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GitLab

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<h3>

Andreas Tille 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/93f448c6b3746a181babb0c0a6b9c6f41686c0fe">93f448c6</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-05-23T07:10:05+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 938</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/commit/9ae39417a8f1ae245177ea8f36d549090a5ca7da">9ae39417</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-05-23T07:10:06+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/938'

Update to upstream version '938'

with Debian dir 1811318611cd61e17698e98a2c6e214d330a8432</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/commit/2307f6c73d9151a411a45551236e8faf732e3d8d">2307f6c7</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-05-23T07:10:06+02:00</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/commit/54f0b1f06cf4f118ee23f5da391f6776a40cbc36">54f0b1f0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-05-23T07:13:07+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>21 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="#bf84e628cb46c973b6c3732520db7e90c068aa9a">

doc/.htaccess

</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="#095e933658235fc5dd1c9f7aa5ad547270953ccb">

doc/last-tuning.html

</a>

</li>

<li class="file-stats">

<a href="#88b73917dd12cf720f9b24d29280ea7564d1e586">

doc/last-tuning.txt

</a>

</li>

<li class="file-stats">

<a href="#1d2db1d5c1263541e178e5c6d1a664dcaee43e97">

doc/lastal.html

</a>

</li>

<li class="file-stats">

<a href="#30d864ed8925787ee70643db49814772753a5f2c">

doc/lastal.txt

</a>

</li>

<li class="file-stats">

<a href="#0bf0c2b9afb77a75953faf3468b6707da7098872">

doc/lastdb.html

</a>

</li>

<li class="file-stats">

<a href="#485665224376f8470c80c62ef464a2a01e61c7e7">

doc/lastdb.txt

</a>

</li>

<li class="file-stats">

<a href="#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">

scripts/last-dotplot

</a>

</li>

<li class="file-stats">

<a href="#91df1cfad6631f83b9c232630119e09896361a09">

scripts/last-map-probs

</a>

</li>

<li class="file-stats">

<a href="#09de00a2f5fb0a5a61122f0d649401a900bbb57b">

scripts/last-postmask

</a>

</li>

<li class="file-stats">

<a href="#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">

scripts/last-train

</a>

</li>

<li class="file-stats">

<a href="#0c8579b85a61ba3e2feb036884e3e6d6da75cf0e">

scripts/maf-convert

</a>

</li>

<li class="file-stats">

<a href="#c647c36ae9d03ba272edef63f9a8da1d719e4c7d">

scripts/maf-join

</a>

</li>

<li class="file-stats">

<a href="#350d50b528bcd24a057c181965b2a50120bca4c7">

scripts/maf-swap

</a>

</li>

<li class="file-stats">

<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">

src/LastalArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#c41d15f61c8e13ecbdb96a800b59fc069d2c6695">

src/LastalArguments.hh

</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/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2018-05-14  Martin C. Frith  <Martin C. Frith></span>

</pre>

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

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

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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="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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">      * scripts/last-dotplot, scripts/last-postmask, test/102.maf, test</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="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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      /last-postmask-test.out, test/last-postmask-test.sh, test/last-</span>

</pre>

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

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      split-test.out, test/last-split-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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">      postmask: fix bug for unusual alignment headers</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="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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">      [65969d4d464d] [tip]</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"></span>

</pre>

</td>

</tr>

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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="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">

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      * scripts/last-dotplot, scripts/last-map-probs, scripts/last-postmask,</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">     scripts/last-train, scripts/maf-convert, scripts/maf-swap:</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="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="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">

11

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     Make last-train find LAST programs more robustly</span>

</pre>

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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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">     [8a4fadbe6080]</span>

</pre>

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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">

13

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

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

</pre>

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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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">2018-05-07  Martin C. Frith  <Martin C. Frith></span>

</pre>

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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">

15

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<pre style="margin: 0;">+<span id="LC15" 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="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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">     * scripts/last-postmask, scripts/last-train, scripts/maf-convert,</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="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-join, scripts/maf-swap:</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     Modernize the Python code</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">     [b1c09fdd12fe]</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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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

</pre>

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">     * doc/last-tuning.txt, doc/lastal.txt, doc/lastdb.txt,</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">     src/LastalArguments.cc, src/LastalArguments.hh, test/last-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">

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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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">     test/last-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="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">     Change lastal -x & -z options</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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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">     [b09d82479c91]</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"></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">     * doc/last-train.txt, scripts/last-train:</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="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">     Make last-train use last-postmask</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="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">     [2755c8f0dc79]</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="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"></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="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="plaintext">     * scripts/last-postmask, test/last-postmask-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">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">     postmask: bugfix for strand-asymmetric scores</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">     [9caca45429d8]</span>

</pre>

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34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>

</pre>

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1

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">2018-04-20  Martin C. Frith  <Martin C. Frith></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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<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">     * doc/Makefile, doc/lastal.txt, doc/maf-cut.txt, scripts/maf-cut:</span>

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">      [482845444bcd]<span class="idiff left right"> [tip]</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">     [482845444bcd]</span>

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

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">2018-04-18  Martin C. Frith  <Martin C. Frith></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>

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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (938-1) unstable; urgency=medium</span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

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

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Wed, 23 May 2018 07:10:11 +0200</span>

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">last-align (932-1) unstable; urgency=medium</span>

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

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

</pre>

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<li id="bf84e628cb46c973b6c3732520db7e90c068aa9a">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#bf84e628cb46c973b6c3732520db7e90c068aa9a"><strong>doc/.htaccess</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,4 +5,4 @@ IndexIgnore last-map-probs.txt last-matrices.txt last-pair-probs.txt</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="apache"><span class="nc" style="color: #458; font-weight: 600;">IndexIgnore</span> last-papers.txt last-parallel.txt last-postmask.txt</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="apache"><span class="nc" style="color: #458; font-weight: 600;">IndexIgnore</span> last-repeats.txt last-seeds.txt last-split.txt last-train.txt</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="apache"><span class="nc" style="color: #458; font-weight: 600;">IndexIgnore</span> last-tuning.txt last-tutorial.txt last.txt lastal.txt lastdb.txt</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="apache"><span class="nc" style="color: #458; font-weight: 600;">IndexIgnore</span> maf-convert.txt</span></pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="apache"><span class="nc" style="color: #458; font-weight: 600;">IndexIgnore</span> maf-convert.txt<span class="idiff left right"> maf-cut.txt</span></span></pre>

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<li id="bf068196d49b041029d9a269a6e3d52acda15f9f">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#bf068196d49b041029d9a269a6e3d52acda15f9f"><strong>doc/last-train.html</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -334,7 +334,7 @@ final score parameters, in a format that can be read by <a class="reference exte</td>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="html">option<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can also pipe sequences into last-train, for example:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="html"><span class="idiff left right">zcat queries.fasta.gz</span> | last-train mydb</span>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="html"><span class="idiff left right">bzcat queries.fasta.bz2</span> | last-train mydb</span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"options"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Options<span class="nt" style="color: navy;"></h2></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="377" style="width: 35px; color: rgba(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="377" style="width: 35px; color: rgba(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">@@ -377,6 +377,11 @@ e.g. score(A→G) = score(G→A).</td></tr></td>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="html">optimize the parameters for low-similarity alignments,</span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="html">similarly to the BLOSUM matrices.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--postmask=<span class="nt" style="color: navy;"><var></span>NUMBER<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>By default, last-train ignores alignments of mostly-lowercase</span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="html">sequence (by using <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"last-postmask.html"</span><span class="nt" style="color: navy;">></span>last-postmask<span class="nt" style="color: navy;"></a></span>).</span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="html">To turn this off, do <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>--postmask=0<span class="nt" style="color: navy;"></span></tt></span>.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--sample-number=<span class="nt" style="color: navy;"><var></span>N<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Use N randomly-chosen chunks of the query sequences.  The</span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="html">queries are chopped into fixed-length chunks (as if they were</span>

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<br>

</li>

<li id="03dd50d6a64beb7787e3bcc9eb6da79c482759d5">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#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">@@ -20,7 +20,7 @@ option <lastal.html#score-options>`_.</td>

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

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">You can also pipe sequences into last-train, for example::</span>

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

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">  <span class="idiff left right">zcat queries.fasta.gz</span> | last-train mydb</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">  <span class="idiff left right">bzcat queries.fasta.bz2</span> | last-train mydb</span>

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

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">-------</span>

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<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">@@ -46,6 +46,10 @@ Training options</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">         Ignore alignments with > PID% identity.  This aims to</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">         optimize the parameters for low-similarity alignments,</span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">         similarly to the BLOSUM matrices.</span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">  --postmask=NUMBER</span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">         By default, last-train ignores alignments of mostly-lowercase</span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">         sequence (by using `last-postmask <last-postmask.html>`_).</span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">         To turn this off, do ``--postmask=0``.</span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">  --sample-number=N</span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">         Use N randomly-chosen chunks of the query sequences.  The</span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">         queries are chopped into fixed-length chunks (as if they were</span>

