1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cutRanges1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">biggestSeqs1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="774" 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">

774

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC774" class="line" lang="python">    <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignments</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">biggestSeqs1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="775" 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">

775

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC775" class="line" lang="python">    <span class="n" style="color: #333;">cutRanges2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remainingSequenceRanges</span><span class="p">(</span><span class="n" style="color: #333;">cutRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="776" 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">

776

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC776" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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="777" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC777" class="line" lang="python">    <span class="n" style="color: #333;">biggestSeqs2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biggestSequences</span><span class="p">(</span><span class="n" style="color: #333;">cutRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maxseqs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="778" 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">

778

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC778" class="line" lang="python">    <span class="n" style="color: #333;">cutRanges2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cutRanges2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">biggestSeqs2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="779" 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">

779

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC779" class="line" lang="python">    <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignments</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">biggestSeqs2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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="780" 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">

780

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC780" class="line" lang="python">    <span class="n" style="color: #333;">cutRanges1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remainingSequenceRanges</span><span class="p">(</span><span class="n" style="color: #333;">cutRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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="781" 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">

781

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="758" 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="782" 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">

782

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC782" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"reading secondary alignments..."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="758" 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">

758

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<td class="diff-line-num new_line" data-linenumber="783" 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">

783

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC783" class="line" lang="python">    <span class="n" style="color: #333;">alnDataB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readSecondaryAlignments</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">cutRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">cutRanges2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="759" 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">

759

</td>

<td class="diff-line-num new_line" data-linenumber="784" 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">

784

</td>

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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python">    <span class="n" style="color: #333;">alignmentsB</span><span class="p">,</span> <span class="n" style="color: #333;">seqRangesB1</span><span class="p">,</span> <span class="n" style="color: #333;">coverDictB1</span><span class="p">,</span> <span class="n" style="color: #333;">seqRangesB2</span><span class="p">,</span> <span class="n" style="color: #333;">coverDictB2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnDataB</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="760" 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">

760

</td>

<td class="diff-line-num new_line old" data-linenumber="785" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC760" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"cutting..."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="761" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="785" 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">

785

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC785" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"cutting..."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="761" 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">

761

</td>

<td class="diff-line-num new_line" data-linenumber="786" 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">

786

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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python">    <span class="n" style="color: #333;">coverDictB1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">mergedRangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">coverDictB1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="762" 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">

762

</td>

<td class="diff-line-num new_line" data-linenumber="787" 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">

787

</td>

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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python">    <span class="n" style="color: #333;">coverDictB2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">mergedRangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">coverDictB2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="763" 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">

763

</td>

<td class="diff-line-num new_line" data-linenumber="788" 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">

788

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC788" class="line" lang="python">    <span class="n" style="color: #333;">cutRangesB1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimmed</span><span class="p">(</span><span class="n" style="color: #333;">seqRangesB1</span><span class="p">,</span> <span class="n" style="color: #333;">coverDictB1</span><span class="p">,</span> <span class="n" style="color: #333;">minAlignedBases</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="790" 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">@@ -765,7 +790,7 @@ def lastDotplot(opts, args):</td>

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<td class="diff-line-num old_line" data-linenumber="765" 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">

765

</td>

<td class="diff-line-num new_line" data-linenumber="790" 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">

790

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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python">    <span class="n" style="color: #333;">cutRangesB2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimmed</span><span class="p">(</span><span class="n" style="color: #333;">seqRangesB2</span><span class="p">,</span> <span class="n" style="color: #333;">coverDictB2</span><span class="p">,</span> <span class="n" style="color: #333;">minAlignedBases</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="766" 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">

766

</td>

<td class="diff-line-num new_line" data-linenumber="791" 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">

791

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC791" class="line" lang="python">                          <span class="n" style="color: #333;">maxGapB2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="767" 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">

767

</td>

<td class="diff-line-num new_line" data-linenumber="792" 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">

792

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="768" 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">

768

</td>

<td class="diff-line-num new_line old" data-linenumber="793" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC768" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"sorting..."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="769" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="793" 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">

793

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC793" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"sorting..."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="769" 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">

769

</td>

<td class="diff-line-num new_line" data-linenumber="794" 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">

794

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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python">    <span class="n" style="color: #333;">sortOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allSortedRanges</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">alignmentsB</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="770" 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">

770

</td>

<td class="diff-line-num new_line" data-linenumber="795" 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">

795

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC795" class="line" lang="python">                              <span class="n" style="color: #333;">cutRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">cutRangesB1</span><span class="p">,</span> <span class="n" style="color: #333;">cutRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">cutRangesB2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="771" 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">

771

</td>

<td class="diff-line-num new_line" data-linenumber="796" 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">

796

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC796" class="line" lang="python">    <span class="n" style="color: #333;">sortedRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortOut</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="810" 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">@@ -785,7 +810,7 @@ def lastDotplot(opts, args):</td>

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<td class="diff-line-num old_line" data-linenumber="785" 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">

785

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<td class="diff-line-num new_line" data-linenumber="810" 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">

810

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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python">    <span class="n" style="color: #333;">bpPerPix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_bp_per_pix</span><span class="p">(</span><span class="n" style="color: #333;">rangeSizes1</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">border_pixels</span><span class="p">,</span> <span class="n" style="color: #333;">maxPixels1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="786" 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">

786

</td>

<td class="diff-line-num new_line" data-linenumber="811" 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">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python">    <span class="n" style="color: #333;">bpPerPix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_bp_per_pix</span><span class="p">(</span><span class="n" style="color: #333;">rangeSizes2</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">border_pixels</span><span class="p">,</span> <span class="n" style="color: #333;">maxPixels2</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="787" 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">

787

</td>

<td class="diff-line-num new_line" data-linenumber="812" 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">

