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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

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/9b12cf2cc27e3510c27c132a8e698b155d8b853f">9b12cf2c</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-06-19T16:43:07+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import Upstream version 1066</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/e1d8e7ffb17d07a95396beed25a56b5b330949b3">e1d8e7ff</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-06-19T16:43:07+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import Debian changes 1066-1

last-align (1066-1) unstable; urgency=medium

  * Team upload.

  [ Michael R. Crusoe ]

  * i386: enable avx2, avx, and sse4.1 specific builds as well

  * Demote GNU parallel to a recommends; only used by parallel-fasta

  [ Steffen Moeller ]

  * New upstream version.

  * debhelper-compat 13 (routine-update)

</pre>

</li>

</ul>

<h4>25 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#57bf262130f956caf76c405086f0815caf4e0a89">

ChangeLog.txt

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">

debian/patches/2to3.patch

</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="#a3473a36b447c7d33b488e9643dadb1f77a412f6">

doc/maf-convert.html

</a>

</li>

<li class="file-stats">

<a href="#2ac8fe07ee85c38c0ea51f42223721b9dfabe8f8">

doc/maf-convert.txt

</a>

</li>

<li class="file-stats">

<a href="#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">

scripts/last-dotplot

</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="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">

src/LastalArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#54925a3b3158a751c06af7acce6d06070e5ac813">

src/LastdbArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#39b07776472abcba47ba556e9f044177918c142c">

src/SequenceFormat.hh

</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="#c25b47eef38e528e2fca11a7df7ca42c6fe59707">

src/split/cbrc_split_aligner.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/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-06-11  Martin C. Frith  <Martin C. Frith></span>

</pre>

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2

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

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      Make inconsistent last-train/lastal -Q an error</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      [f2071b3c3173] [tip]</span>

</pre>

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6

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

<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">      * doc/last-train.txt, doc/lastal.txt, doc/lastdb.txt, scripts/last-</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      train, src/LastalArguments.cc, src/LastdbArguments.cc,</span>

</pre>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      src/SequenceFormat.hh, src/last.hh, src/lastdb.cc,</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">     src/split/cbrc_split_aligner.cc, src/split/last-split.cc, test/last-</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     test.out, test/last-test.sh:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">     Add option to keep but ignore fastq quals</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">     [0315c96a5a9b]</span>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">2020-06-08  Martin C. Frith  <Martin C. Frith></span>

</pre>

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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">

16

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></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="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">     * scripts/maf-convert:</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">

</td>

<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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     Fix small bug in maf-convert -J</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="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">     [cd67e8009c78]</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">

</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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></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="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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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">     * doc/maf-convert.txt, scripts/maf-convert, test/maf-convert-test.out,</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">

</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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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">     test/maf-convert-test.sh:</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">     Add maf-convert -J 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">

</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="plaintext">     [bc7b2cdbcb32]</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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></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="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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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">     * doc/maf-convert.txt, scripts/last-dotplot, scripts/last-train,</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">

</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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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">     scripts/maf-convert, scripts/maf-cut, test/maf-convert-test.out,</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">

</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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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">     test/maf-convert-test.sh:</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">

</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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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">     Add maf-convert to gff (with help from C. Plessy)</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">

</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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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">     [6d8d56a74b14]</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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<pre style="margin: 0;">+<span id="LC31" 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="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="plaintext">2020-05-07  Martin C. Frith  <Martin C. Frith></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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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">

33

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<pre style="margin: 0;"> <span id="LC33" 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="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">     * src/tantan.cc:</span>

</pre>

</td>

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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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<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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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">     Make tantan repeat-finding faster</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">      [543d36d39ce3]<span class="idiff left right"> [tip]</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">     [543d36d39ce3]</span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">2020-03-16  Martin C. Frith  <Martin C. Frith></span>

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

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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">last-align (106<span class="idiff left right">1-2) UNRELEASED</span>; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (106<span class="idiff left right">6-1) unstable</span>; urgency=medium</span>

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2

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  [ Michael R. Crusoe ]</span>

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4

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * i386: enable avx2, avx, and sse4.1 specific builds as well</span>

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5

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">  * Demote GNU parallel to a recommends; only used by parallel-fasta</span>

</pre>

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6

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(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="LC9" class="line" lang="plaintext">  [ Steffen Moeller ]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(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="LC10" class="line" lang="plaintext">  * New upstream version.</span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(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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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  * debhelper-compat 13 (routine-update)</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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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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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="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 17 May 2020 12:32:51 +0200</span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">last-align (1061-1) unstable; urgency=medium</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,11 +4,11 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">           Andreas Tille <tille@debian.org></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>

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

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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(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="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               help2man,</span>

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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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<td class="diff-line-num new_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="plaintext">               python3-pil,</span>

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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="plaintext">               zlib1g-dev,</span>

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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="plaintext">               libsimde-dev<span class="idiff left right"> ( >= 0.0.0.git.20200419 )</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">               libsimde-dev</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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.0</span>

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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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/last-align</span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/last-align.git</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,12 +17,12 @@ Rules-Requires-Root: no</td>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Package: last-align</span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: any</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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="20" 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="LC20" class="line" lang="plaintext">Built-Using: ${Built-Using}</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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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Depends: ${shlibs:Depends},</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="21" 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="plaintext">         ${misc:Depends}<span class="idiff left right">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">         ${misc:Depends}</span>

</pre>

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23

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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="plaintext">Recommends: python3,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">            python3-pil,</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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num new old_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">

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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">

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Built-Using: ${Built-Using}</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">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: genome-scale comparison of biological sequences</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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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> LAST is software for comparing and aligning sequences, typically DNA or</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="plaintext"> protein sequences. LAST is similar to BLAST, but it copes better with very</span>

</pre>

</td>

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<br>

</li>

<li id="555c85016bd79aa8bbb523506af81b69d9c69534">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,15 +3,17 @@ Bug-Debian: https://bugs.debian.org/943148</td>

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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="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">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(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="5" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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="6" style="width: 35px; color: rgba(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="LC6" class="line" lang="diff">Index: last-align/scripts/last-dotplot</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/last-dotplot</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/last-dotplot</span></span>

</pre>

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<td class="diff-line-num 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">

8

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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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</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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<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">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num new old_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="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#! /usr/bin/python3</span></span>

</pre>

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # Author: Martin C. Frith 2008</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # SPDX-License-Identifier: GPL-3.0-or-later</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="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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="16" 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="LC12" class="line" lang="diff"> # Read pair-wise alignments in MAF or LAST tabular format: write an</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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="16" 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="LC13" class="line" lang="diff"> # "Oxford grid", a.k.a. dotplot.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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="16" 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="LC14" class="line" lang="diff"><span class="p">@@ -262,12 +262,12 @@</span></span>

</pre>

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<td class="diff-line-num new old_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="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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -264,12 +264,12 @@</span> def mergedRanges(ranges):</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="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="diff">     yield oldBeg, maxEnd</span>

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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="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="diff"> </span>

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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="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="diff"> def mergedRangesPerSeq(coverDict):</span>

</pre>

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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="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">...</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 +28,7 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</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="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="diff"> </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="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="diff"> def trimmed(seqRanges, coverDict, minAlignedBases, maxGapFrac, endPad, midPad):</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="diff">     maxEndGapFrac, maxMidGapFrac = twoValuesFromOption(maxGapFrac, ",")</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">

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

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">08,7 +308,7 @@</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">

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left">10,7 +310,7 @@</span></span><span class="idiff right"> def rangesWithStrandInfo(seqRanges, stra</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="diff"> def natural_sort_key(my_string):</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="diff">     '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''</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="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="diff">     parts = re.split(r'(\d+)', my_string)</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,7 +37,7 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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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="diff">     return parts</span>

</pre>

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

</pre>

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<td class="diff-line-num old_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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<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="diff"> def nameKey(oneSeqRanges):</span>

</pre>

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="p">@@ -57<span class="idiff left right">7,7 +577,7 @@</span></span></span>

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(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="LC40" class="line" lang="diff"><span class="p">@@ -57<span class="idiff left">9,7 +579,7 @@</span></span><span class="idiff right"> def drawJoins(im, alignments, bpPerPix,</span></span>

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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="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">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> def expandedSeqDict(seqDict):</span>

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<td class="diff-line-num old_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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<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">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff">     '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''</span>

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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">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff">     newDict = seqDict.copy()</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +46,7 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff">         if "." in name:</span>

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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">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="diff">             base = name.split(".")[-1]</span>

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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">

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff">             if base in newDict:  # an ambiguous case was found:</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">

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

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="p">@@ -61<span class="idiff left right">1,7 +611,7 @@</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="48" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -61<span class="idiff left">3,7 +613,7 @@</span></span><span class="idiff right"> def readBed(fileName, rangeDict):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff">         yield layer, color, seqName, beg, end</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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </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">

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(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="LC52" class="line" lang="diff"> def commaSeparatedInts(text):</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(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="55" style="width: 35px; color: rgba(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">@@ -53,6 +55,8 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(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="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="diff"> def readGenePred(opts, fileName, rangeDict):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="diff">     for line in myOpen(fileName):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" style="width: 35px; color: rgba(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="LC58" class="line" lang="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/last-map-probs</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/last-map-probs</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(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="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/last-map-probs</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(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">@@ -61,6 +65,8 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> # Copyright 2010, 2011, 2012, 2014 Martin C. Frith</span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> </span>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(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="LC68" class="line" lang="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/last-postmask</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(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">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/last-postmask</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(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="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/last-postmask</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" style="width: 35px; color: rgba(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="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">...</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> # Copyright 2014 Martin C. Frith</span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span><span class="idiff left right"> def complement(base):</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> def fastScoreMatrix(rowHeads, colHeads, matrix, deleteCost, insertCost):</span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff">     matrixLen = 128</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,7 +84,7 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff">     fastMatrix = [[defaultScore for i in range(matrixLen)]</span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff">                   for j in range(matrixLen)]</span>

</pre>

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<td class="diff-line-num new_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="diff">     for i, x in enumerate(rowHeads):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" 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="87" 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="LC81" class="line" lang="diff"><span class="p">@@ -111,7 +111,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="82" style="width: 35px; color: rgba(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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -111,7 +111,7 @@</span><span class="idiff left right"> def doOneFile(lines):</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="88" style="width: 35px; color: rgba(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="LC88" class="line" lang="diff">                     if i.startswith("B="): bIns = int(i[2:])</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">

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="diff">                     if i.startswith("e="): minScore = int(i[2:])</span>

</pre>

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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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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff">                     if i.startswith("S="): strandParam = int(i[2:])</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(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">@@ -87,15 +93,17 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(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="LC93" class="line" lang="diff">                     colHeads = fields[1:]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(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="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="diff">             elif nf == len(colHeads) + 2 and len(fields[1]) == 1:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(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="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="diff">                 rowHeads.append(fields[1])</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/last-train</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/last-train</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/last-train</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(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="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(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">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(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">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="diff"> # Copyright 2015 Martin C. Frith</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> # SPDX-License-Identifier: GPL-3.0-or-later</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="97" 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="106" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> # References:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="98" 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="LC98" class="line" lang="diff"><span class="p">@@ -248,7 +248,7 @@</span></span>

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="p">@@ -249,7 +249,7 @@</span> def writeScoreMatrix(outFile, matrix, pr</span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff">     writeMatrixBody(outFile, prefix, alphabet, matrix, "%6s")</span>