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<br>

</li>

<li id="095e933658235fc5dd1c9f7aa5ad547270953ccb">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#095e933658235fc5dd1c9f7aa5ad547270953ccb"><strong>doc/last-tuning.html</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -370,7 +370,7 @@ alphabetically earliest.</p></td>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"lastdb8-lastal8"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>lastdb8 <span class="ni" style="color: purple;">&amp;</span> lastal8<span class="nt" style="color: navy;"></h2></span></span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If your reference has more than about 4 billion letters, 8-byte LAST</span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="html"><span class="nt" style="color: navy;"><span class="idiff left"><em></span></span><span class="idiff">may</span><span class="nt" style="color: navy;"><span class="idiff right"></em></span></span> be beneficial.  Ordinary (4-byte) LAST cannot directly handle so</span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="html"><span class="idiff left right">may</span> be beneficial.  Ordinary (4-byte) LAST cannot directly handle so</span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="html">much data, so it splits it into volumes, which is inefficient.  8-byte</span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="html">LAST can handle such data without voluming, but it uses more memory.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>8-byte LAST combines well with lastdb option -w or -W, which reduce</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="401" style="width: 35px; color: rgba(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="401" style="width: 35px; color: rgba(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">@@ -401,15 +401,27 @@ high-identity matches.</p></td>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>This option (gapless alignment culling) can make lastal <span class="nt" style="color: navy;"><strong></span>faster<span class="nt" style="color: navy;"></strong></span> but</span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="html"><span class="nt" style="color: navy;"><strong></span>less sensitive<span class="nt" style="color: navy;"></strong></span>.  It can also <span class="nt" style="color: navy;"><strong></span>reduce redundant output<span class="nt" style="color: navy;"></strong></span>.  For</span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="html">example, -C2 makes it discard alignments (before gapped extension)</span>

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="html">whose query coordinates lie in those of 2 or more stronger alignments.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="html">whose query coordinates lie in those of 2 or more stronger alignments.</span>

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html">This works well for aligning long, repeat-rich, indel-poor sequences</span>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="html">(e.g. mammal chromosomes) without repeat-masking.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"lastal-<span class="idiff left right">x</span>"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="html"><span class="nt" style="color: navy;"><h3></span>lastal -<span class="idiff left right">x</span><span class="nt" style="color: navy;"></h3></span></span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"lastal-<span class="idiff left right">z</span>"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="html"><span class="nt" style="color: navy;"><h3></span>lastal -<span class="idiff left right">z</span><span class="nt" style="color: navy;"></h3></span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>This option can make lastal <span class="nt" style="color: navy;"><strong></span>faster<span class="nt" style="color: navy;"></strong></span> but <span class="nt" style="color: navy;"><strong></span>less sensitive<span class="nt" style="color: navy;"></strong></span>.  It</span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="html">sets the maximum score drop in alignments, in the gapped extension</span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="html">phase.  Lower values make it faster, by quitting unpromising</span>

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="html">extensions sooner.  The default aims at best accuracy.  For example,</span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="html">use -x50% to specify 50% of the default value.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="html">extensions sooner.  The default aims at best accuracy.<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can set this option in several ways: perhaps the most intuitive is</span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="html">via maximum gap length.  For example, -z10g sets the maximum score</span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="html">drop such that the longest possible gap length is 10.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"lastal-x"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="html"><span class="nt" style="color: navy;"><h3></span>lastal -x<span class="nt" style="color: navy;"></h3></span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>This option (preliminary gapped extension) can make lastal <span class="nt" style="color: navy;"><strong></span>faster<span class="nt" style="color: navy;"></strong></span></span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="html">but <span class="nt" style="color: navy;"><strong></span>less sensitive<span class="nt" style="color: navy;"></strong></span>.  For example, -x2g makes it extend gapped</span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="html">alignments with a maximum gap length of 2, discard those with score</span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="html">below the gapped score threshold, then redo the survivors with the</span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="html">final max score drop (z).<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"id2"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="html"><span class="nt" style="color: navy;"><h3></span>lastal -M<span class="nt" style="color: navy;"></h3></span></span>

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<br>

</li>

<li id="88b73917dd12cf720f9b24d29280ea7564d1e586">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#88b73917dd12cf720f9b24d29280ea7564d1e586"><strong>doc/last-tuning.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">@@ -65,7 +65,7 @@ lastdb8 & lastal8</td>

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

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">If your reference has more than about 4 billion letters, 8-byte LAST</span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"><span class="idiff left right">*may*</span> be beneficial.  Ordinary (4-byte) LAST cannot directly handle so</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"><span class="idiff left right">may</span> be beneficial.  Ordinary (4-byte) LAST cannot directly handle so</span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">much data, so it splits it into volumes, which is inefficient.  8-byte</span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">LAST can handle such data without voluming, but it uses more memory.</span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,15 +102,29 @@ This option (gapless alignment culling) can make lastal **faster** but</td>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">**less sensitive**.  It can also **reduce redundant output**.  For</span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">example, -C2 makes it discard alignments (before gapped extension)</span>

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104

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<td class="diff-line-num new_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">

104

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

<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">whose query coordinates lie in those of 2 or more stronger alignments.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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

<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">This works well for aligning long, repeat-rich, indel-poor sequences</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

106

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

<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">(e.g. mammal chromosomes) without repeat-masking.</span>

</pre>

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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">

105

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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

<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"></span>

</pre>

</td>

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

106

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<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">lastal -<span class="idiff left right">x</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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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

<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">lastal -<span class="idiff left right">z</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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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="plaintext">---------</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">

108

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<td class="diff-line-num new_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">

110

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

<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"></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">

109

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<td class="diff-line-num new_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">

111

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

<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">This option can make lastal **faster** but **less sensitive**.  It</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">

110

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<td class="diff-line-num 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">

112

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

<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">sets the maximum score drop in alignments, in the gapped extension</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">

111

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<td class="diff-line-num new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

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

<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">phase.  Lower values make it faster, by quitting unpromising</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

112

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<td class="diff-line-num new_line old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">extensions sooner.  The default aims at best accuracy.  For example,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

113

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<td class="diff-line-num new_line old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">use -x50% to specify 50% of the default value.</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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

<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">extensions sooner.  The default aims at best accuracy.</span>

</pre>

</td>

</tr>

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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="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"></span>

</pre>

</td>

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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">

</td>

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

<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">You can set this option in several ways: perhaps the most intuitive is</span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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

<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">via maximum gap length.  For example, -z10g sets the maximum score</span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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

<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">drop such that the longest possible gap length is 10.</span>

</pre>

</td>

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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="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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

</pre>

</td>

</tr>

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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="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">

120

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

<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">lastal -x</span>

</pre>

</td>

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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="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">---------</span>

</pre>

</td>

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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="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"></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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">This option (preliminary gapped extension) can make lastal **faster**</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="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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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">but **less sensitive**.  For example, -x2g makes it extend gapped</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="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="plaintext">alignments with a maximum gap length of 2, discard those with score</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">below the gapped score threshold, then redo the survivors with the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">final max score drop (z).</span>

</pre>

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114

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"></span>

</pre>

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

</pre>

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

</pre>

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<br>

</li>

<li id="1d2db1d5c1263541e178e5c6d1a664dcaee43e97">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#1d2db1d5c1263541e178e5c6d1a664dcaee43e97"><strong>doc/lastal.html</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="520" style="width: 35px; color: rgba(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="520" style="width: 35px; color: rgba(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">@@ -520,25 +520,37 @@ looks like this:</p></td>

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<td class="diff-line-num old_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC520" class="line" lang="html"><span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: navy;">></span>The <span class="ni" style="color: purple;">&quot;</span>-1<span class="ni" style="color: purple;">&quot;</span> indicates the reverse frameshift.<span class="nt" style="color: navy;"></p></span></span>

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521

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

<pre style="margin: 0;"> <span id="LC521" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC522" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="523" style="width: 35px; color: rgba(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="LC523" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-<span class="idiff left right">x</span> <span class="nt" style="color: navy;"><var></span>DROP<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-<span class="idiff left right">z</span> <span class="nt" style="color: navy;"><var></span>DROP<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC524" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>Maximum score drop for gapped alignments.  Gapped alignments are</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC525" class="line" lang="html">forbidden from having any internal region with score <span class="ni" style="color: purple;">&lt;</span> -DROP.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="526" style="width: 35px; color: rgba(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="526" style="width: 35px; color: rgba(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="LC526" class="line" lang="html">This serves two purposes: accuracy (avoid spurious internal</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="526" style="width: 35px; color: rgba(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="LC527" class="line" lang="html">regions in alignments) and speed (the smaller the faster).<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC528" class="line" lang="html"><span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: navy;">></span>You can specify either a score (e.g. -x20), or a percentage; for</span>

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<pre style="margin: 0;">-<span id="LC529" class="line" lang="html">example, -x50% specifies 50% of the default value (rounded down</span>

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530

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="html">to the nearest integer).<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="html">The default value is e-1, which arguably produces the best</span>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="html">alignments.  Lower values improve speed, by quitting unpromising</span>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="html">extensions sooner.  You can specify this parameter in 3 ways:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="html"><span class="nt" style="color: navy;"><ul</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="html"><span class="nt" style="color: navy;"><li><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>A score (e.g. -z20).<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="html"><span class="nt" style="color: navy;"></li></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="html"><span class="nt" style="color: navy;"><li><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>A percentage.  For example, -z50% specifies 50% of the default</span>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="html">value (rounded down to the nearest integer).<span class="nt" style="color: navy;"></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="html"><span class="nt" style="color: navy;"></li></span></span>

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="html"><span class="nt" style="color: navy;"><li><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>A maximum gap length.  For example, -z8g sets the maximum</span>

</pre>

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="html">score drop to: min[a+8b, A+8B].  However, this never increases</span>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="html">the value above the default.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="html"><span class="nt" style="color: navy;"></li></span></span>

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="html"><span class="nt" style="color: navy;"></ul></span></span>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-x <span class="nt" style="color: navy;"><var></span>DROP<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>This option makes lastal extend gapped alignments twice.  First,</span>

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="html">it extends gapped alignments with a maximum score drop of x, and</span>

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="html">discards those with score <span class="ni" style="color: purple;">&lt;</span> e.  The surviving alignments are</span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="html">redone with a (presumably higher) maximum score drop of z.  This</span>

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="html">aims to improve speed with minimal effect on the final</span>