812

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<pre style="margin: 0;"> <span id="LC812" class="line" lang="python">    <span class="n" style="color: #333;">bpPerPix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">bpPerPix1</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix2</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="788" 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">

788

</td>

<td class="diff-line-num new_line old" data-linenumber="813" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC788" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"bp per pixel = "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">bpPerPix</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="789" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="813" 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">

813

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC813" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"bp per pixel = "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">bpPerPix</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="789" 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">

789

</td>

<td class="diff-line-num new_line" data-linenumber="814" 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">

814

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="790" 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">

790

</td>

<td class="diff-line-num new_line" data-linenumber="815" 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">

815

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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python">    <span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pixelData</span><span class="p">(</span><span class="n" style="color: #333;">rangeSizes1</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">border_pixels</span><span class="p">,</span> <span class="n" style="color: #333;">lMargin</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="791" 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">

791

</td>

<td class="diff-line-num new_line" data-linenumber="816" 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">

816

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC816" class="line" lang="python">    <span class="n" style="color: #333;">rangePixBegs1</span><span class="p">,</span> <span class="n" style="color: #333;">rangePixLens1</span><span class="p">,</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p1</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="822" 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">@@ -797,14 +822,14 @@ def lastDotplot(opts, args):</td>

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<td class="diff-line-num old_line" data-linenumber="797" 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">

797

</td>

<td class="diff-line-num new_line" data-linenumber="822" 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">

822

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC822" class="line" lang="python">    <span class="n" style="color: #333;">rangeDict2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">rangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">sortedRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">rangePixBegs2</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="798" 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">

798

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<td class="diff-line-num new_line" data-linenumber="823" 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">

823

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC823" class="line" lang="python">                                   <span class="n" style="color: #333;">rangePixLens2</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="799" 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">

799

</td>

<td class="diff-line-num new_line" data-linenumber="824" 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">

824

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC824" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="800" 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">

800

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<td class="diff-line-num new_line old" data-linenumber="825" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC800" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"width:  "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="801" 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">

801

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<td class="diff-line-num new_line old" data-linenumber="825" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC801" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"height: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">height</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="802" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="825" 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">

825

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC825" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"width:  "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="802" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="826" 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">

826

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC826" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"height: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">height</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="802" 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">

802

</td>

<td class="diff-line-num new_line" data-linenumber="827" 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">

827

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="803" 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">

803

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<td class="diff-line-num new_line old" data-linenumber="828" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC803" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"processing alignments..."</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="804" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="828" 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">

828

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC828" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"processing alignments..."</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="804" 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">

804

</td>

<td class="diff-line-num new_line" data-linenumber="829" 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">

829

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC829" class="line" lang="python">    <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentPixels</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignmentsB</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="805" 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">

805

</td>

<td class="diff-line-num new_line" data-linenumber="830" 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">

830

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC830" class="line" lang="python">                           <span class="n" style="color: #333;">rangeDict1</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict2</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="806" 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">

806

</td>

<td class="diff-line-num new_line" data-linenumber="831" 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">

831

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="807" 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">

807

</td>

<td class="diff-line-num new_line old" data-linenumber="832" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC807" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"reading annotations..."</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="808" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="832" 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">

832

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC832" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"reading annotations..."</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="808" 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">

808

</td>

<td class="diff-line-num new_line" data-linenumber="833" 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">

833

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="809" 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">

809

</td>

<td class="diff-line-num new_line" data-linenumber="834" 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">

834

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC834" class="line" lang="python">    <span class="n" style="color: #333;">rangeDict1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expandedSeqDict</span><span class="p">(</span><span class="n" style="color: #333;">rangeDict1</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="810" 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">

810

</td>

<td class="diff-line-num new_line" data-linenumber="835" 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">

835

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC835" class="line" lang="python">    <span class="n" style="color: #333;">beds1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">readBed</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bed1</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict1</span><span class="p">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="847" 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">@@ -822,7 +847,7 @@ def lastDotplot(opts, args):</td>

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<td class="diff-line-num old_line" data-linenumber="822" 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">

822

</td>

<td class="diff-line-num new_line" data-linenumber="847" 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">

847

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC847" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="823" 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">

823

</td>

<td class="diff-line-num new_line" data-linenumber="848" 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">

848

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC848" class="line" lang="python">    <span class="n" style="color: #333;">boxes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="n" style="color: #333;">b2</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="824" 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">

824

</td>

<td class="diff-line-num new_line" data-linenumber="849" 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">

849

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC849" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="825" 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">

825

</td>

<td class="diff-line-num new_line old" data-linenumber="850" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC825" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"drawing..."</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="826" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="850" 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">

850

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC850" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">(</span><span class="s" style="color: #d14;">"drawing..."</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="826" 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">

826

</td>

<td class="diff-line-num new_line" data-linenumber="851" 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">

851

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC851" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="827" 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">

827

</td>

<td class="diff-line-num new_line" data-linenumber="852" 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">

852

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC852" class="line" lang="python">    <span class="n" style="color: #333;">image_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="828" 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">

828

</td>

<td class="diff-line-num new_line" data-linenumber="853" 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">

853

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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python">    <span class="n" style="color: #333;">im</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Image</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">image_mode</span><span class="p">,</span> <span class="n" style="color: #333;">image_size</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">background_color</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="893" 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">@@ -868,17 +893,20 @@ if __name__ == "__main__":</td>

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<td class="diff-line-num old_line" data-linenumber="868" 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">

868

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<td class="diff-line-num new_line" data-linenumber="893" 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">

893

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<pre style="margin: 0;"> <span id="LC893" class="line" lang="python">    <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OptionParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="869" 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">

869

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<td class="diff-line-num new_line" data-linenumber="894" 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">

894

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--verbose"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="870" 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">

870

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<td class="diff-line-num new_line" data-linenumber="895" 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">