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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">

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

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(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="LC109" class="line" lang="diff"> def matProbsFromCounts(counts, opts):</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" style="width: 35px; color: rgba(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="112" style="width: 35px; color: rgba(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">@@ -104,23 +112,27 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(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="LC112" class="line" lang="diff">     if opts.revsym:  # add complement (reverse strand) substitutions</span>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(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="LC113" class="line" lang="diff">         counts = [[counts[i][j] + counts[-1-i][-1-j] for j in r] for i in r]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(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="LC114" class="line" lang="diff">     if opts.matsym:  # symmetrize the substitution matrix</span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/maf-convert</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/maf-convert</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(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="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/maf-convert</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(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="LC119" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(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="120" style="width: 35px; color: rgba(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="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(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="121" style="width: 35px; color: rgba(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="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(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="122" style="width: 35px; color: rgba(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="LC122" class="line" lang="diff"> # Copyright 2010, 2011, 2013, 2014 Martin C. Frith</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">

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<td class="diff-line-num new_line old" data-linenumber="123" 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="LC113" class="line" lang="diff"> # <span class="idiff left right">Read MAF-format alignments: write them in other formats.</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(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="LC123" class="line" lang="diff"> # <span class="idiff left right">SPDX-License-Identifier: GPL-3.0-or-later</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="diff"> # Seems to work with Python 2.x, x>=6</span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/maf-cut</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/maf-cut</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(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="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/maf-cut</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="117" style="width: 35px; color: rgba(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="LC129" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(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="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" 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="131" 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="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#! /usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> # Author: Martin C. Frith 2018</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(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="134" style="width: 35px; color: rgba(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="diff"> from __future__ import print_function</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" 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="135" 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="LC122" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" 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="135" 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="LC123" class="line" lang="diff"><span class="p">@@ -70,12 +70,12 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(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="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="diff"><span class="p">@@ -71,12 +71,12 @@</span> def cutMafRecords(mafLines, alnBeg, alnE</span>

</pre>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(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="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="diff"> def mafFieldWidths(mafRecords):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(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="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="LC138" class="line" lang="diff">     sRecords = (i for i in mafRecords if i[0] == "s")</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" style="width: 35px; color: rgba(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="148" style="width: 35px; color: rgba(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">@@ -136,6 +148,8 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<td class="diff-line-num new_line" data-linenumber="148" style="width: 35px; color: rgba(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="LC148" class="line" lang="diff">     print("%*s %-*s %*s %*s %*s %*s %*s" % tuple(formatParams))</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(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="LC149" class="line" lang="diff"> </span>

</pre>

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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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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(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="LC150" class="line" lang="diff"> def cutOneMaf(cutRange, mafLines):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="139" style="width: 35px; color: rgba(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="151" style="width: 35px; color: rgba(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="LC151" class="line" lang="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/maf-join</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="139" style="width: 35px; color: rgba(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="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/maf-join</span></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/maf-join</span></span>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(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="155" style="width: 35px; color: rgba(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="LC155" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(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="158" style="width: 35px; color: rgba(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">@@ -144,7 +158,7 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="diff"> </span>

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<td class="diff-line-num old_line" data-linenumber="145" style="width: 35px; color: rgba(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="159" style="width: 35px; color: rgba(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="LC159" class="line" lang="diff"> # Copyright 2009, 2010, 2011 Martin C. Frith</span>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC160" class="line" lang="diff"> </span>

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<td class="diff-line-num old old_line" data-linenumber="147" 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="161" 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="LC147" class="line" lang="diff"><span class="p">@@ -229,7 +229,7 @@</span></span>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(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="161" style="width: 35px; color: rgba(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="LC161" class="line" lang="diff"><span class="p">@@ -229,7 +229,7 @@</span><span class="idiff left right"> def nextWindow(window, theInput, referen</span></span>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(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="162" style="width: 35px; color: rgba(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="LC162" class="line" lang="diff">         while True:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(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="163" style="width: 35px; color: rgba(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="LC163" class="line" lang="diff">             maf = theInput.peek()</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(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="164" style="width: 35px; color: rgba(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="LC164" class="line" lang="diff">             if maf.after(referenceMaf): break</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" style="width: 35px; color: rgba(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">@@ -153,6 +167,8 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(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="LC167" class="line" lang="diff">             if not maf.before(referenceMaf): yield maf</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(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="LC168" class="line" lang="diff">     except StopIteration: pass</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(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="169" style="width: 35px; color: rgba(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="LC169" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(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="diff"><span class="gh" style="color: #999;">Index: last-align/scripts/maf-swap</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(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="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="156" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/scripts/maf-swap</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(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="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/scripts/maf-swap</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(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="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(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="177" style="width: 35px; color: rgba(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">@@ -161,7 +177,7 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="diff"> # Read MAF-format alignments, and write them, after moving the Nth</span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="diff"> # sequence to the top in each alignment.</span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="p">@@ -69,12 +69,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="p">@@ -69,12 +69,12 @@</span><span class="idiff left right"> def flippedMafRecords(mafLines):</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="diff"> def sLineFieldWidths(mafLines):</span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="diff">     sLines = (i for i in mafLines if i[0] == "s")</span>

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<br>

</li>

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<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#bf068196d49b041029d9a269a6e3d52acda15f9f"><strong>doc/last-train.html</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="491" style="width: 35px; color: rgba(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">@@ -491,22 +491,23 @@ Ns/Xs as ambiguous.</p></td>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="html">output, so it will override lastal's default.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="html"><span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new_line old" data-linenumber="494" 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="LC494" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-Q <span class="nt" style="color: #000080;"><var></span>NUMBER<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<td class="diff-line-num new_line old" data-linenumber="494" 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="html"><span class="nt" style="color: #000080;"><td><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>How to read the query sequences.  By default, they must</span>

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<td class="diff-line-num new_line old" data-linenumber="494" 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="LC496" class="line" lang="html">be in <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>fasta<span class="nt" style="color: #000080;"></tt></span> format.  <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-Q0<span class="nt" style="color: #000080;"></span></tt></span> means <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>fasta<span class="nt" style="color: #000080;"></tt></span> or</span>

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

497

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<td class="diff-line-num new_line old" data-linenumber="494" 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="LC497" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>fastq-ignore<span class="nt" style="color: #000080;"></span></tt></span>.  <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-Q1<span class="nt" style="color: #000080;"></span></tt></span> means <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>fastq-sanger<span class="nt" style="color: #000080;"></span></tt></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-Q <span class="nt" style="color: #000080;"><var></span>NAME<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="html"><span class="nt" style="color: #000080;"><td><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>How to read the query sequences (the NAME is not</span>

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="html">case-sensitive):<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="html">Default         fasta</span>

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>0<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>fastx<span class="ni" style="color: #800080;">&quot;</span>    fasta or fastq: discard per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>1<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>sanger<span class="ni" style="color: #800080;">&quot;</span>   fastq-sanger</span>

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>fastq<span class="nt" style="color: #000080;"></tt></span> formats are described here:</span>

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<pre style="margin: 0;">-<span id="LC499" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>.  <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>fastq-ignore<span class="nt" style="color: #000080;"></span></tt></span> means that the</span>

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="html">quality data is ignored, so the results will be the same</span>

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<pre style="margin: 0;">-<span id="LC501" class="line" lang="html">as for <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>fasta<span class="nt" style="color: #000080;"></tt></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>For <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>fastq-sanger<span class="nt" style="color: #000080;"></span></tt></span>, last-train assumes the quality</span>

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="html">codes indicate substitution error probabilities, <span class="nt" style="color: #000080;"><em></span>not<span class="nt" style="color: #000080;"></em></span></span>

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="html">insertion or deletion error probabilities.  If this</span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>.  last-train assumes the per-base</span>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="html">quality codes indicate substitution error probabilities,</span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="html"><span class="nt" style="color: #000080;"><em></span>not<span class="nt" style="color: #000080;"></em></span> insertion or deletion error probabilities.  If this</span>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="html">assumption is dubious (e.g. for data with many insertion</span>

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<pre style="margin: 0;">-<span id="LC506" class="line" lang="html">or deletion errors), it may be better to <span class="idiff left right">us</span>e</span>

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">fastq-ignore</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff">.  For </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">fastq-sanger</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right">, last-train finds</span></span>

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<td class="diff-line-num new_line old" data-linenumber="507" 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="LC508" class="line" lang="html"><span class="idiff left right">the rates of substitutions not explained by the quality</span></span>

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<pre style="margin: 0;">-<span id="LC509" class="line" lang="html"><span class="idiff left right">data </span>(ideally, real substitutions as opposed to errors).<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="html">or deletion errors), it may be better to <span class="idiff left right">discard th</span>e</span>

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="html"><span class="idiff left">quality data.  For </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">fastq-sanger</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right">, last-train finds the</span></span>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="html"><span class="idiff left right">rates of substitutions not explained by the quality data</span></span>

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="html">(ideally, real substitutions as opposed to errors).<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span>If specified, this parameter is written in last-train's</span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="html">output, so it will override lastal's default.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="html"><span class="nt" style="color: #000080;"></td></tr></span></span>

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<br>

</li>

<li id="03dd50d6a64beb7787e3bcc9eb6da79c482759d5">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#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">@@ -114,23 +114,22 @@ Alignment options</td>

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<pre style="margin: 0;"> <span id="LC114" 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="LC115" class="line" lang="plaintext">             output, so it will override lastal's default.</span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">  -Q NUMBER  How to read the query sequences.  By default, they must</span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">             be in ``fasta`` format.  ``-Q0`` means ``fasta`` or</span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">             ``fastq-ignore``.  ``-Q1`` means ``fastq-sanger``.</span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">  -Q NAME    How to read the query sequences (the NAME is not</span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">             case-sensitive)::</span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">             The ``fastq`` formats are described here:</span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">             `<lastal.html>`_.  ``fastq-ignore`` means that the</span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">             quality data is ignored, so the results will be the same</span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">             as for ``fasta``.</span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">               Default         fasta</span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">               "0", "fastx"    fasta or fastq: discard per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">               "1", "sanger"   fastq-sanger</span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">             For ``fastq-sanger``, last-train assumes the quality</span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">             codes indicate substitution error probabilities, *not*</span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">             insertion or deletion error probabilities.  If this</span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">             The ``fastq`` formats are described here:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">             `<lastal.html>`_.  last-train assumes the per-base</span>

</pre>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">             quality codes indicate substitution error probabilities,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">             *not* insertion or deletion error probabilities.  If this</span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext">             assumption is dubious (e.g. for data with many insertion</span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">             or deletion errors), it may be better to <span class="idiff left right">us</span>e</span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">             <span class="idiff left right">``fastq-ignore``.  For ``fastq-sanger``, last-train finds</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">             <span class="idiff left right">the rates of substitutions not explained by the quality</span></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">             <span class="idiff left right">data </span>(ideally, real substitutions as opposed to errors).</span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">             or deletion errors), it may be better to <span class="idiff left right">discard th</span>e</span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">             <span class="idiff left right">quality data.  For ``fastq-sanger``, last-train finds the</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">             <span class="idiff left right">rates of substitutions not explained by the quality data</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">             (ideally, real substitutions as opposed to errors).</span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC134" 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="LC135" class="line" lang="plaintext">             output, so it will override lastal's default.</span>