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="html">alignments.  You can specify -x in the same ways as -z (with the</span>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="html">default value of x being z).<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-y <span class="nt" style="color: navy;"><var></span>DROP<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum score drop for gapless alignments.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC536" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-z <span class="nt" style="color: navy;"><var></span>DROP<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;">-<span id="LC537" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Maximum score drop for final gapped alignments.  Setting z</span>

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<pre style="margin: 0;">-<span id="LC538" class="line" lang="html">different from x causes lastal to extend gapless alignments</span>

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<pre style="margin: 0;">-<span id="LC539" class="line" lang="html">twice: first with a maximum score drop of x, and then with a</span>

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<pre style="margin: 0;">-<span id="LC540" class="line" lang="html">(presumably higher) maximum score drop of z.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">-<span id="LC541" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-d <span class="nt" style="color: navy;"><var></span>SCORE<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Minimum score for gapless alignments.<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<br>

</li>

<li id="30d864ed8925787ee70643db49814772753a5f2c">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#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">@@ -187,25 +187,34 @@ Score options</td>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext">      The "-1" indicates the reverse frameshift.</span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">  -<span class="idiff left right">x</span> DROP</span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">  -<span class="idiff left right">z</span> DROP</span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext">      Maximum score drop for gapped alignments.  Gapped alignments are</span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext">      forbidden from having any internal region with score < -DROP.</span>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext">      This serves two purposes: accuracy (avoid spurious internal</span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">      regions in alignments) and speed (the smaller the faster).</span>

</pre>

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<td class="diff-line-num new old_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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<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="plaintext">      The default value is e-1, which arguably produces the best</span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">      alignments.  Lower values improve speed, by quitting unpromising</span>

</pre>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">      extensions sooner.  You can specify this parameter in 3 ways:</span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">      * A score (e.g. -z20).</span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">      * A percentage.  For example, -z50% specifies 50% of the default</span>

</pre>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">        value (rounded down to the nearest integer).</span>

</pre>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext">      You can specify either a score (e.g. -x20), or a percentage; for</span>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">      example, -x50% specifies 50% of the default value (rounded down</span>

</pre>

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">      to the nearest integer).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">      * A maximum gap length.  For example, -z8g sets the maximum</span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">        score drop to: min[a+8b, A+8B].  However, this never increases</span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">        the value above the default.</span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">  -x DROP</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">      This option makes lastal extend gapped alignments twice.  First,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">      it extends gapped alignments with a maximum score drop of x, and</span>

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">      discards those with score < e.  The surviving alignments are</span>

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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">      redone with a (presumably higher) maximum score drop of z.  This</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">      aims to improve speed with minimal effect on the final</span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">      alignments.  You can specify -x in the same ways as -z (with the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">      default value of x being z).</span>

</pre>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext">  -y DROP</span>

</pre>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext">      Maximum score drop for gapless alignments.</span>

</pre>

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

</pre>

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<td class="diff-line-num new_line old" data-linenumber="218" style="width: 35px; color: rgba(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="LC203" class="line" lang="plaintext">  -z DROP</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="218" style="width: 35px; color: rgba(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="LC204" class="line" lang="plaintext">      Maximum score drop for final gapped alignments.  Setting z</span>

</pre>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext">      different from x causes lastal to extend gapless alignments</span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">      twice: first with a maximum score drop of x, and then with a</span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">      (presumably higher) maximum score drop of z.</span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">      Minimum score for gapless alignments.</span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"></span>

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<li id="0bf0c2b9afb77a75953faf3468b6707da7098872">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#0bf0c2b9afb77a75953faf3468b6707da7098872"><strong>doc/lastdb.html</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -569,8 +569,7 @@ bytes.</p></td>

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>lastdb can become catastrophically slow for highly redundant</span>

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="html">sequences, e.g. two almost-identical genomes.  It usually processes</span>

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="html">several GB per hour, but if it becomes much slower, try option <span class="ni" style="color: purple;">&quot;</span>-i</span>

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<pre style="margin: 0;">-<span id="LC572" class="line" lang="html">10<span class="ni" style="color: purple;">&quot;</span>, which is likely to solve the problem.  (If even that is too slow,</span>

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<pre style="margin: 0;">-<span id="LC573" class="line" lang="html">try <span class="ni" style="color: purple;">&quot;</span>-i 100<span class="ni" style="color: purple;">&quot;</span> or so.)<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="html">10<span class="ni" style="color: purple;">&quot;</span>, which is likely to solve the problem.<span class="nt" style="color: navy;"></p></span></span>

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

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<pre style="margin: 0;"> <span id="LC574" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="html"><span class="nt" style="color: navy;"></body></span></span>

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<li id="485665224376f8470c80c62ef464a2a01e61c7e7">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#485665224376f8470c80c62ef464a2a01e61c7e7"><strong>doc/lastdb.txt</strong></a>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="plaintext">lastdb can become catastrophically slow for highly redundant</span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext">sequences, e.g. two almost-identical genomes.  It usually processes</span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="plaintext">several GB per hour, but if it becomes much slower, try option "-i</span>

</pre>

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237

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<td class="diff-line-num new_line old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext">10", which is likely to solve the problem.  (If even that is too slow,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

238

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<td class="diff-line-num new_line old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext">try "-i 100" or so.)</span></pre>

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<td class="diff-line-num new old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); 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="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

237

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">10", which is likely to solve the problem.</span></pre>

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</table>

<br>

</li>

<li id="d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8"><strong>scripts/last-dotplot</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,8 +18,15 @@ import subprocess</td>

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18

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18

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

<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span><span class="p">,</span> <span class="n" style="color: #333;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>

</pre>

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19

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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">

19

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Try to make PIL/PILLOW work:</span></span>

</pre>

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

21

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

<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">PIL</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Image</span><span class="p">,</span> <span class="n" style="color: #333;">ImageDraw</span><span class="p">,</span> <span class="n" style="color: #333;">ImageFont</span><span class="p">,</span> <span class="n" style="color: #333;">ImageColor</span></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">

22

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

<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Image</span><span class="p">,</span> <span class="n" style="color: #333;">ImageDraw</span><span class="p">,</span> <span class="n" style="color: #333;">ImageFont</span><span class="p">,</span> <span class="n" style="color: #333;">ImageColor</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">PIL</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Image</span><span class="p">,</span> <span class="n" style="color: #333;">ImageDraw</span><span class="p">,</span> <span class="n" style="color: #333;">ImageFont</span><span class="p">,</span> <span class="n" style="color: #333;">ImageColor</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</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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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Image</span><span class="p">,</span> <span class="n" style="color: #333;">ImageDraw</span><span class="p">,</span> <span class="n" style="color: #333;">ImageFont</span><span class="p">,</span> <span class="n" style="color: #333;">ImageColor</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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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></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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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num 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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<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="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">future_builtins</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">zip</span></span>

</pre>

</td>

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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">

</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">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

</td>

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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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<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="python">    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

</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">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span>  <span class="c" style="color: #998; font-style: italic;"># faster than fileinput</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +82,7 @@ def tabBlocks(beg1, beg2, blocks):</td>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafBlocks</span><span class="p">(</span><span class="n" style="color: #333;">beg1</span><span class="p">,</span> <span class="n" style="color: #333;">beg2</span><span class="p">,</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">    <span class="s" style="color: #d14;">'''Get the gapless blocks of an alignment, from MAF format.'''</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python">    <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="85" style="width: 35px; color: rgba(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="LC78" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">itertools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>zip</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">):</span></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="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">size</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">beg1</span><span class="p">,</span> <span class="n" style="color: #333;">beg2</span><span class="p">,</span> <span class="n" style="color: #333;">size</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,8 +156,8 @@ def updateSeqs(coverDict, seqRanges, seqName, ranges, coveredRange):</td>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></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="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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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readAlignments</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">    <span class="s" style="color: #d14;">'''Get alignments and sequence limits, from MAF or tabular format.'''</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(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="159" style="width: 35px; color: rgba(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="LC152" class="line" lang="python">    <span class="n" style="color: #333;">seqRequests1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqRequestFromText</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq1</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python">    <span class="n" style="color: #333;">seqRequests2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqRequestFromText</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq2</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); 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="159" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC159" class="line" lang="python">    <span class="n" style="color: #333;">seqRequests1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">seqRequestFromText</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq1</span></span><span class="p"><span class="idiff right">]</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="154" style="width: 35px; color: rgba(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="160" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC160" class="line" lang="python">    <span class="n" style="color: #333;">seqRequests2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">seqRequestFromText</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq2</span></span><span class="p"><span class="idiff right">]</span></span></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="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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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></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">

155

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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">

162

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">    <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</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">

156

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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="python">    <span class="n" style="color: #333;">seqRanges1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="91df1cfad6631f83b9c232630119e09896361a09">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#91df1cfad6631f83b9c232630119e09896361a09"><strong>scripts/last-map-probs</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,6 +120,6 @@ if __name__ == "__main__":</td>

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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">

120

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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">

120

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

<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

</pre>

</td>

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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">

121

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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="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="n" style="color: #333;">lastMapProbs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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">

122

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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="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyboardInterrupt</span><span class="p">:</span> <span class="k" style="font-weight: 600;">pass</span>  <span class="c" style="color: #998; font-style: italic;"># avoid silly error message</span></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">

123

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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="LC123" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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

</td>

<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="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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

124

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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="python">        <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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<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">

125

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="09de00a2f5fb0a5a61122f0d649401a900bbb57b">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#09de00a2f5fb0a5a61122f0d649401a900bbb57b"><strong>scripts/last-postmask</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +12,15 @@</td>

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12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Limitations: doesn't (yet) handle sequence quality data,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># frameshifts, or generalized affine gaps.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></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="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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__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 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>