895

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<pre style="margin: 0;"> <span id="LC895" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"show progress messages & data about the plot"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="871" 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="896" 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">

896

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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Replace "width" & "height" with a single "length" option?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="871" 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="897" 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">

897

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC897" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--width"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"INT"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="871" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="898" 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">

898

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC898" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximum width in pixels (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="871" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="899" 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">

899

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC899" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--height"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"INT"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="871" 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="900" 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">

900

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC900" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximum height in pixels (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="871" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="901" 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">

901

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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--maxseqs"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"M"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="871" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="902" 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">

902

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC902" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximum number of horizontal or vertical sequences "</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="871" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="903" 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">

903

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC903" class="line" lang="python">                  <span class="s" style="color: #d14;">"(default=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="871" 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">

871

</td>

<td class="diff-line-num new_line" data-linenumber="904" 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">

904

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC904" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--seq1"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PATTERN"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"append"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="872" 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">

872

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<td class="diff-line-num new_line" data-linenumber="905" 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">

905

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC905" class="line" lang="python">                  <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="873" 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">

873

</td>

<td class="diff-line-num new_line" data-linenumber="906" 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">

906

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC906" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"which sequences to show from the 1st genome"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="874" 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">

874

</td>

<td class="diff-line-num new_line" data-linenumber="907" 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">

907

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC907" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--seq2"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PATTERN"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"append"</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="875" 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">

875

</td>

<td class="diff-line-num new_line" data-linenumber="908" 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">

908

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC908" class="line" lang="python">                  <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="876" 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">

876

</td>

<td class="diff-line-num new_line" data-linenumber="909" 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">

909

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC909" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"which sequences to show from the 2nd genome"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="877" 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">

877

</td>

<td class="diff-line-num new_line old" data-linenumber="910" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC877" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Replace "width" & "height" with a single "length" option?</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="878" 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">

878

</td>

<td class="diff-line-num new_line old" data-linenumber="910" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC878" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--width"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="879" 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">

879

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<td class="diff-line-num new_line old" data-linenumber="910" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC879" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximum width in pixels (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="880" 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">

880

</td>

<td class="diff-line-num new_line old" data-linenumber="910" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC880" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--height"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="881" 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">

881

</td>

<td class="diff-line-num new_line old" data-linenumber="910" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC881" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximum height in pixels (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="882" 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">

882

</td>

<td class="diff-line-num new_line" data-linenumber="910" 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">

910

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC910" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--forwardcolor"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"red"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="883" 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">

883

</td>

<td class="diff-line-num new_line" data-linenumber="911" 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">

911

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC911" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"color for forward alignments (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="884" 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">

884

</td>

<td class="diff-line-num new_line" data-linenumber="912" 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">

912

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC912" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--reversecolor"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"blue"</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="91df1cfad6631f83b9c232630119e09896361a09">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#91df1cfad6631f83b9c232630119e09896361a09"><strong>scripts/last-map-probs</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" 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">@@ -16,7 +16,7 @@ def myOpen(fileName):</td>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line" data-linenumber="18" 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">

18

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="19" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="20" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rt"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx dubious for Python2</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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">

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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">logsum</span><span class="p">(</span><span class="n" style="color: #333;">numbers</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="09de00a2f5fb0a5a61122f0d649401a900bbb57b">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#09de00a2f5fb0a5a61122f0d649401a900bbb57b"><strong>scripts/last-postmask</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" 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">@@ -26,7 +26,7 @@ def myOpen(fileName):</td>

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<td class="diff-line-num old_line" data-linenumber="26" 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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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line" data-linenumber="27" 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">

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line old" data-linenumber="29" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" 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">

</td>

<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">

29

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rt"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx dubious for Python2</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line" data-linenumber="30" 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="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line" data-linenumber="31" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line" data-linenumber="32" 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">

32

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">complement</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">):</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0"><strong>scripts/last-train</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">@@ -10,7 +10,7 @@ def myOpen(fileName):  # faster than fileinput</td>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="14" 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="13" 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="LC13" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rt"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx dubious for Python2</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">randomSample</span><span class="p">(</span><span class="n" style="color: #333;">things</span><span class="p">,</span> <span class="n" style="color: #333;">sampleSize</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="499" 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">@@ -499,8 +499,9 @@ if __name__ == "__main__":</td>

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<td class="diff-line-num new_line" data-linenumber="499" 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="LC499" class="line" lang="python">                  <span class="s" style="color: #d14;">"every STEP-th position in each query (default: 1)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="500" 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="LC500" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-P"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"THREADS"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of parallel threads"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="502" 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="LC502" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-Q"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NUMBER"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="502" 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="LC503" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"input format: 0=fasta, 1=fastq-sanger"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="504" 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="502" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC502" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-Q"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NUMBER"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="504" 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="LC503" class="line" lang="python">                  <span class="s" style="color: #d14;">"input format: 0=fasta or fastq-ignore, 1=fastq-sanger "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python">                  <span class="s" style="color: #d14;">"(default=fasta)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="505" 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="LC505" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python">    <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<br>

</li>

<li id="0c8579b85a61ba3e2feb036884e3e6d6da75cf0e">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#0c8579b85a61ba3e2feb036884e3e6d6da75cf0e"><strong>scripts/maf-convert</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ def myOpen(fileName):</td>

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<td class="diff-line-num old_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">

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="html">    if fileName == "-":</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="html">        return sys.stdin</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="23" 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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="html">    if fileName.endswith(".gz"):</span>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC24" class="line" lang="html">        return gzip.open(fileName<span class="idiff left right">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="html">        return gzip.open(fileName<span class="idiff left right">, "rt")  # xxx dubious for Python2</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="html">    return open(fileName)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line" data-linenumber="26" 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">

26

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line" data-linenumber="27" 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">