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<li id="1d2db1d5c1263541e178e5c6d1a664dcaee43e97">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#1d2db1d5c1263541e178e5c6d1a664dcaee43e97"><strong>doc/lastal.html</strong></a>

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<pre style="margin: 0;"> <span id="LC844" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

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<pre style="margin: 0;"> <span id="LC846" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new_line old" data-linenumber="847" 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="LC847" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-Q <span class="nt" style="color: #000080;"><var></span>NUMBER<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<td class="diff-line-num new_line old" data-linenumber="847" 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="LC848" class="line" lang="html"><span class="nt" style="color: #000080;"><td><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Specify how to read the query sequences:<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC847" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-Q <span class="nt" style="color: #000080;"><var></span>NAME<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<td class="diff-line-num new new_line" data-linenumber="848" style="width: 35px; color: rgba(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="LC848" class="line" lang="html"><span class="nt" style="color: #000080;"><td><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Specify how to read the query sequences (the NAME is not</span>

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<pre style="margin: 0;">+<span id="LC849" class="line" lang="html">case-sensitive):<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC850" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC850" class="line" lang="html">Default    fasta</span>

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851

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<pre style="margin: 0;">-<span id="LC851" class="line" lang="html">   0       fasta or fastq-ignore</span>

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852

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<pre style="margin: 0;">-<span id="LC852" class="line" lang="html">   1       fastq-sanger</span>

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853

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<pre style="margin: 0;">-<span id="LC853" class="line" lang="html">   2       fastq-solexa</span>

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854

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<pre style="margin: 0;">-<span id="LC854" class="line" lang="html">   3       fastq-illumina</span>

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855

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<pre style="margin: 0;">-<span id="LC855" class="line" lang="html">   4       prb</span>

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856

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<pre style="margin: 0;">-<span id="LC856" class="line" lang="html">   5       PSSM</span>

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="html">Default           fasta</span>

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<td class="diff-line-num new old_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">

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852

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>0<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>fastx<span class="ni" style="color: #800080;">&quot;</span>      fasta or fastq: discard per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>keep<span class="ni" style="color: #800080;">&quot;</span>            fasta or fastq: keep but ignore per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>1<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>sanger<span class="ni" style="color: #800080;">&quot;</span>     fastq-sanger</span>

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<pre style="margin: 0;">+<span id="LC855" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>2<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>solexa<span class="ni" style="color: #800080;">&quot;</span>     fastq-solexa</span>

</pre>

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856

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>3<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>illumina<span class="ni" style="color: #800080;">&quot;</span>   fastq-illumina</span>

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857

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>4<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>prb<span class="ni" style="color: #800080;">&quot;</span>        prb</span>

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<pre style="margin: 0;">+<span id="LC858" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>5<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>pssm<span class="ni" style="color: #800080;">&quot;</span>       PSSM</span>

</pre>

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859

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<pre style="margin: 0;"> <span id="LC859" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="html"><span class="nt" style="color: #000080;"><p><em></span>Warning<span class="nt" style="color: #000080;"></em></span>: Illumina data is not necessarily in fastq-illumina</span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC861" class="line" lang="html">format; it is often in fastq-sanger format.<span class="nt" style="color: #000080;"></p></span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="867" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -867,12 +869,10 @@ TTTTTTTTGCCTCGGGCCTGAGTTCTTAGCCGCG</td>

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<pre style="margin: 0;"> <span id="LC869" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="ni" style="color: #800080;">&quot;</span>+<span class="ni" style="color: #800080;">&quot;</span> may be followed by text (ignored).  The symbols below</span>

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<pre style="margin: 0;"> <span id="LC870" class="line" lang="html">the <span class="ni" style="color: #800080;">&quot;</span>+<span class="ni" style="color: #800080;">&quot;</span> are quality codes, one per sequence letter.  The</span>

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<pre style="margin: 0;"> <span id="LC871" class="line" lang="html">sequence and quality codes may wrap onto more than one line.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC870" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>fastq-ignore means that the quality codes are ignored.  For the</span>

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<pre style="margin: 0;">-<span id="LC871" class="line" lang="html">other fastq variants, lastal assumes the quality codes indicate</span>

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<pre style="margin: 0;">-<span id="LC872" class="line" lang="html">substitution error probabilities, <span class="nt" style="color: #000080;"><em></span>not<span class="nt" style="color: #000080;"></em></span> insertion or deletion</span>

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<pre style="margin: 0;">-<span id="LC873" 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="LC874" 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="LC875" class="line" lang="html">to use fastq-ignore.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC872" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>lastal assumes the quality codes indicate substitution error</span>

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<pre style="margin: 0;">+<span id="LC873" class="line" lang="html">probabilities, <span class="nt" style="color: #000080;"><em></span>not<span class="nt" style="color: #000080;"></em></span> insertion or deletion error probabilities.</span>

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="html">If this assumption is dubious (e.g. for data with many insertion</span>

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="html">or deletion errors), it may be better to discard or ignore them.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC876" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>For fastq-sanger, quality scores are obtained by subtracting 33</span>

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<pre style="margin: 0;"> <span id="LC877" 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="LC878" class="line" lang="html">and fastq-illumina, they are obtained by subtracting 64.<span class="nt" style="color: #000080;"></p></span></span>

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</li>

<li id="30d864ed8925787ee70643db49814772753a5f2c">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#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">@@ -474,16 +474,18 @@ Miscellaneous options</td>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="plaintext">      * The count of delete opens (= count of delete closes).</span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="plaintext">      * The count of insert opens (= count of insert closes).</span>

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

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<pre style="margin: 0;">-<span id="LC477" class="line" lang="plaintext">  -Q NUMBER</span>

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<pre style="margin: 0;">-<span id="LC478" class="line" lang="plaintext">      Specify how to read the query sequences::</span>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC480" class="line" lang="plaintext">        Default    fasta</span>

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<pre style="margin: 0;">-<span id="LC481" class="line" lang="plaintext">           0       fasta or fastq-ignore</span>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="plaintext">           1       fastq-sanger</span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="plaintext">           2       fastq-solexa</span>

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<pre style="margin: 0;">-<span id="LC484" class="line" lang="plaintext">           3       fastq-illumina</span>

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="plaintext">           4       prb</span>

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<pre style="margin: 0;">-<span id="LC486" class="line" lang="plaintext">           5       PSSM</span>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">  -Q NAME</span>

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext">      Specify how to read the query sequences (the NAME is not</span>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext">      case-sensitive)::</span>

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">        Default           fasta</span>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">        "0", "fastx"      fasta or fastq: discard per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">        "keep"            fasta or fastq: keep but ignore per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">        "1", "sanger"     fastq-sanger</span>

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">        "2", "solexa"     fastq-solexa</span>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext">        "3", "illumina"   fastq-illumina</span>

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">        "4", "prb"        prb</span>

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext">        "5", "pssm"       PSSM</span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="plaintext">      *Warning*: Illumina data is not necessarily in fastq-illumina</span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="plaintext">      format; it is often in fastq-sanger format.</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">@@ -499,12 +501,10 @@ Miscellaneous options</td>

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext">      the "+" are quality codes, one per sequence letter.  The</span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="plaintext">      sequence and quality codes may wrap onto more than one line.</span>

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line old" data-linenumber="504" 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="plaintext">      fastq-ignore means that the quality codes are ignored.  For the</span>

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="plaintext">      other fastq variants, lastal assumes the quality codes indicate</span>

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="plaintext">      substitution error probabilities, *not* insertion or deletion</span>

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<pre style="margin: 0;">-<span id="LC505" class="line" lang="plaintext">      error probabilities.  If this assumption is dubious (e.g. for</span>

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<td class="diff-line-num new_line old" data-linenumber="504" 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="LC506" class="line" lang="plaintext">      data with many insertion or deletion errors), it may be better</span>

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="plaintext">      to use fastq-ignore.</span>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext">      lastal assumes the quality codes indicate substitution error</span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext">      probabilities, *not* insertion or deletion error probabilities.</span>

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext">      If this assumption is dubious (e.g. for data with many insertion</span>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext">      or deletion errors), it may be better to discard or ignore them.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="plaintext">      For fastq-sanger, quality scores are obtained by subtracting 33</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="510" style="width: 35px; color: rgba(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="LC510" class="line" lang="plaintext">      from the ASCII values of the quality codes.  For fastq-solexa</span>

</pre>

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<br>

</li>

<li id="0bf0c2b9afb77a75953faf3468b6707da7098872">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#0bf0c2b9afb77a75953faf3468b6707da7098872"><strong>doc/lastdb.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="diff-line-num unfold js-unfold old_line" data-linenumber="456" style="width: 35px; color: rgba(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="456" style="width: 35px; color: rgba(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">@@ -456,11 +456,18 @@ lastdb will refuse to process any single sequence longer than</td>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="html">about 4 billion.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="html"><span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-Q <span class="nt" style="color: #000080;"><var></span>NUMBER<span class="nt" style="color: #000080;"></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: #000080;"><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: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-Q <span class="nt" style="color: #000080;"><var></span>NAME<span class="nt" style="color: #000080;"></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: #000080;"><td><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Specify how to read the sequences (the NAME is not case-sensitive):<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="html">Default           fasta</span>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>0<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>fastx<span class="ni" style="color: #800080;">&quot;</span>      fasta or fastq: discard per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>keep<span class="ni" style="color: #800080;">&quot;</span>            fasta or fastq: keep but ignore per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>1<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>sanger<span class="ni" style="color: #800080;">&quot;</span>     fastq-sanger</span>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>2<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>solexa<span class="ni" style="color: #800080;">&quot;</span>     fastq-solexa</span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="html"><span class="ni" style="color: #800080;">&quot;</span>3<span class="ni" style="color: #800080;">&quot;</span>, <span class="ni" style="color: #800080;">&quot;</span>illumina<span class="ni" style="color: #800080;">&quot;</span>   fastq-illumina</span>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span>The fastq formats are described in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="html"><span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-P <span class="nt" style="color: #000080;"><var></span>THREADS<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="html"><span class="nt" style="color: #000080;"><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/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#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">@@ -124,11 +124,17 @@ Advanced Options</td>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext">      lastdb will refuse to process any single sequence longer than</span>

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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 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="LC127" class="line" lang="plaintext">  -Q NAME</span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">      Specify how to read the sequences (the NAME is not case-sensitive)::</span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">        Default           fasta</span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">        "0", "fastx"      fasta or fastq: discard per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">        "keep"            fasta or fastq: keep but ignore per-base quality data</span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">        "1", "sanger"     fastq-sanger</span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">        "2", "solexa"     fastq-solexa</span>

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="plaintext">        "3", "illumina"   fastq-illumina</span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"></span>

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="plaintext">      The fastq formats are described in `<lastal.html>`_.</span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">  -P THREADS</span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">      Divide the work between this number of threads running in</span>