</pre>

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<td class="diff-line-num old 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">

16

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

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span><span class="p">,</span> <span class="n" style="color: #333;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">future_builtins</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">zip</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="python">    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +29,17 @@ def myOpen(fileName):</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>

</pre>

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25

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<td class="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">,</span> <span class="n" style="color: #333;">colHeads</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">deleteCost</span><span class="p">,</span> <span class="n" style="color: #333;">insertCost</span><span class="p">):</span></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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">complement</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">):</span></span>

</pre>

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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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">    <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGTRYKMBDHV"</span></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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">    <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TGCAYRMKVHDB"</span></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="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python">    <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">)</span></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="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</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="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">base</span></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="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></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="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fastScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">,</span> <span class="n" style="color: #333;">colHeads</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">deleteCost</span><span class="p">,</span> <span class="n" style="color: #333;">insertCost</span><span class="p">):</span></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="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">    <span class="n" style="color: #333;">matrixLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">128</span></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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">    <span class="n" style="color: #333;">defaultScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">scoreMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">defaultScore</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">128</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">128</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">    <span class="n" style="color: #333;">fastMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">defaultScore</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixLen</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">                  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixLen</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">colHeads</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python">            <span class="n" style="color: #333;">xu</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">())</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,70 +48,90 @@ def getScoreMatrix(rowHeads, colHeads, matrix, deleteCost, insertCost):</td>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">            <span class="n" style="color: #333;">yl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">            <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">            <span class="n" style="color: #333;">maskScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python">            <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xu</span><span class="p">][</span><span class="n" style="color: #333;">yu</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span></span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python">            <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xu</span><span class="p">][</span><span class="n" style="color: #333;">yl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskScore</span></span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">            <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xl</span><span class="p">][</span><span class="n" style="color: #333;">yu</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskScore</span></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python">            <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xl</span><span class="p">][</span><span class="n" style="color: #333;">yl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskScore</span></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">128</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python">        <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</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;">deleteCost</span></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python">        <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insertCost</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoreMatrix</span></span>

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

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isGoodAlignment</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">insOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">            <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xu</span><span class="p">][</span><span class="n" style="color: #333;">yu</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">            <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xu</span><span class="p">][</span><span class="n" style="color: #333;">yl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskScore</span></span>

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC53" class="line" lang="python">            <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xl</span><span class="p">][</span><span class="n" style="color: #333;">yu</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskScore</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC54" class="line" lang="python">            <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">xl</span><span class="p">][</span><span class="n" style="color: #333;">yl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskScore</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC55" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixLen</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_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="LC56" class="line" lang="python">        <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</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;">deleteCost</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC57" class="line" lang="python">        <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insertCost</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); 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="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fastMatrix</span></span>

</pre>

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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="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">matrixPerStrand</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">,</span> <span class="n" style="color: #333;">colHeads</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">deleteCost</span><span class="p">,</span> <span class="n" style="color: #333;">insertCost</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">    <span class="n" style="color: #333;">rowComps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">complement</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowHeads</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">    <span class="n" style="color: #333;">colComps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">complement</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">colHeads</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC63" class="line" lang="python">    <span class="n" style="color: #333;">fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">,</span> <span class="n" style="color: #333;">colHeads</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">deleteCost</span><span class="p">,</span> <span class="n" style="color: #333;">insertCost</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_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="LC64" class="line" lang="python">    <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">rowComps</span><span class="p">,</span> <span class="n" style="color: #333;">colComps</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">deleteCost</span><span class="p">,</span> <span class="n" style="color: #333;">insertCost</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC65" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fwd</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isGoodAlignment</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">insOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python">    <span class="s" style="color: #d14;">"""Does the alignment have a segment with score >= minScore?"""</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python">    <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</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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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">    <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(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="LC49" class="line" lang="python">    <span class="n" style="color: #333;">xOld</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python">    <span class="n" style="color: #333;">yOld</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC51" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC70" class="line" lang="python">    <span class="n" style="color: #333;">xOld</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yOld</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); 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="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">columns</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">        <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)][</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="73" style="width: 35px; color: rgba(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="LC53" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minScore</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="73" style="width: 35px; color: rgba(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="LC54" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">xOld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">insOpenCost</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="73" style="width: 35px; color: rgba(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="LC55" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">yOld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">delOpenCost</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="73" style="width: 35px; color: rgba(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="LC56" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</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;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minScore</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); 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="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">xOld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); 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="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC76" class="line" lang="python">            <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">insOpenCost</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); 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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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

<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">yOld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(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="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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

<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">            <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">delOpenCost</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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

<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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

<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">            <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

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

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

57

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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

<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">        <span class="n" style="color: #333;">xOld</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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

82

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

<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">        <span class="n" style="color: #333;">yOld</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num old_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">

60

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<td class="diff-line-num 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">

84

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

<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_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">

61

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

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

<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printIfGood</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">insOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">):</span></span>

</pre>

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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="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

62

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC62" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isGoodAlignment</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">insOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">):</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(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="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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

<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">    <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqs</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

87

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

<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isGoodAlignment</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">insOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">):</span></span>

</pre>

</td>

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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">

63

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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">

88

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

<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">maf</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

64

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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC64" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

65

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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC65" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</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="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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

<pre style="margin: 0;">+<span id="LC89" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

90

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

<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

</pre>

</td>

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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">

66

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<td class="diff-line-num new_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">

91

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

<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="diff-line-num new_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">

92

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

<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doOneFile</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC93" class="line" lang="python">    <span class="n" style="color: #333;">aDel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bDel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aIns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bIns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrices</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(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="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

94

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

<pre style="margin: 0;">+<span id="LC94" class="line" lang="python">    <span class="n" style="color: #333;">strandParam</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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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">

95

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

<pre style="margin: 0;"> <span id="LC95" class="line" lang="python">    <span class="n" style="color: #333;">scoreMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

96

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="python">    <span class="n" style="color: #333;">rowHeads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

97

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

<pre style="margin: 0;">+<span id="LC97" class="line" lang="python">    <span class="n" style="color: #333;">colHeads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

69

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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">

98

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

<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">    <span class="n" style="color: #333;">maf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

70

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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

<pre style="margin: 0;"> <span id="LC99" class="line" lang="python">    <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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

<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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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">

101

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

<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"#"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

74

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<td class="diff-line-num new_line old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC74" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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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="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

75

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<td class="diff-line-num new_line old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC75" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">w</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

76

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<td class="diff-line-num new_line old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC76" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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

<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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">

104

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

<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">fields</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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

<pre style="margin: 0;">+<span id="LC105" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new_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="LC106" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"a="</span><span class="p">):</span> <span class="n" style="color: #333;">aDel</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC107" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"b="</span><span class="p">):</span> <span class="n" style="color: #333;">bDel</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<td class="diff-line-num new_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="LC108" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"A="</span><span class="p">):</span> <span class="n" style="color: #333;">aIns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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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">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"B="</span><span class="p">):</span> <span class="n" style="color: #333;">bIns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"e="</span><span class="p">):</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

82

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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(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="LC82" 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;">w</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">w</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 old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python">                <span class="n" style="color: #333;">colHeads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(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="LC84" class="line" lang="python">                <span class="n" style="color: #333;">rowHeads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(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="LC85" class="line" lang="python">                <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC86" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">w</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;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 old_line" 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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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(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="LC87" class="line" lang="python">                <span class="n" style="color: #333;">rowHeads</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(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="LC88" class="line" lang="python">                <span class="n" style="color: #333;">matrix</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"S="</span><span class="p">):</span> <span class="n" style="color: #333;">strandParam</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="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;">colHeads</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">fields</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 new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">                <span class="n" style="color: #333;">colHeads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</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;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="python">                <span class="n" style="color: #333;">rowHeads</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="python">                <span class="n" style="color: #333;">scoreMatrix</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:]])</span></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="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="LC117" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isspace</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(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="118" style="width: 35px; color: rgba(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="LC90" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqs</span><span class="p">:</span> <span class="n" style="color: #333;">printIfGood</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">scoreM</span>atrix</span><span class="p">,</span> <span class="n" style="color: #333;">aDel</span><span class="p">,</span> <span class="n" style="color: #333;">aIns</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqs</span><span class="p">:</span> <span class="n" style="color: #333;">printIfGood</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">m</span>atrix</span><span class="p">,</span> <span class="n" style="color: #333;">aDel</span><span class="p">,</span> <span class="n" style="color: #333;">aIns</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); 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="python">            <span class="n" style="color: #333;">maf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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="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="python">            <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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="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="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">-<span id="LC94" 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;">scoreMatrix</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python">                <span class="n" style="color: #333;">scoreMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">,</span> <span class="n" style="color: #333;">colHeads</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">                                             <span class="n" style="color: #333;">bDel</span><span class="p">,</span> <span class="n" style="color: #333;">bIns</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); 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="python">            <span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>

</pre>

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

<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span> <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

99

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

<pre style="margin: 0;">-<span id="LC99" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqs</span><span class="p">:</span> <span class="n" style="color: #333;">printIfGood</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">aDel</span><span class="p">,</span> <span class="n" style="color: #333;">aIns</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

124

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

<pre style="margin: 0;">+<span id="LC124" 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;">matrices</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

125

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

<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">aDel</span><span class="p">,</span> <span class="n" style="color: #333;">bDel</span><span class="p">,</span> <span class="n" style="color: #333;">aIns</span><span class="p">,</span> <span class="n" style="color: #333;">bIns</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python">                        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"can't read alignment header"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">                    <span class="n" style="color: #333;">matrices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrixPerStrand</span><span class="p">(</span><span class="n" style="color: #333;">rowHeads</span><span class="p">,</span> <span class="n" style="color: #333;">colHeads</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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