27

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="html">def maxlen(s):</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="177815a02f622695617613b9dc8023a958d68f7b">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#177815a02f622695617613b9dc8023a958d68f7b"><strong>scripts/maf-cut</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" 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">@@ -12,7 +12,7 @@ def myOpen(fileName):  # faster than fileinput</td>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line" data-linenumber="13" 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">

13

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line" data-linenumber="14" 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">

14

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

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<td class="diff-line-num new_line old" data-linenumber="15" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rt"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx dubious for Python2</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line" data-linenumber="17" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">alnBegFromSeqBeg</span><span class="p">(</span><span class="n" style="color: #333;">gappedSequence</span><span class="p">,</span> <span class="n" style="color: #333;">seqBeg</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="350d50b528bcd24a057c181965b2a50120bca4c7">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#350d50b528bcd24a057c181965b2a50120bca4c7"><strong>scripts/maf-swap</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,7 +25,7 @@ def myOpen(fileName):</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="26" 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="LC26" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left right">)</span></span></span>

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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="28" 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="LC28" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rt"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx dubious for Python2</span></span></span>

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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">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">indexOfNthSequence</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="4b7be8c3b80efc62977b307791d1a304c23e1fa4">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" 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>

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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">@@ -172,9 +172,8 @@ Miscellaneous options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="s" style="color: #d14;">                 4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"><span class="s" style="color: #d14;">                 7=expected counts ("</span></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">outputType</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"><span class="s" style="color: #d14;">                  4=prb, 5=PSSM ("</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">inputFormat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: 0=fasta or fastq-ignore, 1=fastq-sanger, 2=fastq-solexa,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"><span class="s" style="color: #d14;">                  3=fastq-illumina, 4=prb, 5=PSSM (fasta)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"><span class="s" style="color: #d14;">Report bugs to: last-align (ATmark) googlegroups (dot) com</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="s" style="color: #d14;">LAST home page: http://last.cbrc.jp/</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</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">@@ -445,7 +444,7 @@ void LastalArguments::setDefaultsFromAlphabet( bool isDna, bool isProtein,</td>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gapExistCost</span>   <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">INT_MIN</span> <span class="p">)</span> <span class="n" style="color: #333;">gapExistCost</span>   <span class="o" style="font-weight: 600;">=</span>  <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gapExtendCost</span>  <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">gapExtendCost</span>  <span class="o" style="font-weight: 600;">=</span>   <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isQuality</span><span class="p">(</span> <span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is<span class="idiff left right">Use</span>Quality</span><span class="p">(</span> <span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">matchScore</span>     <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">matchScore</span>     <span class="o" style="font-weight: 600;">=</span>   <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mismatchCost</span>   <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">mismatchCost</span>   <span class="o" style="font-weight: 600;">=</span>   <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gapExistCost</span>   <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">INT_MIN</span> <span class="p">)</span> <span class="n" style="color: #333;">gapExistCost</span>   <span class="o" style="font-weight: 600;">=</span>   <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="640" 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">@@ -641,7 +640,7 @@ void LastalArguments::writeCommented( std::ostream& stream ) const{</td>

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp">    <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" g="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gamma</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="cpp">  <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" j="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outputType</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="cpp">  <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Q="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left right">inputFormat</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp">  <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Q="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequenceFormat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="cpp">  <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC645" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="cpp">  <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">lastdbName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<li id="54925a3b3158a751c06af7acce6d06070e5ac813">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#54925a3b3158a751c06af7acce6d06070e5ac813"><strong>src/LastdbArguments.cc</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">@@ -70,8 +70,8 @@ Advanced Options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="s" style="color: #d14;">-S: strand: 0=reverse, 1=forward, 2=both ("</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"><span class="s" style="color: #d14;">-s: volume size (unlimited)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: 0=fasta<span class="idiff left right">, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina ("</span></span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp">    <span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stringify</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: 0=fasta<span class="idiff left"> or fastq-ignore,</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">\</span></span></span>

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<td class="diff-line-num new new_line" data-linenumber="74" 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="LC74" class="line" lang="cpp"><span class="s" style="color: #d14;">    <span class="idiff left right">              1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (fasta</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="s" style="color: #d14;">-P: number of parallel threads ("</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="s" style="color: #d14;">-m: seed pattern</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<br>

</li>

<li id="de5a928be30a99dcb150a5f687171caed2e9c00c">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#de5a928be30a99dcb150a5f687171caed2e9c00c"><strong>src/MultiSequence.hh</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">@@ -47,8 +47,15 @@ class MultiSequence{</td>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// may not finish reading the sequence.</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">appendFromFasta</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// As above, but read quality scores too.</span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// As above, but read FASTQ format.</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">                           <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isKeepQualityData</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// As above, but read either FASTA or FASTQ format.  The first</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// sequence may have either format, but subsequent sequences must</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// have the same format.</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">appendFromFastx</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">                           <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isKeepQualityData</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// As above, but read quality scores too.</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">appendFromPrb</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" 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">@@ -133,6 +140,7 @@ class MultiSequence{</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Qsolexa = -10*log10(p/(1-p))</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp">  <span class="n" style="color: #333;">VectorOrMmap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qualityScores</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="135" 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="LC142" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qualityScoresPerLetter</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="136" 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="143" 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="LC143" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isReadingFastq</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Read a fasta/fastq header: read the whole line but store just the</span></span>

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<td class="diff-line-num old_line" data-linenumber="138" 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="LC146" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// 1st word</span></span>

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<br>

</li>

<li id="a06897230734e5ba8f58dabb84ae90af66f731e9">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#a06897230734e5ba8f58dabb84ae90af66f731e9"><strong>src/MultiSequenceQual.cc</strong></a>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span></span>