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<li id="a3473a36b447c7d33b488e9643dadb1f77a412f6">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#a3473a36b447c7d33b488e9643dadb1f77a412f6"><strong>doc/maf-convert.html</strong></a>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This script reads alignments in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://genome.ucsc.edu/FAQ/FAQformat.html#format5"</span><span class="nt" style="color: #000080;">></span>maf<span class="nt" style="color: #000080;"></a></span> format, and writes them in</span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="html">another format.  It can write them in these formats: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.ucsc.edu/goldenPath/help/axt.html"</span><span class="nt" style="color: #000080;">></span>axt<span class="nt" style="color: #000080;"></a></span>, blast,</span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="html">blasttab, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.ucsc.edu/goldenPath/help/chain.html"</span><span class="nt" style="color: #000080;">></span>chain<span class="nt" style="color: #000080;"></a></span>, html, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.ucsc.edu/FAQ/FAQformat.html#format2"</span><span class="nt" style="color: #000080;">></span>psl<span class="nt" style="color: #000080;"></a></span>, sam, tab.  You can use it like this:<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="html">blasttab, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.ucsc.edu/goldenPath/help/chain.html"</span><span class="nt" style="color: #000080;">></span>chain<span class="nt" style="color: #000080;"></a></span>, <span class="idiff left right">gff, </span>html, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.ucsc.edu/FAQ/FAQformat.html#format2"</span><span class="nt" style="color: #000080;">></span>psl<span class="nt" style="color: #000080;"></a></span>, sam, tab.  You can use it like this:<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="html">maf-convert psl my-alignments.maf <span class="ni" style="color: #800080;">&gt;</span> my-alignments.psl</span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="html"><span class="nt" style="color: #000080;"></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">@@ -350,9 +350,17 @@ nucleotides.  This affects psl format only (the first 4</td>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="html">columns).<span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-j <span class="nt" style="color: #000080;"><var></span>N<span class="nt" style="color: #000080;"></var></span></span>, <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--join=<span class="nt" style="color: #000080;"><var></span>N<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Join neighboring alignments if they are co-linear and</span>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="html">separated by at most N letters.  This affects psl format</span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="html">only.<span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Join alignments that are co-linear (align different parts of</span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="html">the same sequences and strands, with the parts being in the</span>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="html">same order in each sequence), are separated by at most N</span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="html">letters in each sequence, and are consecutive in the input.</span>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="html">This affects psl and gff formats only.<span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-J <span class="nt" style="color: #000080;"><var></span>N<span class="nt" style="color: #000080;"></var></span></span>, <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--Join=<span class="nt" style="color: #000080;"><var></span>N<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Join alignments that are co-linear, are separated by at most</span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="html">N letters in each sequence, and are nearest in each sequence.</span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="html">This affects psl and gff formats only, and reads the whole</span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="html">input into memory.<span class="nt" style="color: #000080;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-n<span class="nt" style="color: #000080;"></span></span>, <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--noheader<span class="nt" style="color: #000080;"></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Omit any header lines from the output.  This may be useful if</span>

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<br>

</li>

<li id="2ac8fe07ee85c38c0ea51f42223721b9dfabe8f8">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#2ac8fe07ee85c38c0ea51f42223721b9dfabe8f8"><strong>doc/maf-convert.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">@@ -3,7 +3,7 @@ maf-convert</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">This script reads alignments in maf_ format, and writes them in</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">another format.  It can write them in these formats: axt_, blast,</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">blasttab, chain_, html, psl_, sam, tab.  You can use it like this::</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">blasttab, chain_, <span class="idiff left right">gff, </span>html, psl_, sam, tab.  You can use it like this::</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">  maf-convert psl my-alignments.maf > my-alignments.psl</span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

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

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

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">  -j N, --join=N</span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">         Join neighboring alignments if they are co-linear and</span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">         separated by at most N letters.  This affects psl format</span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">         only.</span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">         Join alignments that are co-linear (align different parts of</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">         the same sequences and strands, with the parts being in the</span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">         same order in each sequence), are separated by at most N</span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">         letters in each sequence, and are consecutive in the input.</span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">         This affects psl and gff formats only.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">  -J N, --Join=N</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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

<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">         Join alignments that are co-linear, are separated by at most</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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

<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">         N letters in each sequence, and are nearest in each sequence.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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

<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">         This affects psl and gff formats only, and reads the whole</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">         input into memory.</span>

</pre>

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<td class="diff-line-num 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">

41

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">  -n, --noheader</span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">         Omit any header lines from the output.  This may be useful if</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8"><strong>scripts/last-dotplot</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 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="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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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Author: Martin C. Frith 2008</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="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># SPDX-License-Identifier: GPL-3.0-or-later</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_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="LC4" class="line" lang="python"></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="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Read pair-wise alignments in MAF or LAST tabular format: write an</span></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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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># "Oxford grid", a.k.a. dotplot.</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0"><strong>scripts/last-train</strong></a>

<hr>

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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="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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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright 2015 Martin C. Frith</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(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="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># SPDX-License-Identifier: GPL-3.0-or-later</span></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="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="LC4" class="line" lang="python"></span>

</pre>

</td>

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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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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># References:</span></span>

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5

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># [Fri19] How sequence alignment scores correspond to probability models,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="576" style="width: 35px; color: rgba(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="577" style="width: 35px; color: rgba(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">@@ -576,14 +577,14 @@ if __name__ == "__main__":</td>

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576

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<td class="diff-line-num new_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="p">.</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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<td class="diff-line-num old_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

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<td class="diff-line-num new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

578

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<pre style="margin: 0;"> <span id="LC578" 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;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Initial parameter options"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

578

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<td class="diff-line-num new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

579

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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</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="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SCORE"</span><span class="p">,</span></span>

</pre>

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579

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<td class="diff-line-num new_line old" data-linenumber="580" 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="LC579" 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;">"match score (default: 6 if Q><span class="idiff left right">0</span>, else 5)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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

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<pre style="margin: 0;">+<span id="LC580" 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;">"match score (default: 6 if Q><span class="idiff left right">=1</span>, else 5)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="580" style="width: 35px; color: rgba(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="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</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;">"COST"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="581" 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">

581

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<td class="diff-line-num new_line old" data-linenumber="582" 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="LC581" 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;">"mismatch cost (default: 18 if Q><span class="idiff left right">0</span>, else 5)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="582" style="width: 35px; color: rgba(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="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

582

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<pre style="margin: 0;">+<span id="LC582" 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;">"mismatch cost (default: 18 if Q><span class="idiff left right">=1</span>, else 5)"</span><span class="p">)</span></span>

</pre>

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582

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<td class="diff-line-num new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</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;">"NAME"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"match/mismatch score matrix"</span><span class="p">)</span></span>

</pre>

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583

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<td class="diff-line-num new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-a"</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;">"COST"</span><span class="p">,</span></span>

</pre>

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584

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<td class="diff-line-num new_line old" data-linenumber="585" 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="LC584" 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;">"gap existence cost (default: 21 if Q><span class="idiff left right">0</span>, else 15)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="585" style="width: 35px; color: rgba(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="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

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

<pre style="margin: 0;">+<span id="LC585" 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;">"gap existence cost (default: 21 if Q><span class="idiff left right">=1</span>, else 15)"</span><span class="p">)</span></span>

</pre>

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585

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<td class="diff-line-num new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

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

<pre style="margin: 0;"> <span id="LC586" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</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;">"COST"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new_line old" data-linenumber="587" 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="LC586" 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;">"gap extension cost (default: 9 if Q><span class="idiff left right">0</span>, else 3)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="587" style="width: 35px; color: rgba(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="LC587" 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;">"gap extension cost (default: 9 if Q><span class="idiff left right">=1</span>, else 3)"</span><span class="p">)</span></span>

</pre>

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587

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<td class="diff-line-num new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-A"</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;">"COST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"insertion existence cost"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<td class="diff-line-num new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

589

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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-B"</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;">"COST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"insertion extension cost"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

589

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<td class="diff-line-num new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="p">.</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="610" style="width: 35px; color: rgba(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="611" style="width: 35px; color: rgba(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">@@ -610,16 +611,15 @@ if __name__ == "__main__":</td>

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610

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<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</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="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 class="s" style="color: #d14;">"N/X is ambiguous in: "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

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<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python">                  <span class="s" style="color: #d14;">"0=neither sequence, 1=reference, 2=query, 3=both "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python">                  <span class="s" style="color: #d14;">"(default=0)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="613" 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">

613

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<td class="diff-line-num new_line old" data-linenumber="614" 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="LC613" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</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 old old_line" data-linenumber="614" 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">

614

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<td class="diff-line-num new_line old" data-linenumber="614" 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="LC614" 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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<td class="diff-line-num old old_line" data-linenumber="615" 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">

615

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<td class="diff-line-num new_line old" data-linenumber="614" 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="LC615" 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 old_line" data-linenumber="616" style="width: 35px; color: rgba(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="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

614

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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="p">.</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;">"NAME"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="616" style="width: 35px; color: rgba(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="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

615

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

<pre style="margin: 0;">+<span id="LC615" 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: fastx, sanger (default=fasta)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

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<td class="diff-line-num new_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python">    <span class="n" style="color: #333;">op</span><span class="p">.</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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<td class="diff-line-num old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

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<td class="diff-line-num new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

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<pre style="margin: 0;"> <span id="LC617" 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="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

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<td class="diff-line-num new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

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

<pre style="margin: 0;"> <span id="LC618" 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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<td class="diff-line-num old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

619

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<td class="diff-line-num new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

619

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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python">        <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"I need a lastdb index and query sequences"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

</td>

<td class="diff-line-num new_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

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<pre style="margin: 0;"> <span id="LC620" 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;">opts</span><span class="p">.</span><span class="n" style="color: #333;">sample_number</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</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;">2</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>

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621

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621

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python">        <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"sorry, can't use stdin when --sample-number=0"</span><span class="p">)</span></span>

</pre>

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622

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<td class="diff-line-num new_line old" data-linenumber="622" 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="LC622" 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;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;"><span class="idiff left">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"0"</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="623" style="width: 35px; color: rgba(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="LC622" 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;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">in</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"0"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"fastx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"keep"</span></span><span class="p"><span class="idiff right">)</span>):</span></span>

</pre>

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623

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<pre style="margin: 0;"> <span id="LC623" 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;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5"</span></span>

</pre>

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624

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<pre style="margin: 0;"> <span id="LC624" 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;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5"</span></span>

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625

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<td class="diff-line-num new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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<pre style="margin: 0;"> <span id="LC625" 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;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"15"</span></span>

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<br>

</li>

<li id="0c8579b85a61ba3e2feb036884e3e6d6da75cf0e">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#0c8579b85a61ba3e2feb036884e3e6d6da75cf0e"><strong>scripts/maf-convert</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="html">#! /usr/bin/env python</span>

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2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="html"># Copyright 2010, 2011, 2013, 2014 Martin C. Frith</span>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="html"># <span class="idiff left right">Read MAF-format alignments: write them in other formats.</span></span>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="html"># <span class="idiff left right">SPDX-License-Identifier: GPL-3.0-or-later</span></span>

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4

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<td class="diff-line-num new_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="LC4" class="line" lang="html"># Seems to work with Python 2.x, x>=6</span>

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5

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="html"></span>

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6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="html"># By "MAF" we mean "multiple alignment format" described in the UCSC</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,8 +9,15 @@</td>

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9

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="html">from __future__ import print_function</span>

</pre>

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10

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10

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

</pre>

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11

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="html">from itertools import *</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">

</td>

<td class="diff-line-num new new_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">

12

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

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

</td>

<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">

13

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="html">import functools</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">

12

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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="html">import gzip</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

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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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<pre style="margin: 0;">-<span id="LC13" class="line" lang="html">import math, optparse, os, signal, sys</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">