<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">                                               <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">bDel</span><span class="p">,</span> <span class="n" style="color: #333;">bIns</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python">                <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="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;">seqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strandParam</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

131

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

<pre style="margin: 0;">+<span id="LC131" class="line" lang="python">                    <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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="python">                    <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrices</span><span class="p">[</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python">                <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqs</span><span class="p">:</span> <span class="n" style="color: #333;">printIfGood</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">aDel</span><span class="p">,</span> <span class="n" style="color: #333;">aIns</span><span class="p">,</span> <span class="n" style="color: #333;">minScore</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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

<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>

</pre>

</td>

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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">

101

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<td class="diff-line-num new_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">

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

<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lastPostmask</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC137" 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;">args</span><span class="p">:</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(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">@@ -116,6 +151,6 @@ if __name__ == "__main__":</td>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></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="LC152" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="n" style="color: #333;">lastPostmask</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

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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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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyboardInterrupt</span><span class="p">:</span> <span class="k" style="font-weight: 600;">pass</span>  <span class="c" style="color: #998; font-style: italic;"># avoid silly error message</span></span>

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<td class="diff-line-num new_line old" data-linenumber="154" style="width: 35px; color: rgba(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="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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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="154" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC154" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">        <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span></pre>

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<br>

</li>

<li id="37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0"><strong>scripts/last-train</strong></a>

<hr>

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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">

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

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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">

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

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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="python"></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<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>

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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">

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

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span><span class="p">,</span> <span class="n" style="color: #333;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">random</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">subprocess</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">tempfile</span></span>

</pre>

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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="python"></span>

</pre>

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

<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">@@ -157,7 +159,7 @@ def countsFromLastOutput(lines, opts):</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">            <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span>  <span class="c" style="color: #998; font-style: italic;"># slow?</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"c"</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python">            <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">()[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:])</span></span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python">            <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">()[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:]]</span></span></span>

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<pre style="margin: 0;"> <span id="LC163" 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;">matrix</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">                <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">                <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrixSize</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">)]</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -236,14 +238,16 @@ def matProbsFromCounts(counts, opts):</td>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python">    <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">    <span class="n" style="color: #333;">probs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"# substitution percent identity: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"# count matrix (query letters = columns, reference letters = rows):"</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# substitution percent identity: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# count matrix "</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python">          <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python">    <span class="n" style="color: #333;">writeCountMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"# probability matrix (query letters = columns, reference letters = rows):"</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# probability matrix "</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python">          <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">    <span class="n" style="color: #333;">writeProbMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">probs</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">probs</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></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">@@ -264,19 +268,19 @@ def gapProbsFromCounts(counts, opts):</td>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python">        <span class="n" style="color: #333;">delExtendProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">deletes</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python">        <span class="n" style="color: #333;">insExtendProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">inserts</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC267" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# aligned letter pairs:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

268

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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(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="LC268" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# deletes:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">deletes</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC269" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# inserts:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">inserts</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

270

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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC270" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# delOpens:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delOpens</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(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="LC271" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# insOpens:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insOpens</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="272" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(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="LC272" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# alignments:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alignments</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

273

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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC273" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# mean delete size: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">deletes</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delOpens</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

274

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<td class="diff-line-num new_line old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC274" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# mean insert size: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">inserts</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insOpens</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="275" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC275" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# delOpenProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delOpenProb</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC276" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# insOpenProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insOpenProb</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="277" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC277" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# delExtendProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delExtendProb</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC278" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# insExtendProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insExtendProb</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC279" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC271" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# aligned letter pairs:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC272" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# deletes:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">deletes</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

273

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# inserts:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">inserts</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

274

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# delOpens:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delOpens</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

275

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# insOpens:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insOpens</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

276

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# alignments:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignments</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

277

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# mean delete size: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">deletes</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">delOpens</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

278

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# mean insert size: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">inserts</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">insOpens</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); 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="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

279

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# delOpenProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</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">delOpenProb</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(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="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

280

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# insOpenProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</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">insOpenProb</span></span><span class="p"><span class="idiff right">)</span></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="280" style="width: 35px; color: rgba(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="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

281

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# delExtendProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</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">delExtendProb</span></span><span class="p"><span class="idiff right">)</span></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="280" style="width: 35px; color: rgba(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="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

282

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

<pre style="margin: 0;">+<span id="LC282" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# insExtendProb: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">g"</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">insExtendProb</span></span><span class="p"><span class="idiff right">)</span></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="280" style="width: 35px; color: rgba(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="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

283

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

280

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<td class="diff-line-num new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

284

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

<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

281

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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">

285

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

<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">    <span class="n" style="color: #333;">delCloseProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delExtendProb</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

282

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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="python">    <span class="n" style="color: #333;">insCloseProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insExtendProb</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="301" style="width: 35px; color: rgba(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="305" style="width: 35px; color: rgba(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">@@ -301,8 +305,8 @@ def scoreFromLetterProbs(scale, pairProb, prob1, prob2):</td>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoreFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">probRatio</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">probs</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python">    <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">sum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">probs</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python">    <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">sum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">probs</span></span><span class="p"><span class="idiff right">))</span></span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python">    <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">sum</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">probs</span></span><span class="p"><span class="idiff right">]</span></span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python">    <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">sum</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">probs</span></span><span class="p"><span class="idiff right">)]</span></span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[[</span><span class="n" style="color: #333;">scoreFromLetterProbs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">probs</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"></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">@@ -328,17 +332,17 @@ def writeGapCosts(gapCosts, out):</td>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python">    <span class="n" style="color: #333;">delExistCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExistCost</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span></span>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# delExistCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delExistCost</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# insExistCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insExistCost</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# delExtendCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delExtendCost</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# insExtendCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insExtendCost</span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="335" style="width: 35px; color: rgba(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="LC335" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC335" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# delExistCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delExistCost</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC336" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# insExistCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insExistCost</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="337" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC337" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# delExtendCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delExtendCost</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="338" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC338" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# insExtendCost:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insExtendCost</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tryToMakeChildProgramsFindable</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">myDir</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">srcDir</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">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">myDir</span></span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pardir</span><span class="p">,</span> <span class="s" style="color: #d14;">"src"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># put <span class="idiff left right">srcDir</span> first, to avoid getting older versions of LAST:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python">    <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"PATH"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">srcDir</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pathsep</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"PATH"</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">d</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">e</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">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">d</span></span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pardir</span><span class="p">,</span> <span class="s" style="color: #d14;">"src"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># put <span class="idiff left right">them</span> first, to avoid getting older versions of LAST:</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python">    <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"PATH"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">d</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">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pathsep</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">e</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pathsep</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"PATH"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readLastalProgName</span><span class="p">(</span><span class="n" style="color: #333;">lastdbIndexName</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">    <span class="n" style="color: #333;">bitsPerInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"32"</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">@@ -377,8 +381,11 @@ def doTraining(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-B"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python">    <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">args</span></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">    <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"last-split"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-n"</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python">    <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"last-postmask"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">    <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python">    <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">postmask</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python">        <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">    <span class="n" style="color: #333;">lastalVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionFromHeader</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">    <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaleFromHeader</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">    <span class="n" style="color: #333;">internalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaleIncrease</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">@@ -387,15 +394,15 @@ def doTraining(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">        <span class="n" style="color: #333;">internalMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaledMatrix</span><span class="p">(</span><span class="n" style="color: #333;">externalMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">scaleIncrease</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">    <span class="n" style="color: #333;">oldParameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# lastal version:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lastalVersion</span></span></span>

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# maximum percent identity:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">pid</span></span></span>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# scale of score parameters:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">externalScale</span></span></span>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"# scale used while training:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">internalScale</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# lastal version:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalVersion</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC398" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# maximum percent identity:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pid</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC399" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# scale of score parameters:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">externalScale</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"# scale used while training:"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">internalScale</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python">    <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"#"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">x</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span></span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"#"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python">        <span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">gapCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</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="LC408" class="line" lang="python">        <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="414" style="width: 35px; color: rgba(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">@@ -407,9 +414,10 @@ def doTraining(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python">            <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</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="LC416" class="line" lang="python">            <span class="n" style="color: #333;">matScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">internalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"# score matrix (query letters = columns, reference letters = rows):"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# score matrix "</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python">                  <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python">            <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span></span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python">            <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span></span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parameters</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oldParameters</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span></span>

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<td class="diff-line-num new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC423" class="line" lang="python">            <span class="n" style="color: #333;">oldParameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" style="width: 35px; color: rgba(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="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -423,6 +431,8 @@ def doTraining(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">        <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># in python2.6, the next line must come after p.stdin.close()</span></span>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python">        <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">postmask</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python">            <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python">    <span class="n" style="color: #333;">gapCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">externalScale</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">    <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="441" style="width: 35px; color: rgba(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">@@ -431,7 +441,8 @@ def doTraining(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC441" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Q</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python">        <span class="n" style="color: #333;">matScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">externalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python">        <span class="n" style="color: #333;">externalMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrixWithLetters</span><span class="p">(</span><span class="n" style="color: #333;">matScores</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"# score matrix (query letters = columns, reference letters = rows):"</span></span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# score matrix "</span></span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python">          <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">    <span class="n" style="color: #333;">writeMatrixWithLetters</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">externalMatrix</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lastTrain</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>

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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">@@ -464,6 +475,8 @@ if __name__ == "__main__":</td>