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<td class="diff-line-num old old_line" data-linenumber="15" 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="LC15" class="line" lang="cpp"><span class="n" style="color: #333;">MultiSequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span> <span class="p">){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="LC15" class="line" lang="cpp"><span class="n" style="color: #333;">MultiSequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">appendFromFastx</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="LC16" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isKeepQualityData</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp">    <span class="n" style="color: #333;">isReadingFastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp">    <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp">      <span class="n" style="color: #333;">isReadingFastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">      <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"bad sequence data: missing '>' or '@'"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">    <span class="n" style="color: #333;">readFastxName</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">stream</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stream</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<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">

29

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isReadingFastq</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">    <span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span> <span class="n" style="color: #333;">isKeepQualityData</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<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">

32

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">    <span class="n" style="color: #333;">appendFromFasta</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="34" 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">

34

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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="35" 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">

35

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="36" 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">

36

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">MultiSequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isKeepQualityData</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// initForAppending:</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp">  <span class="n" style="color: #333;">qualityScoresPerLetter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="18" 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="LC39" class="line" lang="cpp">  <span class="n" style="color: #333;">qualityScoresPerLetter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">isKeepQualityData</span></span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="18" 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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<td class="diff-line-num new_line" data-linenumber="40" 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="LC40" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">qualityScores</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">appendQualPad</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isFinished</span><span class="p">()</span> <span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp">    <span class="n" style="color: #333;"><span class="idiff left right">u</span>char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">    <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'@'</span> <span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"bad FASTQ data: missing '@'"</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp">    <span class="n" style="color: #333;">readFastxName</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" 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">@@ -41,11 +63,16 @@ MultiSequence::appendFromFastq( std::istream& stream, indexT maxSeqLen ){</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp">      <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sbumpc</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">streambuf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">traits_type</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">eof</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">while</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qualityScores</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="66" 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">

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ends</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">back</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line" data-linenumber="67" 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">

67

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">      <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sbumpc</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" 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">

46

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<td class="diff-line-num new_line" data-linenumber="68" 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">

68

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">streambuf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">traits_type</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">eof</span><span class="p">())</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"bad FASTQ data"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="69" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">126</span><span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"non-printable-ASCII in FASTQ quality data"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

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<td class="diff-line-num new_line old" data-linenumber="69" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">></span> <span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="n" style="color: #333;">qualityScores</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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="69" 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">

69

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">></span> <span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="70" 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">

70

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isKeepQualityData</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="71" 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">

71

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">126</span><span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"non-printable-ASCII in FASTQ quality data"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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="72" 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">

72

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">     <span class="n" style="color: #333;">qualityScores</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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="73" 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">

73

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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="74" 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">

74

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">   <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="75" 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">

75

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line" data-linenumber="76" 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">

76

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" 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">

50

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<td class="diff-line-num new_line" data-linenumber="77" 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">

77

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>

</pre>

</td>

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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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<td class="diff-line-num new_line" data-linenumber="78" 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">

78

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">    <span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

</pre>

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<br>

</li>

<li id="39b07776472abcba47ba556e9f044177918c142c">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#39b07776472abcba47ba556e9f044177918c142c"><strong>src/SequenceFormat.hh</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" 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">@@ -8,7 +8,7 @@</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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="LC9" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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="LC10" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">sequenceFormat</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" 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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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">Enum</span> <span class="p">{</span> <span class="n" style="color: #333;">fast<span class="idiff left">a</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fastqSanger</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fastqSolexa</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fastqIllumina</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">prb</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pssm</span></span> <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="11" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">Enum</span> <span class="p">{</span> <span class="n" style="color: #333;">fast<span class="idiff left">x</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fastqSanger</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fastqSolexa</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fastqIllumina</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">prb</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pssm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span> <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -19,17 +19,17 @@ inline std::istream &operator>>(std::istream &s, sequenceFormat::Enum &f) {</td>

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<td class="diff-line-num old_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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="20" 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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<td class="diff-line-num new_line" data-linenumber="20" 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="LC20" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_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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<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="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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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<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="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isQuality</span><span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></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="LC23" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pssm</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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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<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="LC24" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="25" 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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<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="LC25" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" 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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<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="LC26" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isFastq</span><span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="27" 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="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="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isUseFastq</span><span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line" data-linenumber="23" 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">

23

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_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">

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp">      <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastqSanger</span> <span class="o" style="font-weight: 600;">||</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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<td class="diff-line-num new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp">      <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastqSolexa</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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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<td class="diff-line-num new_line" data-linenumber="26" 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">

26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp">      <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastqIllumina</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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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<td class="diff-line-num new_line" data-linenumber="28" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" 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="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="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isUseQuality</span><span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" 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="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isUseFastq</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prb</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" 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="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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" 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="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="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" 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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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qualityOffset</span><span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" 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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<td class="diff-line-num new_line" data-linenumber="34" 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="LC34" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastqSanger</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">33</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">64</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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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<td class="diff-line-num new_line" data-linenumber="35" 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="LC35" class="line" lang="cpp"><span class="p">}</span>  <span class="c1" style="color: #998; font-style: italic;">// The result is meaningless for non-quality formats.</span></span>

</pre>

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<br>

</li>

<li id="cbc8995f0e52a1d4b5b18e7df92014c01ec2dea1">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#cbc8995f0e52a1d4b5b18e7df92014c01ec2dea1"><strong>src/SubsetSuffixArray.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" 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">@@ -66,13 +66,13 @@ void SubsetSuffixArray::fromFiles( const std::string& baseName,</td>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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="LC67" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">    <span class="n" style="color: #333;">childTable</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".chi"</span><span class="p">,</span> <span class="n" style="color: #333;">indexedPositions</span> <span class="p">);</span></span>

</pre>

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69

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp">  <span class="p">}</span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span> <span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">  <span class="p">}</span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="p">){</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" 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">