</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">

15

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="html">import math</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="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">

16

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="html">import operator</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="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="html">import optparse</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="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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="html">import os</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="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="html">import signal</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="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="html">import sys</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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

15

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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">try:</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="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">    from future_builtins import map, zip</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(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">@@ -161,6 +168,41 @@ def mafGroupInput(opts, lines):</td>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="html">        <span class="na" style="color: #008080;">fixOrder</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="html">        <span class="na" style="color: #008080;">yield</span> <span class="na" style="color: #008080;">x</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

170

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">linkedMafBegSortKey</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">sequenceNumber</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">mafAndLinks</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="html">    <span class="na" style="color: #008080;">return</span> <span class="na" style="color: #008080;">operator</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">itemgetter</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">2</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">4</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)(</span><span class="na" style="color: #008080;">mafAndLinks</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">][</span><span class="na" style="color: #008080;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">][</span><span class="na" style="color: #008080;">sequenceNumber</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="html"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="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="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">colinearMafInput</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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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="html">    <span class="na" style="color: #008080;">mafs = </span><span class="s" style="color: #d14;">list(mafInput(opts,</span> <span class="na" style="color: #008080;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>

</pre>

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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="html">    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">not</span> <span class="na" style="color: #008080;">mafs:</span></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">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="html">        <span class="na" style="color: #008080;">return</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="html">    <span class="na" style="color: #008080;">numOfSeqs = </span><span class="s" style="color: #d14;">max(len(maf[1])</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">maf</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">mafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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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="html">    <span class="na" style="color: #008080;">linkedMafs = </span><span class="s" style="color: #d14;">[(maf,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">None</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">numOfSeqs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">maf</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">mafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></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="html">    <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">s</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">range</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">numOfSeqs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></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="html">        <span class="na" style="color: #008080;">begFunc = </span><span class="s" style="color: #d14;">functools.partial(linkedMafBegSortKey,</span> <span class="na" style="color: #008080;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(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="LC182" class="line" lang="html">        <span class="na" style="color: #008080;">linkedMafs.sort(key=</span><span class="s" style="color: #d14;">begFunc)</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="html">        <span class="na" style="color: #008080;">maxEnd = </span><span class="s" style="color: #d14;">""</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"+",</span> <span class="na" style="color: #008080;">0</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="html">        <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">j</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">range</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">len</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">linkedMafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="html">            <span class="na" style="color: #008080;">xMaf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">xLinks = </span><span class="s" style="color: #d14;">linkedMafs[j</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="html">            <span class="na" style="color: #008080;">yMaf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">yLinks = </span><span class="s" style="color: #d14;">linkedMafs[j]</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="html">            <span class="na" style="color: #008080;">x = </span><span class="s" style="color: #d14;">xMaf[1][s]</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="html">            <span class="na" style="color: #008080;">y = </span><span class="s" style="color: #d14;">yMaf[1][s]</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="html">            <span class="na" style="color: #008080;">newEnd = </span><span class="s" style="color: #d14;">x[0],</span> <span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">2</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">],</span> <span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">5</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="html">            <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">newEnd</span> <span class="nt" style="color: #000080;">></span> maxEnd:</span>

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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="html">                maxEnd = newEnd</span>

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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">

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="html">                if (x[:4] == y[:4] and 0 <span class="nt" style="color: #000080;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="na" style="color: #008080;">y</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">4</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">5</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><=</span> <span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">Join</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="html">                    <span class="na" style="color: #008080;">k = </span><span class="s" style="color: #d14;">j</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="na" style="color: #008080;">1</span></span>

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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="html">                    <span class="na" style="color: #008080;">yBeg = </span><span class="s" style="color: #d14;">y[0],</span> <span class="na" style="color: #008080;">y</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">2</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">],</span> <span class="na" style="color: #008080;">y</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">4</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="html">                    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">k =</span><span class="s" style="color: #d14;">=</span> <span class="na" style="color: #008080;">len</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">linkedMafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="na" style="color: #008080;">or</span> <span class="na" style="color: #008080;">yBeg</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="na" style="color: #008080;">begFunc</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">linkedMafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">k</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">])</span><span class="na" style="color: #008080;">:</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="html">                        <span class="na" style="color: #008080;">yLinks[s] = </span><span class="s" style="color: #d14;">xMaf</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="html">    <span class="na" style="color: #008080;">colinearMafs = </span><span class="s" style="color: #d14;">[]</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="html">    <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">maf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">links</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">linkedMafs:</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="html">        <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">colinearMafs:</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="html">            <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">any</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">i</span> <span class="na" style="color: #008080;">is</span> <span class="na" style="color: #008080;">not</span> <span class="na" style="color: #008080;">colinearMafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">-1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">i</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">links</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="html">                <span class="na" style="color: #008080;">yield</span> <span class="na" style="color: #008080;">colinearMafs</span></span>

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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="html">                <span class="na" style="color: #008080;">colinearMafs = </span><span class="s" style="color: #d14;">[]</span></span>

</pre>

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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="html">        <span class="na" style="color: #008080;">colinearMafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">maf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">+<span id="LC204" class="line" lang="html">    <span class="na" style="color: #008080;">yield</span> <span class="na" style="color: #008080;">colinearMafs</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="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="html"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<td class="diff-line-num new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

206

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="html"><span class="na" style="color: #008080;">#####</span> <span class="na" style="color: #008080;">Routines</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">converting</span> <span class="na" style="color: #008080;">to</span> <span class="na" style="color: #008080;">AXT</span> <span class="na" style="color: #008080;">format:</span> <span class="na" style="color: #008080;">#####</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<td class="diff-line-num new_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">

207

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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<td class="diff-line-num new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="html"><span class="na" style="color: #008080;">axtCounter = </span><span class="s" style="color: #d14;">count()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(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="227" style="width: 35px; color: rgba(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">@@ -185,7 +227,7 @@ def writeAxt(maf):</td>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(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="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

227

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="html">    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">score:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(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="228" style="width: 35px; color: rgba(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="LC228" class="line" lang="html">        <span class="na" style="color: #008080;">outWords</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">score</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" 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="230" 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="LC188" class="line" lang="html">    <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(<span class="idiff left">"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">".</span></span><span class="na" style="color: #008080;"><span class="idiff">join</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">(</span></span><span class="na" style="color: #008080;"><span class="idiff">outWords</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="230" style="width: 35px; color: rgba(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="LC230" class="line" lang="html">    <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;"><span class="idiff left right">*outWords</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(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="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

231

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="html">    <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">i</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">sLines:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="html">        <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">6</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(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="233" style="width: 35px; color: rgba(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="LC233" class="line" lang="html">    <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">()</span>  <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">print</span> <span class="na" style="color: #008080;">a</span> <span class="na" style="color: #008080;">blank</span> <span class="na" style="color: #008080;">line</span> <span class="na" style="color: #008080;">at</span> <span class="na" style="color: #008080;">the</span> <span class="na" style="color: #008080;">end</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="285" style="width: 35px; color: rgba(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 +285,7 @@ def writeChain(maf):</td>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(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="LC285" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(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="286" style="width: 35px; color: rgba(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="LC286" class="line" lang="html">    <span class="na" style="color: #008080;">outWords</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">str</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">next</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">axtCounter</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="na" style="color: #008080;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="287" style="width: 35px; color: rgba(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="LC287" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="html">    <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(<span class="idiff left">"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">".</span></span><span class="na" style="color: #008080;"><span class="idiff">join</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">(</span></span><span class="na" style="color: #008080;"><span class="idiff">outWords</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(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="LC288" class="line" lang="html">    <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;"><span class="idiff left right">*outWords</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="html"></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="LC290" class="line" lang="html">    <span class="na" style="color: #008080;">letterSizes = </span><span class="s" style="color: #d14;">[i[3]</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">i</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">sLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="html">    <span class="na" style="color: #008080;">rows = </span><span class="s" style="color: #d14;">[i[6]</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">i</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">sLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="360" style="width: 35px; color: rgba(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">@@ -360,15 +402,16 @@ def writePsl(opts, mafs):</td>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="html">    blockCount = len(blocks)</span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="html">    blockSizes, blockStartsA, blockStartsB = map(pslCommaString, zip(*blocks))</span>

</pre>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="html">    outWords = (matches, mismatches, repMatches, nCount,</span>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="html">                numInsertB, baseInsertB, numInsertA, baseInsertA, strand,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="html">                seqNameB, seqLenB, begB, endB, seqNameA, seqLenA, begA, endA,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="html">                blockCount, blockSizes, blockStartsB, blockStartsA)</span>

</pre>

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="368" 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="LC368" class="line" lang="html">    print("\t".join(map(str, outWords)))</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="369" style="width: 35px; color: rgba(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="405" style="width: 35px; color: rgba(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="LC405" class="line" lang="html">    print(matches, mismatches, repMatches, nCount,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(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="LC406" class="line" lang="html">          numInsertB, baseInsertB, numInsertA, baseInsertA, strand,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(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="LC407" class="line" lang="html">          seqNameB, seqLenB, begB, endB, seqNameA, seqLenA, begA, endA,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(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="LC408" class="line" lang="html">          blockCount, blockSizes, blockStartsB, blockStartsA, sep="\t")</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="409" style="width: 35px; color: rgba(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="LC409" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

370

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<td class="diff-line-num new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

410

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="html">def mafConvertToPsl(opts, lines):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="371" 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">

371

</td>

<td class="diff-line-num new_line old" data-linenumber="411" 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="LC371" class="line" lang="html">    if opts.join:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="372" style="width: 35px; color: rgba(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="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

411

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="html">    if opts.Join:</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="372" style="width: 35px; color: rgba(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="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

412

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="html">        for i in colinearMafInput(opts, lines):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="372" style="width: 35px; color: rgba(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="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

413

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="html">            writePsl(opts, i)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="372" style="width: 35px; color: rgba(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="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

414

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="html">    elif opts.join:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

372

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<td class="diff-line-num new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

415

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="html">        for i in mafGroupInput(opts, lines):</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

373

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<td class="diff-line-num new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

416

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

<pre style="margin: 0;"> <span id="LC416" class="line" lang="html">            writePsl(opts, i)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

374

</td>

<td class="diff-line-num new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

417

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="html">    else:</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="679" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -679,8 +722,8 @@ def writeBlastTab(opts, maf):</td>

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<td class="diff-line-num old_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

679

</td>

<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC722" class="line" lang="html">    mismatches = alnSize - matches - rowA.count("-") - rowB.count("-")</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

680

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<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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<pre style="margin: 0;"> <span id="LC723" class="line" lang="html">    gapOpens = gapRunCount(rowA) + gapRunCount(rowB)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

681

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<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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<pre style="margin: 0;"> <span id="LC724" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="682" 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">

682

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<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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<pre style="margin: 0;">-<span id="LC682" class="line" lang="html">    out = [seqNameB, seqNameA, matchPercent, <span class="idiff left right">str(alnSize), str(mismatches)</span>,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="683" 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">

683

</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">

</td>

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<pre style="margin: 0;">-<span id="LC683" class="line" lang="html">           <span class="idiff left right">str(gapOpens)</span>, begB, endB, begA, endA]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="684" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC725" class="line" lang="html">    out = [seqNameB, seqNameA, matchPercent, <span class="idiff left right">alnSize, mismatches</span>,</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="684" style="width: 35px; color: rgba(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="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