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<pre style="margin: 0;"> <span id="LC475" 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;">"force insertion/deletion symmetry"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--pid"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"float"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python">                  <span class="s" style="color: #d14;">"skip alignments with > PID</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">identity (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--postmask"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python">                  <span class="s" style="color: #d14;">"skip mostly-lowercase alignments (default=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample-number"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">500</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;">"N"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python">                  <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of random sequence samples (default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">default)"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python">    <span class="n" style="color: #333;">og</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample-length"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2000</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;">"L"</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="518" style="width: 35px; color: rgba(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="531" style="width: 35px; color: rgba(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">@@ -518,6 +531,6 @@ if __name__ == "__main__":</td>

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531

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

<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

519

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="n" style="color: #333;">lastTrain</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyboardInterrupt</span><span class="p">:</span> <span class="k" style="font-weight: 600;">pass</span>  <span class="c" style="color: #998; font-style: italic;"># avoid silly error message</span></span>

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<td class="diff-line-num new_line old" data-linenumber="534" style="width: 35px; color: rgba(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="LC521" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC534" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">        <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span></pre>

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<br>

</li>

<li id="0c8579b85a61ba3e2feb036884e3e6d6da75cf0e">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#0c8579b85a61ba3e2feb036884e3e6d6da75cf0e"><strong>scripts/maf-convert</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,8 @@</td>

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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="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">

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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>

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="html"># Genome FAQ, not e.g. "MIRA assembly format".</span>

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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="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="html"></span>

</pre>

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<td class="diff-line-num new old_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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<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">

9

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

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); 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="html"></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="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="html">from itertools import *</span>

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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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="html">import math, optparse, os, signal, sys</span>

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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="128" style="width: 35px; color: rgba(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 +128,7 @@ def mafInput(opts, lines):</td>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="html">        <span class="na" style="color: teal;">elif</span> <span class="na" style="color: teal;">line</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: teal;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</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: teal;">:</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="html">            <span class="na" style="color: teal;">updateEvalueParameters</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">line</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="html">            <span class="na" style="color: teal;">if</span> <span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">isKeepComments:</span></span>

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<td class="diff-line-num old old_line" 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="html">                <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="na" style="color: teal;"><span class="idiff">line</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">,</span></span></span>

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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="html">                <span class="na" style="color: teal;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">(</span></span><span class="na" style="color: teal;"><span class="idiff">line</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">end=</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="html">    <span class="na" style="color: teal;">if</span> <span class="na" style="color: teal;">sLines:</span> <span class="na" style="color: teal;">yield</span> <span class="na" style="color: teal;">aLine</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">sLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">qLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">pLines</span></span>

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

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="html"><span class="na" style="color: teal;">def</span> <span class="na" style="color: teal;">isJoinable</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">oldMaf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">newMaf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(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="180" style="width: 35px; color: rgba(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">@@ -178,10 +180,10 @@ def writeAxt(maf):</td>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="html">    <span class="na" style="color: teal;">if</span> <span class="na" style="color: teal;">score:</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="html">        <span class="na" style="color: teal;">outWords</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">score</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

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

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<td class="diff-line-num new_line old" data-linenumber="183" style="width: 35px; color: rgba(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="LC181" class="line" lang="html">    <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">"</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: teal;"><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: teal;"><span class="idiff right">outWords</span></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="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: teal;">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: teal;"><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: teal;"><span class="idiff">outWords</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">)</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="html">    <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">i</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">sLines:</span></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="html">        <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="na" style="color: teal;"><span class="idiff">i</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">[</span></span><span class="na" style="color: teal;"><span class="idiff">6</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">]</span></span></span>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="html">    <span class="na" style="color: teal;">print</span>  <span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> <span class="na" style="color: teal;">print</span> <span class="na" style="color: teal;">a</span> <span class="na" style="color: teal;">blank</span> <span class="na" style="color: teal;">line</span> <span class="na" style="color: teal;">at</span> <span class="na" style="color: teal;">the</span> <span class="na" style="color: teal;">end</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="html">        <span class="na" style="color: teal;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">(</span></span><span class="na" style="color: teal;"><span class="idiff">i</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">[</span></span><span class="na" style="color: teal;"><span class="idiff">6</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">])</span></span></span>

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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: teal;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">()</span></span>  <span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> <span class="na" style="color: teal;">print</span> <span class="na" style="color: teal;">a</span> <span class="na" style="color: teal;">blank</span> <span class="na" style="color: teal;">line</span> <span class="na" style="color: teal;">at</span> <span class="na" style="color: teal;">the</span> <span class="na" style="color: teal;">end</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="html"><span class="na" style="color: teal;">def</span> <span class="na" style="color: teal;">mafConvertToAxt</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="html">    <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">maf</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">mafInput</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(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="214" style="width: 35px; color: rgba(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">@@ -212,7 +214,7 @@ def writeTab(maf):</td>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="html"><span class="s" style="color: #d14;">    gapWord = "</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,".</span><span class="na" style="color: teal;">join</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">matchAndInsertSizes</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">alignmentColumns</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">letterSizes</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="html">    <span class="na" style="color: teal;">outWords</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">gapWord</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC216" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(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="217" style="width: 35px; color: rgba(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="LC215" class="line" lang="html">    <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">"\</span></span><span class="na" style="color: teal;"><span class="idiff">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">".</span></span><span class="na" style="color: teal;"><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: teal;"><span class="idiff">outWords</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff right">endWords</span></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="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC217" class="line" lang="html">    <span class="na" style="color: teal;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">("\</span></span><span class="na" style="color: teal;"><span class="idiff">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">".</span></span><span class="na" style="color: teal;"><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: teal;"><span class="idiff">outWords</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">endWords</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_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC218" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="html"><span class="na" style="color: teal;">def</span> <span class="na" style="color: teal;">mafConvertToTab</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="html">    <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">maf</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">mafInput</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" style="width: 35px; color: rgba(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="238" style="width: 35px; color: rgba(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">@@ -236,7 +238,7 @@ def writeChain(maf):</td>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="html"></span>

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<td class="diff-line-num old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); 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="239" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC239" class="line" lang="html">    <span class="na" style="color: teal;">outWords</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">str</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">next</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">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: teal;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>

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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC240" class="line" lang="html"></span>

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<td class="diff-line-num old old_line" data-linenumber="239" style="width: 35px; color: rgba(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="241" style="width: 35px; color: rgba(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="LC239" class="line" lang="html">    <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">"</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: teal;"><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: teal;"><span class="idiff 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 new old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="241" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC241" class="line" lang="html">    <span class="na" style="color: teal;">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: teal;"><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: teal;"><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_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC242" class="line" lang="html"></span>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;"> <span id="LC243" class="line" lang="html">    <span class="na" style="color: teal;">letterSizes =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">[i[3]</span> <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">i</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">sLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC244" class="line" lang="html">    <span class="na" style="color: teal;">rows =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">[i[6]</span> <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">i</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="246" style="width: 35px; color: rgba(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">@@ -244,11 +246,11 @@ def writeChain(maf):</td>

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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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<pre style="margin: 0;"> <span id="LC246" class="line" lang="html">    <span class="na" style="color: teal;">size =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">"0"</span></span>

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC247" class="line" lang="html">    <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">i</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">matchAndInsertSizes</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">alignmentColumns</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">letterSizes</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="html">        <span class="na" style="color: teal;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: teal;">:</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">i:</span></span>

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(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="LC247" class="line" lang="html">            <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="na" style="color: teal;"><span class="idiff">size</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">+</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: teal;"><span class="idiff">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">i</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">replace</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">("</span></span><span class="na" style="color: teal;"><span class="idiff">:</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">",</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: teal;"><span class="idiff">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">"</span>)</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="html">            <span class="na" style="color: teal;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">(</span></span><span class="na" style="color: teal;"><span class="idiff">size</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">+</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: teal;"><span class="idiff">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">i</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">replace</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">("</span></span><span class="na" style="color: teal;"><span class="idiff">:</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">",</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: teal;"><span class="idiff">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">")</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="html">            <span class="na" style="color: teal;">size =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">"0"</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="html">        <span class="na" style="color: teal;">else:</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="html">            <span class="na" style="color: teal;">size =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">i</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="html">    <span class="na" style="color: teal;">print</span><span class="idiff left"> </span><span class="na" style="color: teal;"><span class="idiff right">size</span></span></span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="html">    <span class="na" style="color: teal;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">(</span></span><span class="na" style="color: teal;"><span class="idiff">size</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="html"><span class="na" style="color: teal;">def</span> <span class="na" style="color: teal;">mafConvertToChain</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="html">    <span class="na" style="color: teal;">for</span> <span class="na" style="color: teal;">maf</span> <span class="na" style="color: teal;">in</span> <span class="na" style="color: teal;">mafInput</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: teal;">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="358" style="width: 35px; color: rgba(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">@@ -358,7 +360,7 @@ def writePsl(opts, mafs):</td>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="html">                seqNameB, seqLenB, begB, endB, seqNameA, seqLenA, begA, endA,</span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="html">                blockCount, blockSizes, blockStartsB, blockStartsA)</span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="html"></span>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="html">    print<span class="idiff left right"> "\t".join(map(str, outWords</span>))</span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="html">    print<span class="idiff left right">("\t".join(map(str, outWords)</span>))</span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html">def mafConvertToPsl(opts, lines):</span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="html">    if opts.join:</span>

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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -409,12 +411,12 @@ def copyDictFile(lines):</td>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC411" class="line" lang="html">            break</span>

</pre>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="html"></span>

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<td class="diff-line-num new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC413" class="line" lang="html">def writeSamHeader(opts, fileNames):</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="414" style="width: 35px; color: rgba(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="LC412" class="line" lang="html">    print<span class="idiff left right"> "@HD\tVN:1.3\tSO:unsorted"</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="html">    print<span class="idiff left right">("@HD\tVN:1.3\tSO:unsorted")</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="html"></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="html">    if opts.dictionary:</span>