71

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71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">      <span class="n" style="color: #333;">kiddyTable</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".chi2"</span><span class="p">,</span> <span class="n" style="color: #333;">indexedPositions</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp">    <span class="p">}</span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span> <span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="p">}</span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="p">){</span></span>

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73

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" 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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<td class="diff-line-num new_line" data-linenumber="74" 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="LC74" class="line" lang="cpp">   <span class="n" style="color: #333;">chibiTable</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".chi1"</span><span class="p">,</span> <span class="n" style="color: #333;">indexedPositions</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp">      <span class="p">}</span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span> <span class="p">){}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">      <span class="p">}</span><span class="k" style="font-weight: 600;">catch</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="p">){}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" 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="LC77" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" 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="LC78" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="6f06cc5de9b7ac057e2bab4944683b3802e6b62f">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#6f06cc5de9b7ac057e2bab4944683b3802e6b62f"><strong>src/last.hh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,12 +25,14 @@ inline std::istream &appendSequence(MultiSequence &m, std::istream &in,</td>

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25

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<td class="diff-line-num new_line" data-linenumber="25" 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">

25

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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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<td class="diff-line-num new_line" data-linenumber="26" 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">

26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fasta</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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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<td class="diff-line-num new_line" data-linenumber="27" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">    <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">appendFromFasta</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastx</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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="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="cpp">    <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">appendFromFastx</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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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<td class="diff-line-num new_line" data-linenumber="30" 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="LC30" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prb</span><span class="p">)</span> <span class="p">{</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">

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<td class="diff-line-num new_line" data-linenumber="31" 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="LC31" class="line" lang="cpp">    <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">appendFromPrb</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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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<td class="diff-line-num new_line" data-linenumber="32" 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="LC32" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pssm</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" class="line" lang="cpp">    <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">appendFromPssm</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="34" 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="LC34" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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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<td class="diff-line-num new_line old" data-linenumber="35" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp">    <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" 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="35" 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="LC35" class="line" lang="cpp">    <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">appendFromFastq</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">true</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" 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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<td class="diff-line-num new_line" data-linenumber="36" 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="LC36" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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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<td class="diff-line-num new_line" data-linenumber="37" 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="LC37" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">isFinished</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">finishedSequences</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<br>

</li>

<li id="a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" 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">@@ -80,7 +80,7 @@ namespace {</td>

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<td class="diff-line-num new_line" data-linenumber="80" 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="LC80" class="line" lang="cpp">  <span class="n" style="color: #333;">OneQualityExpMatrix</span> <span class="n" style="color: #333;">oneQualityExpMatrixRev</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" 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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<td class="diff-line-num new_line" data-linenumber="81" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp">  <span class="n" style="color: #333;">QualityPssmMaker</span> <span class="n" style="color: #333;">qualityPssmMaker</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" 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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<td class="diff-line-num new_line" data-linenumber="82" 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="LC82" class="line" lang="cpp">  <span class="n" style="color: #333;">QualityPssmMaker</span> <span class="n" style="color: #333;">qualityPssmMakerRev</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" 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="LC83" class="line" lang="cpp">  <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">referenceFormat</span><span class="p"><span class="idiff left">;</span></span><span class="idiff">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// defaults to 0</span></span></span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">  <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">referenceFormat</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequenceFormat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="p"><span class="idiff right">;</span></span></span>

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<td class="diff-line-num old_line" data-linenumber="84" 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="LC84" class="line" lang="cpp">  <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="n" style="color: #333;">twoQualityMatrix</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="85" 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="LC85" class="line" lang="cpp">  <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="n" style="color: #333;">twoQualityMatrixMasked</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="86" 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="LC86" class="line" lang="cpp">  <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="n" style="color: #333;">twoQualityMatrixRev</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,7 @@ static void calculateSubstitutionScoreMatrixStatistics() {</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">  <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">caseSensitive</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">isBad</span><span class="p">()</span> <span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isQuality</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">is<span class="idiff left right">Use</span>Quality</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp">        <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">      <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't calculate probabilities: "</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">     <span class="s" style="color: #d14;">"maybe the mismatch costs are too weak"</span> <span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="179" 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">@@ -179,7 +179,7 @@ void makeQualityScorers(){</td>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isTranslated</span><span class="p">()</span> <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">is<span class="idiff left">Quality</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">is</span>Quality</span><span class="p">(</span> <span class="n" style="color: #333;">referenceFormat</span> <span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">is<span class="idiff left">UseQuality</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isUse</span>Quality</span><span class="p">(</span> <span class="n" style="color: #333;">referenceFormat</span> <span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">warn</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">programName</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp">             <span class="s" style="color: #d14;">"quality data not used for DNA-versus-protein alignment"</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="199" 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">@@ -199,8 +199,8 @@ void makeQualityScorers(){</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lp2rev</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp">  <span class="n" style="color: #333;">permuteComplement</span><span class="p">(</span> <span class="n" style="color: #333;">lp2</span><span class="p">,</span> <span class="n" style="color: #333;">lp2rev</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;"><span class="idiff left">referenceFormat</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequenceFormat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span> <span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isFastq</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="p">){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="204" 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="202" 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="LC202" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">isUseFastq</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">referenceFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">)</span></span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" 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="203" 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="LC203" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">is<span class="idiff left right">Use</span>Fastq</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" 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="LC204" class="line" lang="cpp">      <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"calculating per-quality scores..."</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp">  <span class="n" style="color: #333;">oneQualityMatrixMasked</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" 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>