726

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

<pre style="margin: 0;">+<span id="LC726" class="line" lang="html">           <span class="idiff left right">gapOpens</span>, begB, endB, begA, endA]</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

684

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<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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC727" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

685

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC728" class="line" lang="html">    score, evalue = scoreAndEvalue(aLine)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

686

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<td class="diff-line-num new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

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<pre style="margin: 0;"> <span id="LC729" class="line" lang="html">    if evalue:</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="689" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -689,12 +732,79 @@ def writeBlastTab(opts, maf):</td>

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<td class="diff-line-num old_line" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

689

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

<pre style="margin: 0;"> <span id="LC732" class="line" lang="html">            bitScore = opts.bitScoreA * float(score) - opts.bitScoreB</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

690

</td>

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

<pre style="margin: 0;"> <span id="LC733" class="line" lang="html">            out.append("%.3g" % bitScore)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

691

</td>

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

<pre style="margin: 0;"> <span id="LC734" class="line" lang="html"></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="692" 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">

692

</td>

<td class="diff-line-num new_line old" data-linenumber="735" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC692" class="line" lang="html">    print(<span class="idiff left right">"\t".join(out)</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="693" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC735" class="line" lang="html">    print(<span class="idiff left right">*out, sep="\t"</span>)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

</td>

<td class="diff-line-num new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

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

<pre style="margin: 0;"> <span id="LC736" class="line" lang="html"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

</td>

<td class="diff-line-num new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

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

<pre style="margin: 0;"> <span id="LC737" class="line" lang="html">def mafConvertToBlastTab(opts, lines):</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

695

</td>

<td class="diff-line-num new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

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

<pre style="margin: 0;"> <span id="LC738" class="line" lang="html">    for maf in mafInput(opts, lines):</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

</td>

<td class="diff-line-num new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

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

<pre style="margin: 0;"> <span id="LC739" class="line" lang="html">        writeBlastTab(opts, maf)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

697

</td>

<td class="diff-line-num new_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

</td>

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

<pre style="margin: 0;"> <span id="LC740" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC741" class="line" lang="html">##### Routines for converting to GFF format: #####</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="698" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC742" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC743" class="line" lang="html">def writeGffHeader():</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="698" style="width: 35px; color: rgba(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="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">

744

</td>

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

<pre style="margin: 0;">+<span id="LC744" class="line" lang="html">    print("##gff-version 3")</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="698" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC745" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC746" class="line" lang="html">def gffFromMaf(maf):</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="698" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC747" class="line" lang="html">    aLine, sLines, qLines, pLines = maf</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="698" style="width: 35px; color: rgba(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="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">

748

</td>

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

<pre style="margin: 0;">+<span id="LC748" class="line" lang="html">    fieldsA, fieldsB = pairOrDie(sLines, "GFF")</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="698" style="width: 35px; color: rgba(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="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

</td>

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

<pre style="margin: 0;">+<span id="LC749" class="line" lang="html">    seqNameA, seqLenA, strandA, letterSizeA, begA, endA, rowA = fieldsA</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="698" style="width: 35px; color: rgba(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="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

</td>

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

<pre style="margin: 0;">+<span id="LC750" class="line" lang="html">    seqNameB, seqLenB, strandB, letterSizeB, begB, endB, rowB = fieldsB</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="698" style="width: 35px; color: rgba(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="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

751

</td>

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

<pre style="margin: 0;">+<span id="LC751" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

</td>

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

<pre style="margin: 0;">+<span id="LC752" class="line" lang="html">    score = "."</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="698" style="width: 35px; color: rgba(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="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

</td>

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

<pre style="margin: 0;">+<span id="LC753" class="line" lang="html">    for i in aLine.split():</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="698" style="width: 35px; color: rgba(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="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

754

</td>

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

<pre style="margin: 0;">+<span id="LC754" class="line" lang="html">        if i.startswith("score="):</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="698" style="width: 35px; color: rgba(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="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

755

</td>

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

<pre style="margin: 0;">+<span id="LC755" class="line" lang="html">            score = i[6:]</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="698" style="width: 35px; color: rgba(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="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

</td>

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

<pre style="margin: 0;">+<span id="LC756" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

757

</td>

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

<pre style="margin: 0;">+<span id="LC757" class="line" lang="html">    if strandA == "-":</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="698" style="width: 35px; color: rgba(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="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">

758

</td>

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

<pre style="margin: 0;">+<span id="LC758" class="line" lang="html">        begA, endA = seqLenA - endA, seqLenA - begA</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="698" style="width: 35px; color: rgba(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="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

759

</td>

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

<pre style="margin: 0;">+<span id="LC759" class="line" lang="html">    if strandB == "-":</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="698" style="width: 35px; color: rgba(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="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

760

</td>

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

<pre style="margin: 0;">+<span id="LC760" class="line" lang="html">        begB, endB = seqLenB - endB, seqLenB - begB</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="698" style="width: 35px; color: rgba(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="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">

761

</td>

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

<pre style="margin: 0;">+<span id="LC761" class="line" lang="html">    begA += 1</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="698" style="width: 35px; color: rgba(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="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

</td>

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

<pre style="margin: 0;">+<span id="LC762" class="line" lang="html">    begB += 1</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="698" style="width: 35px; color: rgba(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="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

763

</td>

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

<pre style="margin: 0;">+<span id="LC763" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

764

</td>

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

<pre style="margin: 0;">+<span id="LC764" class="line" lang="html">    strand = "+" if strandA == strandB else "-"</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="698" style="width: 35px; color: rgba(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="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

765

</td>

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

<pre style="margin: 0;">+<span id="LC765" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

766

</td>

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

<pre style="margin: 0;">+<span id="LC766" class="line" lang="html">    return seqNameA, begA, endA, strand, score, seqNameB, begB, endB</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="698" style="width: 35px; color: rgba(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="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

767

</td>

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

<pre style="margin: 0;">+<span id="LC767" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

768

</td>

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

<pre style="margin: 0;">+<span id="LC768" class="line" lang="html">def writeOneGff(gff, typeOfThing, parentId):</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="698" style="width: 35px; color: rgba(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="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">

769

</td>

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

<pre style="margin: 0;">+<span id="LC769" class="line" lang="html">    seqNameA, begA, endA, strand, score, seqNameB, begB, endB = gff</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="698" style="width: 35px; color: rgba(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="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

770

</td>

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

<pre style="margin: 0;">+<span id="LC770" class="line" lang="html">    target = "Target={0} {1} {2}".format(seqNameB, begB, endB)</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="698" style="width: 35px; color: rgba(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="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

771

</td>

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

<pre style="margin: 0;">+<span id="LC771" class="line" lang="html">    name = "Name={0}:{1}-{2}".format(seqNameB, begB, endB)</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="698" style="width: 35px; color: rgba(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="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">

772

</td>

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

<pre style="margin: 0;">+<span id="LC772" class="line" lang="html">    attributes = [target, name]</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="698" style="width: 35px; color: rgba(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">

773

</td>

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

<pre style="margin: 0;">+<span id="LC773" class="line" lang="html">    if parentId:</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="698" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC774" class="line" lang="html">        attributes.append("Parent=" + parentId)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC775" class="line" lang="html">    print(seqNameA, "maf-convert", typeOfThing, begA, endA, score, strand, ".",</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC776" class="line" lang="html">          ";".join(attributes), sep="\t")</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="698" style="width: 35px; color: rgba(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="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">

777

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

<pre style="margin: 0;">+<span id="LC777" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC778" class="line" lang="html">def writeGffGroup(qryNameCounts, mafs):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC779" class="line" lang="html">    gffs = [gffFromMaf(i) for i in mafs]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">+<span id="LC780" class="line" lang="html">    seqNameA, begA, endA, strand, score, seqNameB, begB, endB = gffs[0]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="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

</td>

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

<pre style="margin: 0;">+<span id="LC781" class="line" lang="html">    endA = gffs[-1][2]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="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

</td>

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

<pre style="margin: 0;">+<span id="LC782" class="line" lang="html">    if strand == "+":</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

783

</td>

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

<pre style="margin: 0;">+<span id="LC783" class="line" lang="html">        endB = gffs[-1][7]</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="698" style="width: 35px; color: rgba(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="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

784

</td>

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<pre style="margin: 0;">+<span id="LC784" class="line" lang="html">    else:</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="698" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC785" class="line" lang="html">        begB = gffs[-1][6]</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="698" style="width: 35px; color: rgba(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="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

</td>

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

<pre style="margin: 0;">+<span id="LC786" class="line" lang="html">    qryNameCounts[seqNameB] += 1</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="698" style="width: 35px; color: rgba(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="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

</td>

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

<pre style="margin: 0;">+<span id="LC787" class="line" lang="html">    parentId = "{0}.{1}".format(seqNameB, qryNameCounts[seqNameB])</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="698" style="width: 35px; color: rgba(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="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

788

</td>

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

<pre style="margin: 0;">+<span id="LC788" class="line" lang="html">    myId = "ID=" + parentId</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="698" style="width: 35px; color: rgba(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="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">

789

</td>

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

<pre style="margin: 0;">+<span id="LC789" class="line" lang="html">    name = "Name={0}:{1}-{2}".format(seqNameB, begB, endB)</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="698" style="width: 35px; color: rgba(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="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

790

</td>

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

<pre style="margin: 0;">+<span id="LC790" class="line" lang="html">    attributes = [myId, name]</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="698" style="width: 35px; color: rgba(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="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

</td>

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

<pre style="margin: 0;">+<span id="LC791" class="line" lang="html">    print(seqNameA, "maf-convert", "match", begA, endA, ".", strand, ".",</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="698" style="width: 35px; color: rgba(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="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

792

</td>

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

<pre style="margin: 0;">+<span id="LC792" class="line" lang="html">          ";".join(attributes), sep="\t")</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="698" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC793" class="line" lang="html">    for i in gffs:</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="698" style="width: 35px; color: rgba(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="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

794

</td>

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<pre style="margin: 0;">+<span id="LC794" class="line" lang="html">        writeOneGff(i, "match_part", parentId)</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

795

</td>

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

<pre style="margin: 0;">+<span id="LC795" class="line" lang="html"></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="698" style="width: 35px; color: rgba(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="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

796

</td>

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

<pre style="margin: 0;">+<span id="LC796" class="line" lang="html">def mafConvertToGff(opts, lines):</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="698" style="width: 35px; color: rgba(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="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

</td>

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

<pre style="margin: 0;">+<span id="LC797" class="line" lang="html">    qryNameCounts = collections.defaultdict(int)</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="698" style="width: 35px; color: rgba(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="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

798

</td>

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

<pre style="margin: 0;">+<span id="LC798" class="line" lang="html">    if opts.Join:</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="698" style="width: 35px; color: rgba(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="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

799

</td>

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

<pre style="margin: 0;">+<span id="LC799" class="line" lang="html">        for i in colinearMafInput(opts, lines):</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="698" style="width: 35px; color: rgba(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="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

800

</td>

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

<pre style="margin: 0;">+<span id="LC800" class="line" lang="html">            writeGffGroup(qryNameCounts, i)</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="698" style="width: 35px; color: rgba(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="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

</td>

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

<pre style="margin: 0;">+<span id="LC801" class="line" lang="html">    elif opts.join:</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="698" style="width: 35px; color: rgba(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="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">