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<td class="diff-line-num old_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">

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<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">        sequenceLengths = dict(readSequenceLengths(fileNames))</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC418" class="line" lang="html">        for k in sorted(sequenceLengths, key=karyotypicSortKey):</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="419" style="width: 35px; color: rgba(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="LC417" class="line" lang="html">            print<span class="idiff left right"> "@SQ\tSN:%s\tLN:%s" % (k, sequenceLengths[k]</span>)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); 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="419" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC419" class="line" lang="html">            print<span class="idiff left right">("@SQ\tSN:%s\tLN:%s" % (k, sequenceLengths[k])</span>)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="html">    if opts.dictfile:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="html">        f = myOpen(opts.dictfile)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="422" style="width: 35px; color: rgba(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="424" style="width: 35px; color: rgba(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">@@ -422,7 +424,7 @@ def writeSamHeader(opts, fileNames):</td>

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<td class="diff-line-num old_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC424" class="line" lang="html">        f.close()</span>

</pre>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="html">    if opts.readgroup:</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="427" style="width: 35px; color: rgba(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="LC425" class="line" lang="html">        print<span class="idiff left right"> "@RG\t" + "\t".join(opts.readgroup.split(</span>))</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC427" class="line" lang="html">        print<span class="idiff left right">("@RG\t" + "\t".join(opts.readgroup.split()</span>))</span>

</pre>

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<pre style="margin: 0;"> <span id="LC428" 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="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

427

</td>

<td class="diff-line-num new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

429

</td>

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

<pre style="margin: 0;"> <span id="LC429" class="line" lang="html">mapqMissing = "255"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

428

</td>

<td class="diff-line-num new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

</td>

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

<pre style="margin: 0;"> <span id="LC430" class="line" lang="html">mapqMaximum = "254"</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="537" style="width: 35px; color: rgba(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="539" style="width: 35px; color: rgba(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">@@ -537,7 +539,7 @@ def writeSam(readGroup, maf):</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

</td>

<td class="diff-line-num new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

</td>

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

<pre style="margin: 0;"> <span id="LC539" class="line" lang="html">    if score: out.append(score)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

</td>

<td class="diff-line-num new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

</td>

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

<pre style="margin: 0;"> <span id="LC540" class="line" lang="html">    if evalue: out.append(evalue)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

</td>

<td class="diff-line-num new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

</td>

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

<pre style="margin: 0;"> <span id="LC541" class="line" lang="html">    if readGroup: out.append(readGroup)</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="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

540

</td>

<td class="diff-line-num new_line old" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC540" 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="541" style="width: 35px; color: rgba(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="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

</td>

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

<pre style="margin: 0;">+<span id="LC542" class="line" lang="html">    print<span class="idiff left right">("\t".join(out)</span>)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

</td>

<td class="diff-line-num new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

</td>

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

<pre style="margin: 0;"> <span id="LC543" 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="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

542

</td>

<td class="diff-line-num new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

</td>

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

<pre style="margin: 0;"> <span id="LC544" class="line" lang="html">def mafConvertToSam(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="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

</td>

<td class="diff-line-num new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

545

</td>

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

<pre style="margin: 0;"> <span id="LC545" class="line" lang="html">    readGroup = ""</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="598" style="width: 35px; color: rgba(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="600" style="width: 35px; color: rgba(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">@@ -598,13 +600,13 @@ def writeBlast(opts, maf, oldQueryName):</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

</td>

<td class="diff-line-num new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

</td>

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

<pre style="margin: 0;"> <span id="LC600" class="line" lang="html">    seqNameB, seqLenB, strandB, letterSizeB, begB, endB, rowB = fieldsB</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

</td>

<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

</td>

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

<pre style="margin: 0;"> <span id="LC601" 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="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

</td>

<td class="diff-line-num new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

</td>

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

<pre style="margin: 0;"> <span id="LC602" class="line" lang="html">    if seqNameB != oldQueryName:</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="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

601

</td>

<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC601" class="line" lang="html">        print<span class="idiff left right"> "Query= " + seqNameB</span></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="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

602

</td>

<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC602" class="line" lang="html">        print<span class="idiff left right"> "         (%s letters)" % seqLenB</span></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="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

603

</td>

<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC603" class="line" lang="html">        print</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="604" style="width: 35px; color: rgba(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="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

</td>

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

<pre style="margin: 0;">+<span id="LC603" class="line" lang="html">        print<span class="idiff left right">("Query= " + seqNameB)</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="604" style="width: 35px; color: rgba(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="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

</td>

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

<pre style="margin: 0;">+<span id="LC604" class="line" lang="html">        print<span class="idiff left right">("         (%s letters)" % seqLenB)</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="604" style="width: 35px; color: rgba(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="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

</td>

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

<pre style="margin: 0;">+<span id="LC605" class="line" lang="html">        print<span class="idiff left right">()</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

</td>

<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

</td>

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

<pre style="margin: 0;"> <span id="LC606" 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="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

605

</td>

<td class="diff-line-num new_line old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC605" class="line" lang="html">    print<span class="idiff left right"> ">" + seqNameA</span></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="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

606

</td>

<td class="diff-line-num new_line old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC606" class="line" lang="html">    print<span class="idiff left right"> "          Length = %s" % seqLenA</span></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="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

607

</td>

<td class="diff-line-num new_line old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC607" class="line" lang="html">    print</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="608" style="width: 35px; color: rgba(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="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

</td>

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

<pre style="margin: 0;">+<span id="LC607" class="line" lang="html">    print<span class="idiff left right">(">" + seqNameA)</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="608" style="width: 35px; color: rgba(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="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

</td>

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

<pre style="margin: 0;">+<span id="LC608" class="line" lang="html">    print<span class="idiff left right">("          Length = %s" % seqLenA)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="608" style="width: 35px; color: rgba(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="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

609

</td>

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

<pre style="margin: 0;">+<span id="LC609" class="line" lang="html">    print<span class="idiff left right">()</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

</td>

<td class="diff-line-num new_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">

610

</td>

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

<pre style="margin: 0;"> <span id="LC610" 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="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC611" class="line" lang="html">    score, evalue = scoreAndEvalue(aLine)</span>

</pre>

</td>

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

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

610

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC612" class="line" lang="html"></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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -617,7 +619,7 @@ def writeBlast(opts, maf, oldQueryName):</td>

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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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC619" class="line" lang="html">    if evalue:</span>

</pre>

</td>

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

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

</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

</td>

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

<pre style="margin: 0;"> <span id="LC620" class="line" lang="html">        scoreLine += ", Expect = %s" % evalue</span>

</pre>

</td>

</tr>

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

<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

</td>

<td class="diff-line-num new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

</td>

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

<pre style="margin: 0;"> <span id="LC621" 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="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

620

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC620" class="line" lang="html">    print<span class="idiff left right"> scoreLine</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="621" style="width: 35px; color: rgba(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="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

622

</td>

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

<pre style="margin: 0;">+<span id="LC622" class="line" lang="html">    print<span class="idiff left right">(scoreLine)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

</td>

<td class="diff-line-num new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

</td>

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

<pre style="margin: 0;"> <span id="LC623" 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="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

</td>

<td class="diff-line-num new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

</td>

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

<pre style="margin: 0;"> <span id="LC624" class="line" lang="html">    alignmentColumns = zip(rowA, rowB)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC625" class="line" lang="html"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="629" style="width: 35px; color: rgba(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="631" style="width: 35px; color: rgba(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">@@ -629,19 +631,19 @@ def writeBlast(opts, maf, oldQueryName):</td>

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

<td class="diff-line-num old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

</td>

<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

</td>

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

<pre style="margin: 0;"> <span id="LC631" class="line" lang="html">    if gaps:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

</td>

<td class="diff-line-num new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

</td>

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

<pre style="margin: 0;"> <span id="LC632" class="line" lang="html">        gapPercent = 100 * gaps // alnSize  # round down, like BLAST</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

</td>

<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

</td>

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

<pre style="margin: 0;"> <span id="LC633" class="line" lang="html">        identLine += ", Gaps = %s/%s (%s%%)" % (gaps, alnSize, gapPercent)</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="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

632

</td>

<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC632" class="line" lang="html">    print<span class="idiff left right"> identLine</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="633" style="width: 35px; color: rgba(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="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

</td>

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

<pre style="margin: 0;">+<span id="LC634" class="line" lang="html">    print<span class="idiff left right">(identLine)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

</td>

<td class="diff-line-num new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

</td>

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

<pre style="margin: 0;"> <span id="LC635" 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="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

634

</td>

<td class="diff-line-num new_line old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC634" class="line" lang="html">    print<span class="idiff left right"> " Strand = %s / %s" % (strandText(strandB), strandText(strandA</span>))</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

635

</td>

<td class="diff-line-num new_line old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC635" class="line" lang="html">    print</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="636" style="width: 35px; color: rgba(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="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

</td>

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

<pre style="margin: 0;">+<span id="LC636" class="line" lang="html">    print<span class="idiff left right">(" Strand = %s / %s" % (strandText(strandB), strandText(strandA)</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="636" style="width: 35px; color: rgba(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="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

</td>

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

<pre style="margin: 0;">+<span id="LC637" class="line" lang="html">    print<span class="idiff left right">()</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

</td>

<td class="diff-line-num new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

</td>

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

<pre style="margin: 0;"> <span id="LC638" 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="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

637

</td>

<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

</td>

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

<pre style="margin: 0;"> <span id="LC639" class="line" lang="html">    for chunk in blastChunker(sLines, opts.linesize, alignmentColumns):</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

</td>

<td class="diff-line-num 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">

640

</td>

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

<pre style="margin: 0;"> <span id="LC640" class="line" lang="html">        cols, rows, begs, ends = chunk</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