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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">@@ -232,7 +232,7 @@ void makeQualityScorers(){</td>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">oneQualityExpMatrixRev</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">qRev</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="235" 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="LC235" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isQuality</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span><span class="p">)</span> <span class="p">){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="236" 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="LC235" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">is<span class="idiff left right">Use</span>Quality</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span><span class="p">)</span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp">      <span class="n" style="color: #333;">qualityPssmMaker</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">isMatchMismatch</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp">                             <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp">                             <span class="n" style="color: #333;">isPhred2</span><span class="p">,</span> <span class="n" style="color: #333;">offset2</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToUppercase</span> <span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="243" 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">@@ -243,7 +243,7 @@ void makeQualityScorers(){</td>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isFastq</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="p">){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="247" 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="LC246" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">is<span class="idiff left right">Use</span>Fastq</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="248" 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="LC248" class="line" lang="cpp">  <span class="n" style="color: #333;">twoQualityMatrixMasked</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">lp1</span><span class="p">,</span> <span class="n" style="color: #333;">lp2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">                               <span class="n" style="color: #333;">isPhred1</span><span class="p">,</span> <span class="n" style="color: #333;">offset1</span><span class="p">,</span> <span class="n" style="color: #333;">isPhred2</span><span class="p">,</span> <span class="n" style="color: #333;">offset2</span><span class="p">,</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">@@ -336,8 +336,9 @@ void readOuterPrj( const std::string& fileName, unsigned& volumes,</td>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">bad</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">refSequences</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">refLetters</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="cpp">      <span class="n" style="color: #333;">isCaseSensitiveSeeds</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">referenceFormat</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prb</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp">      <span class="n" style="color: #333;">numOfIndexes</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxNumOfIndexes</span> <span class="p">){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="341" 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="LC339" class="line" lang="cpp">      <span class="n" style="color: #333;">isCaseSensitiveSeeds</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">numOfIndexes</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxNumOfIndexes</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp">      <span class="n" style="color: #333;">referenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prb</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp">      <span class="n" style="color: #333;">referenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pssm</span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">setstate</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">failbit</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">f</span> <span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't read file: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fileName</span> <span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="749" 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">@@ -748,7 +749,7 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>

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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line" data-linenumber="750" 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="LC750" class="line" lang="cpp">  <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">setScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="751" 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">

751

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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp">  <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">setLetterProbsPerPosition</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">queryLen</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC751" class="line" lang="cpp">                                     <span class="n" style="color: #333;">isFastq</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp">                                     <span class="n" style="color: #333;">is<span class="idiff left right">Use</span>Fastq</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp">                                     <span class="n" style="color: #333;">qualityPssmMaker</span><span class="p">.</span><span class="n" style="color: #333;">qualToProbRight</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp">                                     <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp">                                     <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToUppercase</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="851" 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">@@ -850,7 +851,7 @@ static void printAndClearAll() {</td>

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<pre style="margin: 0;"> <span id="LC851" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">makeQualityPssm</span><span class="p">(</span> <span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC853" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMask</span> <span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC853" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">isQuality</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isQuality</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">referenceFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">isUseQuality</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isUseQuality</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">referenceFormat</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC855" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isTranslated</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="856" 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="LC856" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC857" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">qualityPssm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">qualityPssm</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1029" 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">@@ -1028,7 +1029,7 @@ static void scanOneVolume(unsigned volume, unsigned volumeCount) {</td>

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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">readIndex</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">baseName</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">seqCount</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

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1030

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<td class="diff-line-num new_line" data-linenumber="1031" 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">

1031

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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="cpp">  <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"reading "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"..."</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1031" 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">

1031

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<td class="diff-line-num new_line old" data-linenumber="1032" 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="LC1031" class="line" lang="cpp">  <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">fromFiles</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">baseName</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqCount</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isFastq</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">referenceFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1032" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1032" 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">

1032

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp">  <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">fromFiles</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">baseName</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqCount</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">referenceFormat</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequenceFormat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1032" 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">

1032

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<td class="diff-line-num new_line" data-linenumber="1033" 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">

1033

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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfIndexes</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x</span> <span class="p">){</span></span>

</pre>

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1033

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<td class="diff-line-num new_line" data-linenumber="1034" 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">

1034

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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">numOfIndexes</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1034" 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">

1034

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<td class="diff-line-num new_line" data-linenumber="1035" 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">

1035

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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="cpp">      <span class="n" style="color: #333;">suffixArrays</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">fromFiles</span><span class="p">(</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">+</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="sc" style="color: #d14;">'a'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span><span class="p">),</span></span>

</pre>

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<br>

</li>

<li id="de4252990d12a909e50ff0b994d1715eae0ea5fd">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#de4252990d12a909e50ff0b994d1715eae0ea5fd"><strong>src/lastdb.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" 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">@@ -98,7 +98,7 @@ void writeLastalOptions( std::ostream& out, const std::string& seedText ){</td>

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98

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98

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writePrjFile</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastdbArguments</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">args</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" 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">

99

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<td class="diff-line-num new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">countT</span> <span class="n" style="color: #333;">sequenceCount</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" 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">