802

</td>

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

<pre style="margin: 0;">+<span id="LC802" class="line" lang="html">        for i in mafGroupInput(opts, lines):</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="698" style="width: 35px; color: rgba(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="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

803

</td>

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

<pre style="margin: 0;">+<span id="LC803" class="line" lang="html">            writeGffGroup(qryNameCounts, i)</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="698" style="width: 35px; color: rgba(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="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">

804

</td>

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

<pre style="margin: 0;">+<span id="LC804" class="line" lang="html">    else:</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="698" style="width: 35px; color: rgba(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="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

805

</td>

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

<pre style="margin: 0;">+<span id="LC805" class="line" lang="html">        for i in mafInput(opts, lines):</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="698" style="width: 35px; color: rgba(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="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

806

</td>

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

<pre style="margin: 0;">+<span id="LC806" class="line" lang="html">            writeOneGff(gffFromMaf(i), "match", None)</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="698" style="width: 35px; color: rgba(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="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

</td>

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

<pre style="margin: 0;">+<span id="LC807" class="line" lang="html"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

698

</td>

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

<pre style="margin: 0;"> <span id="LC808" class="line" lang="html">##### Routines for converting to HTML format: #####</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

</td>

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

<pre style="margin: 0;"> <span id="LC809" class="line" lang="html"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC810" class="line" lang="html">def writeHtmlHeader():</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="922" style="width: 35px; color: rgba(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">@@ -812,6 +922,8 @@ def mafConvertOneFile(opts, formatName, lines):</td>

</tr>

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

<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

922

</td>

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

<pre style="margin: 0;"> <span id="LC922" class="line" lang="html">        mafConvertToBlastTab(opts, lines)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

</td>

<td class="diff-line-num new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

</td>

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

<pre style="margin: 0;"> <span id="LC923" class="line" lang="html">    elif isFormat(formatName, "chain"):</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

924

</td>

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

<pre style="margin: 0;"> <span id="LC924" class="line" lang="html">        mafConvertToChain(opts, lines)</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="815" style="width: 35px; color: rgba(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="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

925

</td>

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

<pre style="margin: 0;">+<span id="LC925" class="line" lang="html">    elif isFormat(formatName, "gff"):</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="815" style="width: 35px; color: rgba(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="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

926

</td>

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

<pre style="margin: 0;">+<span id="LC926" class="line" lang="html">        mafConvertToGff(opts, lines)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

927

</td>

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

<pre style="margin: 0;"> <span id="LC927" class="line" lang="html">    elif isFormat(formatName, "html"):</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

928

</td>

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

<pre style="margin: 0;"> <span id="LC928" class="line" lang="html">        mafConvertToHtml(opts, lines)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

817

</td>

<td class="diff-line-num new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

929

</td>

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

<pre style="margin: 0;"> <span id="LC929" class="line" lang="html">    elif isFormat(formatName, "psl"):</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="832" style="width: 35px; color: rgba(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="944" style="width: 35px; color: rgba(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">@@ -832,6 +944,8 @@ def mafConvert(opts, args):</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

<td class="diff-line-num new_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

944

</td>

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

<pre style="margin: 0;"> <span id="LC944" class="line" lang="html">    opts.bitScoreB = None</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

</td>

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

<pre style="margin: 0;"> <span id="LC945" class="line" lang="html"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

</td>

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

<pre style="margin: 0;"> <span id="LC946" class="line" lang="html">    if not opts.noheader:</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="835" style="width: 35px; color: rgba(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="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

947

</td>

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

<pre style="margin: 0;">+<span id="LC947" class="line" lang="html">        if isFormat(formatName, "gff"):</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="835" style="width: 35px; color: rgba(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="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

948

</td>

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

<pre style="margin: 0;">+<span id="LC948" class="line" lang="html">            writeGffHeader()</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

949

</td>

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

<pre style="margin: 0;"> <span id="LC949" class="line" lang="html">        if isFormat(formatName, "html"):</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="diff-line-num new_line" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

950

</td>

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

<pre style="margin: 0;"> <span id="LC950" class="line" lang="html">            writeHtmlHeader()</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

<td class="diff-line-num new_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

951

</td>

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

<pre style="margin: 0;"> <span id="LC951" class="line" lang="html">        if isFormat(formatName, "sam"):</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="859" style="width: 35px; color: rgba(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="973" style="width: 35px; color: rgba(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">@@ -859,6 +973,7 @@ if __name__ == "__main__":</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

859

</td>

<td class="diff-line-num new_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

973

</td>

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

<pre style="margin: 0;"> <span id="LC973" class="line" lang="html">  %prog blast mafFile(s)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

</td>

<td class="diff-line-num new_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

974

</td>

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

<pre style="margin: 0;"> <span id="LC974" class="line" lang="html">  %prog blasttab mafFile(s)</span>

</pre>

</td>

</tr>

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

<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

</td>

<td class="diff-line-num new_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

975

</td>

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

<pre style="margin: 0;"> <span id="LC975" class="line" lang="html">  %prog chain mafFile(s)</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

976

</td>

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

<pre style="margin: 0;">+<span id="LC976" class="line" lang="html">  %prog gff mafFile(s)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

</td>

<td class="diff-line-num new_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

977

</td>

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

<pre style="margin: 0;"> <span id="LC977" class="line" lang="html">  %prog html mafFile(s)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

863

</td>

<td class="diff-line-num new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

978

</td>

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

<pre style="margin: 0;"> <span id="LC978" class="line" lang="html">  %prog psl mafFile(s)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

979

</td>

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

<pre style="margin: 0;"> <span id="LC979" class="line" lang="html">  %prog sam mafFile(s)</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="984" style="width: 35px; color: rgba(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">@@ -869,8 +984,10 @@ if __name__ == "__main__":</td>

</tr>

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

<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

</td>

<td class="diff-line-num new_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

984

</td>

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

<pre style="margin: 0;"> <span id="LC984" class="line" lang="html">    op = optparse.OptionParser(usage=usage, description=description)</span>

</pre>

</td>

</tr>

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

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870

</td>

<td class="diff-line-num new_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

</td>

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<pre style="margin: 0;"> <span id="LC985" class="line" lang="html">    op.add_option("-p", "--protein", action="store_true",</span>

</pre>

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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="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

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<pre style="margin: 0;"> <span id="LC986" class="line" lang="html">                  help="assume protein alignments, for psl match counts")</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="872" 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">

872

</td>

<td class="diff-line-num new_line old" data-linenumber="987" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC872" class="line" lang="html">    op.add_option("-j", "--join", type="float", metavar="N",</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="873" 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">

873

</td>

<td class="diff-line-num new_line old" data-linenumber="987" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC873" class="line" lang="html">                  help="join co-linear alignments separated by <span class="nt" style="color: #000080;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="na" style="color: #008080;">N</span> <span class="na" style="color: #008080;">letters</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="874" style="width: 35px; color: rgba(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="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

987

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

<pre style="margin: 0;">+<span id="LC987" class="line" lang="html">    op.add_option("-j", "--join", type="float", metavar="N", help="join "</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="874" style="width: 35px; color: rgba(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="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

988

</td>

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

<pre style="margin: 0;">+<span id="LC988" class="line" lang="html">                  "consecutive co-linear alignments separated by <span class="nt" style="color: #000080;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="na" style="color: #008080;">N</span> <span class="na" style="color: #008080;">letters</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="874" style="width: 35px; color: rgba(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="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

989

</td>

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

<pre style="margin: 0;">+<span id="LC989" class="line" lang="html">    <span class="na" style="color: #008080;">op</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">add_option</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">-J</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">--Join</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">metavar=</span><span class="s" style="color: #d14;">"N"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">help=</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="874" style="width: 35px; color: rgba(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="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

990

</td>

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

<pre style="margin: 0;">+<span id="LC990" class="line" lang="html"><span class="na" style="color: #008080;">                  </span><span class="s" style="color: #d14;">"join nearest co-linear alignments separated by <= N letters"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

</td>

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<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="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

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

<pre style="margin: 0;"> <span id="LC991" class="line" lang="html">    <span class="na" style="color: #008080;">op</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">add_option</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">-n</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">--noheader</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="na" style="color: #008080;">action=</span><span class="s" style="color: #d14;">"store_true"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>

</pre>

</td>

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<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="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

992

</td>

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

<pre style="margin: 0;"> <span id="LC992" class="line" lang="html">                  <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"omit any header lines from the output"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

</td>

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<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="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

993

</td>

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

<pre style="margin: 0;"> <span id="LC993" class="line" lang="html">    <span class="na" style="color: #008080;">op</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">add_option</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">-d</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">--dictionary</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="na" style="color: #008080;">action=</span><span class="s" style="color: #d14;">"store_true"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="177815a02f622695617613b9dc8023a958d68f7b">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#177815a02f622695617613b9dc8023a958d68f7b"><strong>scripts/maf-cut</strong></a>

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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="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

</td>

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python</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">

</td>

<td class="diff-line-num new new_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">

2

</td>

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Author: Martin C. Frith 2018</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_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

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

</pre>

</td>

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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="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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></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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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

</pre>

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</tr>

</table>

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<li id="4b7be8c3b80efc62977b307791d1a304c23e1fa4">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.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">@@ -135,13 +135,13 @@ E-value options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="s" style="color: #d14;">-E: maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands)</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="LC136" 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="LC137" class="line" lang="cpp"><span class="s" style="color: #d14;">Score options (default settings):</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="LC138" class="line" lang="cpp"><span class="s" style="color: #d14;">-r: match score   (2 if -M, else  6 if <span class="idiff left right">0<Q<5</span>, else 1 if DNA)</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="LC139" class="line" lang="cpp"><span class="s" style="color: #d14;">-q: mismatch cost (3 if -M, else 18 if <span class="idiff left right">0<Q<5</span>, else 1 if DNA)</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="LC138" class="line" lang="cpp"><span class="s" style="color: #d14;">-r: match score   (2 if -M, else  6 if <span class="idiff left right">1<=Q<=4</span>, else 1 if DNA)</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="LC139" class="line" lang="cpp"><span class="s" style="color: #d14;">-q: mismatch cost (3 if -M, else 18 if <span class="idiff left right">1<=Q<=4</span>, else 1 if DNA)</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="LC140" class="line" lang="cpp"><span class="s" style="color: #d14;">-p: match/mismatch score matrix (protein-protein: BL62, DNA-protein: BL80)</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="LC141" class="line" lang="cpp"><span class="s" style="color: #d14;">-X: N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both ("</span></span>

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<pre style="margin: 0;"> <span id="LC142" 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;">ambiguousLetterOpt</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="LC143" class="line" lang="cpp"><span class="s" style="color: #d14;">-a: gap existence cost (DNA: 7, protein: 11, <span class="idiff left right">0<Q<5</span>: 21)</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="LC144" class="line" lang="cpp"><span class="s" style="color: #d14;">-b: gap extension cost (DNA: 1, protein:  2, <span class="idiff left right">0<Q<5</span>:  9)</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="LC143" class="line" lang="cpp"><span class="s" style="color: #d14;">-a: gap existence cost (DNA: 7, protein: 11, <span class="idiff left right">1<=Q<=4</span>: 21)</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="LC144" class="line" lang="cpp"><span class="s" style="color: #d14;">-b: gap extension cost (DNA: 1, protein:  2, <span class="idiff left right">1<=Q<=4</span>:  9)</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="LC145" class="line" lang="cpp"><span class="s" style="color: #d14;">-A: insertion existence cost (a)</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="LC146" class="line" lang="cpp"><span class="s" style="color: #d14;">-B: insertion extension cost (b)</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="LC147" class="line" lang="cpp"><span class="s" style="color: #d14;">-c: unaligned residue pair cost (off)</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">@@ -178,7 +178,7 @@ Miscellaneous options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"><span class="s" style="color: #d14;">-N: stop after the first N alignments per query strand</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;">-R: repeat-marking options (the same as was used for lastdb)</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="LC180" class="line" lang="cpp"><span class="s" style="color: #d14;">-u: mask lowercase during extensions: 0=never, 1=gapless,</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="LC181" class="line" lang="cpp"><span class="s" style="color: #d14;">    2=gapless+postmask, 3=always (2 if lastdb -c and Q<span class="idiff left right"><5</span>, else 0)</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="LC181" class="line" lang="cpp"><span class="s" style="color: #d14;">    2=gapless+postmask, 3=always (2 if lastdb -c and Q<span class="idiff left right">!=pssm</span>, else 0)</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="LC182" class="line" lang="cpp"><span class="s" style="color: #d14;">-w: suppress repeats inside exact matches, offset by <= this distance ("</span></span>

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<pre style="margin: 0;"> <span id="LC183" 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;">maxRepeatDistance</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="LC184" class="line" lang="cpp"><span class="s" style="color: #d14;">-G: genetic code ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geneticCodeFile</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,8 +189,8 @@ Miscellaneous options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC189" 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="LC190" 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="LC191" 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="LC192" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: <span class="idiff left right">0=fasta or fastq-ignore, 1=fastq-sanger, 2=fastq-solexa,</span></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="LC193" class="line" lang="cpp"><span class="s" style="color: #d14;">                  <span class="idiff left right">3=fastq-illumina, 4=prb, 5=PSSM (</span>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="LC192" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: <span class="idiff left right">fastx, keep, sanger, solexa, illumina, prb, pssm</span></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="LC193" class="line" lang="cpp"><span class="s" style="color: #d14;">                  <span class="idiff left right">(default=</span>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="LC194" 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="LC195" 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="LC196" 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="diff-line-num unfold js-unfold old_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="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">@@ -640,7 +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="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><span class="n" style="color: #333;">inputFormat</span> <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">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="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><span class="n" style="color: #333;">inputFormat</span> <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">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="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">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="mi" style="color: #099;"><span class="idiff right">0</span></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="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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<br>

</li>

<li id="54925a3b3158a751c06af7acce6d06070e5ac813">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#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 +70,7 @@ 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 or fastq-ignore,</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="LC74" class="line" lang="cpp"><span class="s" style="color: #d14;">                  1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (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="LC73" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: fastx, keep, sanger, solexa, illumina (default=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="LC74" class="line" lang="cpp"><span class="s" style="color: #d14;">-P: number of parallel threads ("</span></span>

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<pre style="margin: 0;"> <span id="LC75" 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>

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<pre style="margin: 0;"> <span id="LC76" 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>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" style="width: 35px; color: rgba(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">@@ -160,7 +159,8 @@ LAST home page: http://last.cbrc.jp/\n\</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'Q'</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(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="LC161" class="line" lang="cpp">      <span class="n" style="color: #333;">unstringify</span><span class="p">(</span> <span class="n" style="color: #333;">inputFormat</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span> <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">inputFormat</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="n" style="color: #333;">badopt</span><span class="p">(</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inputFormat</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="LC163" class="line" lang="cpp">    <span class="n" style="color: #333;">inputFormat</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="n" style="color: #333;">badopt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp">      <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"bad option"</span> <span class="p">);</span></span>

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<br>

</li>

<li id="39b07776472abcba47ba556e9f044177918c142c">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#39b07776472abcba47ba556e9f044177918c142c"><strong>src/SequenceFormat.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">@@ -3,19 +3,33 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef SEQUENCE_FORMAT_HH</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define SEQUENCE_FORMAT_HH</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cctype></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <istream></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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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">

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

</pre>

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<td class="diff-line-num 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">

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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="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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<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="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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<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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<pre style="margin: 0;"> <span id="LC13" 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="14" 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;">fastx</span><span class="p">,</span> <span class="n" style="color: #333;">fastqSanger</span><span class="p">,</span> <span class="n" style="color: #333;">fastqSolexa</span><span class="p">,</span> <span class="n" style="color: #333;">fastqIllumina</span><span class="p">,</span> <span class="n" style="color: #333;">prb</span><span class="p">,</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</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="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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<pre style="margin: 0;">+<span id="LC14" 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;">fastx</span><span class="p">,</span> <span class="n" style="color: #333;">fastqSanger</span><span class="p">,</span> <span class="n" style="color: #333;">fastqSolexa</span><span class="p">,</span> <span class="n" style="color: #333;">fastqIllumina</span><span class="p">,</span> <span class="n" style="color: #333;">prb</span><span class="p">,</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</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="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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp">       <span class="n" style="color: #333;">fastxKeep</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="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="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="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="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="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="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 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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<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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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</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 old_line" data-linenumber="16" 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="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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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp">  <span class="n" style="color: #333;">s</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 old_line" data-linenumber="17" 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="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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<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;">i</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;">i</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="n" style="color: #333;">s</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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">

18

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<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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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</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;">Enum</span><span class="o" style="font-weight: 600;">></span><span class="p">(</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 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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">w</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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="cpp">  <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">w</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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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<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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</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="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">

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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="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</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="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">

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<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">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">    <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</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;">tolower</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</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="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">

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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">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/**/</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fastx"</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>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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<pre style="margin: 0;">+<span id="LC26" 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="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"keep"</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;">fastxKeep</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC27" 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="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sanger"</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>

</pre>

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<td class="diff-line-num new old_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">

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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="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;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"2"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"solexa"</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;">fastqSolexa</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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="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;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"3"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"illumina"</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;">fastqIllumina</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC30" 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="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"prb"</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>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="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="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"5"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pssm"</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>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">s</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>

</pre>

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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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<pre style="margin: 0;"> <span id="LC33" 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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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="p">}</span></span>

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

</pre>

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<li id="6f06cc5de9b7ac057e2bab4944683b3802e6b62f">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#6f06cc5de9b7ac057e2bab4944683b3802e6b62f"><strong>src/last.hh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,6 +27,8 @@ inline std::istream &appendSequence(MultiSequence &m, std::istream &in,</td>

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<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>

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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>

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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="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>

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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;">fastxKeep</span><span class="p">)</span> <span class="p">{</span></span>

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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;">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;">true</span><span class="p">);</span></span>

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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;">prb</span><span class="p">)</span> <span class="p">{</span></span>

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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;">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>

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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="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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<li id="a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1143" style="width: 35px; color: rgba(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="1143" style="width: 35px; color: rgba(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">@@ -1143,7 +1143,11 @@ void lastal( int argc, char** argv ){</td>

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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp">    <span class="n" style="color: #333;">matrixFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromName</span><span class="p">(</span> <span class="n" style="color: #333;">matrixName</span> <span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="1144" style="width: 35px; color: rgba(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="LC1144" class="line" lang="cpp">    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">resetCumulativeOptions</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp">    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="n" style="color: #333;">matrixFile</span> <span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// read options from the matrix file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1146" 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;">f</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="p">;</span></span>

</pre>

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1146

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<td class="diff-line-num new_line" data-linenumber="1147" style="width: 35px; color: rgba(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="LC1147" class="line" lang="cpp">    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fromArgs</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// command line overrides matrix file</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1148" style="width: 35px; color: rgba(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="LC1148" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isUseQuality</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;">isUseQuality</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 new new_line" data-linenumber="1149" style="width: 35px; color: rgba(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="LC1149" class="line" lang="cpp">      <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"option -Q is inconsistent with the matrix file"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1150" style="width: 35px; color: rgba(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="LC1150" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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1151

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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1152

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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1153" style="width: 35px; color: rgba(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="LC1153" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">minSeedLimit</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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<br>

</li>

<li id="de4252990d12a909e50ff0b994d1715eae0ea5fd">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#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="126" style="width: 35px; color: rgba(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="126" style="width: 35px; color: rgba(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">@@ -126,7 +126,8 @@ void writePrjFile( const std::string& fileName, const LastdbArguments& args,</td>

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126

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126

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC128" 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>

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<td class="diff-line-num new_line old" data-linenumber="129" 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="LC129" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp">  <span class="o" style="font-weight: 600;"><<</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="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;">fastxKeep</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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132

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<pre style="margin: 0;"> <span id="LC132" 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>

</pre>

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132

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133

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Maybe this should be written (and read) by the indexes, so</span></span>

</pre>

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</li>

<li id="c25b47eef38e528e2fca11a7df7ca42c6fe59707">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#c25b47eef38e528e2fca11a7df7ca42c6fe59707"><strong>src/split/cbrc_split_aligner.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -758,7 +758,7 @@ void SplitAligner::calcBaseScores(unsigned i) {</td>

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758

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758

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<pre style="margin: 0;"> <span id="LC758" class="line" lang="cpp"></span>

</pre>

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759

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759

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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</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;">rAlign</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;">ralign</span><span class="p">;</span></span>

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<td class="diff-line-num old_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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760

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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</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;">qAlign</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;">qalign</span><span class="p">;</span></span>

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761

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<td class="diff-line-num new_line old" data-linenumber="761" 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="LC761" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</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;">qQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">a</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">qQual</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_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">

761

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<pre style="margin: 0;">+<span id="LC761" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</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;">qQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">qualityOffset</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">a</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">qQual</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">0</span></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

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762

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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"></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

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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="cpp">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qAlign</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_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">

764

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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">

764

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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rAlign</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="cff6a16c49a626871ebb6399a31650f25e4f5395">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#cff6a16c49a626871ebb6399a31650f25e4f5395"><strong>src/split/last-split.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="370" style="width: 35px; color: rgba(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="370" style="width: 35px; color: rgba(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">@@ -370,7 +370,8 @@ void lastSplit(LastSplitOptions& opts) {</td>

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<td class="diff-line-num old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

370

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370

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

371

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<td class="diff-line-num new_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

371

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jumpCost</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

372

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<td class="diff-line-num new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

372

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp">      <span class="p">(</span><span class="n" style="color: #333;">jumpProb</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</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;">scoreFromProb</span><span class="p">(</span><span class="n" style="color: #333;">jumpProb</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">INT_MIN</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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<td class="diff-line-num old old_line" data-linenumber="373" 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">

373

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<td class="diff-line-num new_line old" data-linenumber="373" 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="LC373" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qualityOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">64</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qualityOffset</span> <span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp">            <span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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="p">(</span><span class="n" style="color: #333;">sequenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">64</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp">    <span class="n" style="color: #333;">printParameters</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp">    <span class="n" style="color: #333;">sa</span><span class="p">.</span><span class="n" style="color: #333;">setParams</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapExistenceCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapExtensionCost</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp">                 <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>

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<li id="69737f84c540417aafef4e696f66adcc9f92fa66">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/bcc8c5f686990ac3beec20d80595b0168ce0d56c...e1d8e7ffb17d07a95396beed25a56b5b330949b3#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;">"106<span class="idiff left right">1</span>"</span></span></pre>

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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;">"106<span class="idiff left right">6</span>"</span></span></pre>

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