100

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<td class="diff-line-num new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">countT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letterCounts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" 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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<td class="diff-line-num new_line old" data-linenumber="101" 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="LC101" class="line" lang="cpp">             <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">volumes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numOfIndexes</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">             <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isFastq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">volumes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numOfIndexes</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" 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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<td class="diff-line-num new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seedText</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">  <span class="n" style="color: #333;">countT</span> <span class="n" style="color: #333;">letterTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">accumulate</span><span class="p">(</span> <span class="n" style="color: #333;">letterCounts</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp">                                        <span class="n" style="color: #333;">letterCounts</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">countT</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" 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">@@ -124,7 +124,7 @@ void writePrjFile( const std::string& fileName, const LastdbArguments& args,</td>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">      <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"tantansetting="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"masklowercase="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isCaseSensitive</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequenceFormat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span> <span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;"><span class="idiff left right">isFastq</span></span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">      <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sequenceformat="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minimizerWindow</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" 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">@@ -201,7 +201,8 @@ void makeVolume( std::vector< CyclicSubsetSeed >& seeds,</td>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp">  <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"writing..."</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp">  <span class="n" style="color: #333;">writePrjFile</span><span class="p">(</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".prj"</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">numOfSequences</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp">          <span class="n" style="color: #333;">letterCountsInThisVolume</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">numOfIndexes</span><span class="p">,</span> <span class="n" style="color: #333;">seedText</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">          <span class="n" style="color: #333;">letterCountsInThisVolume</span><span class="p">,</span> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">qualsPerLetter</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp">          <span class="n" style="color: #333;">numOfIndexes</span><span class="p">,</span> <span class="n" style="color: #333;">seedText</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp">  <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">toFiles</span><span class="p">(</span> <span class="n" style="color: #333;">baseName</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfIndexes</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x</span> <span class="p">){</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">@@ -240,8 +241,9 @@ void makeVolume( std::vector< CyclicSubsetSeed >& seeds,</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// neglects memory for the sequence names, and the fact that</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// lowercase-masked letters and DNA "N"s aren't indexed.)</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxLettersPerVolume</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastdbArguments</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">args</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">                             <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qualityCodesPerLetter</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">                             <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numOfIndexes</span> <span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bytesPerLetter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">isFastq</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inputFormat</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bytesPerLetter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">qualityCodesPerLetter</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxIndexBytesPerPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">indexT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">  <span class="n" style="color: #333;">maxIndexBytesPerPosition</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">numOfIndexes</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bytesPerLetter</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">indexStep</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maxIndexBytesPerPosition</span><span class="p">;</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">@@ -286,7 +288,7 @@ void lastdb( int argc, char** argv ){</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">volumeNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp">  <span class="n" style="color: #333;">countT</span> <span class="n" style="color: #333;">sequenceCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">countT</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">letterCounts</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp">  <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">maxLettersPerVolume</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seeds</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">)</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">  <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">maxSeqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">defaultInputName</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">defaultInput</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="n" style="color: #333;">defaultInputName</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">};</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">@@ -299,9 +301,13 @@ void lastdb( int argc, char** argv ){</td>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">appendSequence</span><span class="p">(</span><span class="n" style="color: #333;">multi</span><span class="p">,</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">maxSeqLen</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp">                    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isKeepLowercase</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isProtein</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">userAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp">          <span class="n" style="color: #333;">sequenceCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDubiousDna</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">multi</span> <span class="p">)</span> <span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">programName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": that's some funny-lookin DNA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequenceCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">  <span class="n" style="color: #333;">maxSeqLen</span> <span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">    <span class="n" style="color: #333;">maxLettersPerVolume</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">qualsPerLetter</span><span class="p">(),</span> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isProtein</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">userAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">      <span class="n" style="color: #333;">isDubiousDna</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">multi</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">programName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": that's some funny-lookin DNA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">isFinished</span><span class="p">()</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="351" 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">@@ -345,7 +351,8 @@ void lastdb( int argc, char** argv ){</td>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp">  <span class="n" style="color: #333;">writePrjFile</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">lastdbName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".prj"</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">sequenceCount</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp">          <span class="n" style="color: #333;">letterCounts</span><span class="p">,</span> <span class="n" style="color: #333;">volumeNumber</span><span class="p">,</span> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">seedText</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp">          <span class="n" style="color: #333;">letterCounts</span><span class="p">,</span> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">qualsPerLetter</span><span class="p">(),</span> <span class="n" style="color: #333;">volumeNumber</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp">          <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">seedText</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">main</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">argv</span> <span class="p">)</span></span>

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<br>

</li>

<li id="cff6a16c49a626871ebb6399a31650f25e4f5395">

<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#cff6a16c49a626871ebb6399a31650f25e4f5395"><strong>src/split/last-split.cc</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">@@ -134,8 +134,12 @@ static void doOneAlignmentPart(cbrc::SplitAligner& sa,</td>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">)</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="137" 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="LC137" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setprecision</span><span class="p">(</span><span class="n" style="color: #333;">mismapPrecision</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="137" 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="LC138" class="line" lang="cpp">      <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"a score="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" mismap="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mismap</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">no_split</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">linesBeg</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'a'</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">linesBeg</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"a score="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setprecision</span><span class="p">(</span><span class="n" style="color: #333;">mismapPrecision</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" mismap="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mismap</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">printSense</span><span class="p">(</span><span class="n" style="color: #333;">senseStrandLogOdds</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">no_split</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">signal</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" 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>

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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">@@ -383,7 +387,7 @@ void lastSplit(LastSplitOptions& opts) {</td>

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<td class="diff-line-num new_line" data-linenumber="387" 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">

387

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp">    <span class="n" style="color: #333;">mafEnds</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="384" 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">

384

</td>

<td class="diff-line-num new_line" data-linenumber="388" 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">

388

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSpace</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="385" 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">

385

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<td class="diff-line-num new_line" data-linenumber="389" 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">

389

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp">    <span class="n" style="color: #333;">addMaf</span><span class="p">(</span><span class="n" style="color: #333;">mafEnds</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="386" 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">

386

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<td class="diff-line-num new_line old" data-linenumber="390" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="s" style="color: #d14;">"sqpc"</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="387" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">no_split</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"asqpc"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"sqpc"</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="387" 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">

387

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<td class="diff-line-num new_line" data-linenumber="391" 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">

391

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp">    <span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="388" 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">

388

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<td class="diff-line-num new_line" data-linenumber="392" 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">

392

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="389" 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">

389

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<td class="diff-line-num new_line" data-linenumber="393" 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">

393

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<a href="https://salsa.debian.org/med-team/last-align/commit/1d01bfcb813030a4be50b9db3df0318d0579323a#69737f84c540417aafef4e696f66adcc9f92fa66"><strong>src/version.hh</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"9<span class="idiff left right">56</span>"</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="2" 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="1" 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">

1

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"9<span class="idiff left right">61</span>"</span></span></pre>

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