</td>

<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

</td>

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

<pre style="margin: 0;"> <span id="LC641" class="line" lang="html">        begWidth = maxlen(begs)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

640

</td>

<td class="diff-line-num new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

</td>

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

<pre style="margin: 0;"> <span id="LC642" class="line" lang="html">        matchSymbols = ''.join(map(pairwiseMatchSymbol, cols))</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="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

641

</td>

<td class="diff-line-num new_line old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC641" class="line" lang="html">        print<span class="idiff left right"> "Query: %-*s %s %s" % (begWidth, begs[1], rows[1], ends[1]</span>)</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="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

642

</td>

<td class="diff-line-num new_line old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC642" class="line" lang="html">        print<span class="idiff left right"> "       %-*s %s"    % (begWidth, " ", matchSymbols</span>)</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="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

643

</td>

<td class="diff-line-num new_line old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC643" class="line" lang="html">        print<span class="idiff left right"> "Sbjct: %-*s %s %s" % (begWidth, begs[0], rows[0], ends[0]</span>)</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="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

644

</td>

<td class="diff-line-num new_line old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC644" class="line" lang="html">        print</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="645" style="width: 35px; color: rgba(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="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

</td>

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

<pre style="margin: 0;">+<span id="LC643" class="line" lang="html">        print<span class="idiff left right">("Query: %-*s %s %s" % (begWidth, begs[1], rows[1], ends[1])</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="645" style="width: 35px; color: rgba(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="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

644

</td>

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

<pre style="margin: 0;">+<span id="LC644" class="line" lang="html">        print<span class="idiff left right">("       %-*s %s"    % (begWidth, " ", matchSymbols)</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="645" style="width: 35px; color: rgba(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="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

</td>

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

<pre style="margin: 0;">+<span id="LC645" class="line" lang="html">        print<span class="idiff left right">("Sbjct: %-*s %s %s" % (begWidth, begs[0], rows[0], ends[0])</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="645" style="width: 35px; color: rgba(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="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

646

</td>

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

<pre style="margin: 0;">+<span id="LC646" class="line" lang="html">        print<span class="idiff left right">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

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<td class="diff-line-num new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

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

<pre style="margin: 0;"> <span id="LC647" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

646

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<td class="diff-line-num new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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

<pre style="margin: 0;"> <span id="LC648" class="line" lang="html">def mafConvertToBlast(opts, lines):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

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<td class="diff-line-num new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

649

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

<pre style="margin: 0;"> <span id="LC649" class="line" lang="html">    oldQueryName = ""</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="682" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -682,7 +684,7 @@ def writeBlastTab(opts, maf):</td>

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<td class="diff-line-num old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

682

</td>

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

<pre style="margin: 0;"> <span id="LC684" class="line" lang="html">            bitScore = opts.bitScoreA * float(score) - opts.bitScoreB</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

683

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

<pre style="margin: 0;"> <span id="LC685" class="line" lang="html">            out.append("%.3g" % bitScore)</span>

</pre>

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

<pre style="margin: 0;"> <span id="LC686" class="line" lang="html"></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="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

685

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<td class="diff-line-num new_line old" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC685" class="line" lang="html">    print<span class="idiff left right"> "\t".join(out</span>)</span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(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="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

687

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

<pre style="margin: 0;">+<span id="LC687" class="line" lang="html">    print<span class="idiff left right">("\t".join(out)</span>)</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

</td>

<td class="diff-line-num new_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

688

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

<pre style="margin: 0;"> <span id="LC688" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

687

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

<pre style="margin: 0;"> <span id="LC689" class="line" lang="html">def mafConvertToBlastTab(opts, lines):</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

688

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<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC690" class="line" lang="html">    for maf in mafInput(opts, lines):</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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -691,7 +693,7 @@ def mafConvertToBlastTab(opts, lines):</td>

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

<pre style="margin: 0;"> <span id="LC693" class="line" lang="html">##### Routines for converting to HTML format: #####</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

</td>

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

<pre style="margin: 0;"> <span id="LC694" class="line" lang="html"></span>

</pre>

</td>

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<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="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

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

<pre style="margin: 0;"> <span id="LC695" class="line" lang="html">def writeHtmlHeader():</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="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

694

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<td class="diff-line-num new_line old" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC694" class="line" lang="html">    print<span class="idiff left right"> </span>'''</span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="695" style="width: 35px; color: rgba(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="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

696

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

<pre style="margin: 0;">+<span id="LC696" class="line" lang="html">    print<span class="idiff left right">(</span>'''</span>

</pre>

</td>

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

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

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

<pre style="margin: 0;"> <span id="LC697" class="line" lang="html"><span class="cp" style="color: #999; font-weight: 600;"><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"</span></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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC698" class="line" lang="html"><span class="cp" style="color: #999; font-weight: 600;"> "http://www.w3.org/TR/html4/strict.dtd"></span></span>

</pre>

</td>

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

<pre style="margin: 0;"> <span id="LC699" class="line" lang="html"><span class="nt" style="color: navy;"><html</span> <span class="na" style="color: teal;">lang=</span><span class="s" style="color: #d14;">"en"</span><span class="nt" style="color: navy;">><head></span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -718,7 +720,7 @@ pre {font-family: "Courier New", monospace, serif; font-size: 0.8125em}</td>

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<td class="diff-line-num old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

718

</td>

<td class="diff-line-num new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

</td>

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

<pre style="margin: 0;"> <span id="LC720" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"key"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"e"</span><span class="nt" style="color: navy;">></span>  <span class="nt" style="color: navy;"></span></span> prob <span class="ni" style="color: purple;">&gt;</span> 0.5  <span class="nt" style="color: navy;"></pre></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

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<td class="diff-line-num new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

</td>

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

<pre style="margin: 0;"> <span id="LC721" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"key"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"f"</span><span class="nt" style="color: navy;">></span>  <span class="nt" style="color: navy;"></span></span> prob <span class="ni" style="color: purple;">&le;</span> 0.5  <span class="nt" style="color: navy;"></pre></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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

</td>

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

<pre style="margin: 0;"> <span id="LC722" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

721

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<td class="diff-line-num new_line old" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC721" class="line" lang="html">'''</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

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

<pre style="margin: 0;">+<span id="LC723" class="line" lang="html">'''<span class="idiff left right">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

</td>

<td class="diff-line-num new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

</td>

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

<pre style="margin: 0;"> <span id="LC724" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

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<td class="diff-line-num new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

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

<pre style="margin: 0;"> <span id="LC725" class="line" lang="html">def probabilityClass(probabilityColumn):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

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<td class="diff-line-num new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

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

<pre style="margin: 0;"> <span id="LC726" class="line" lang="html">    p = ord(min(probabilityColumn)) - 33</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -756,7 +758,7 @@ def writeHtml(opts, maf):</td>

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<td class="diff-line-num old_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

</td>

<td class="diff-line-num 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">

758

</td>

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

<pre style="margin: 0;"> <span id="LC758" class="line" lang="html">        scoreLine += " score=" + score</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

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<td class="diff-line-num new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

759

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<pre style="margin: 0;"> <span id="LC759" class="line" lang="html">        if evalue:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

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

<pre style="margin: 0;"> <span id="LC760" class="line" lang="html">            scoreLine += ", expect=" + evalue</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="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

759

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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="LC759" class="line" lang="html">    print<span class="idiff left"> "</span><span class="nt" style="color: navy;"><span class="idiff"><h3></span></span><span class="idiff">%s:</span><span class="nt" style="color: navy;"><span class="idiff"></h3></span></span><span class="idiff right">" % scoreLine</span></span>

</pre>

</td>

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

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

</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

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

<pre style="margin: 0;">+<span id="LC761" class="line" lang="html">    print<span class="idiff left">("</span><span class="nt" style="color: navy;"><span class="idiff"><h3></span></span><span class="idiff">%s:</span><span class="nt" style="color: navy;"><span class="idiff"></h3></span></span><span class="idiff right">" % scoreLine)</span></span>

</pre>

</td>

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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

</td>

<td class="diff-line-num new_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

</td>

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

<pre style="margin: 0;"> <span id="LC762" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

761

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

<pre style="margin: 0;"> <span id="LC763" class="line" lang="html">    if pLines:</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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<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="html">        probRows = [i.split()[1] for i in pLines]</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="772" style="width: 35px; color: rgba(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">@@ -770,7 +772,7 @@ def writeHtml(opts, maf):</td>

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<td class="diff-line-num old_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

</td>

<td class="diff-line-num new_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

772

</td>

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

<pre style="margin: 0;"> <span id="LC772" class="line" lang="html">    rows = [i[6] for i in sLines]</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

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<td class="diff-line-num new_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

773

</td>

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

<pre style="margin: 0;"> <span id="LC773" class="line" lang="html">    alignmentColumns = zip(*rows)</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

772

</td>

<td class="diff-line-num new_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

</td>

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

<pre style="margin: 0;"> <span id="LC774" 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="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

773

</td>

<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC773" class="line" lang="html">    print<span class="idiff left"> '</span><span class="nt" style="color: navy;"><span class="idiff"><pre></span></span><span class="idiff right">'</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="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">

</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

</td>

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

<pre style="margin: 0;">+<span id="LC775" class="line" lang="html">    print<span class="idiff left">('</span><span class="nt" style="color: navy;"><span class="idiff"><pre></span></span><span class="idiff right">')</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

</td>

<td class="diff-line-num new_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

</td>

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

<pre style="margin: 0;"> <span id="LC776" class="line" lang="html">    for chunk in blastChunker(sLines, opts.linesize, alignmentColumns):</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

775

</td>

<td class="diff-line-num new_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

777

</td>

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

<pre style="margin: 0;"> <span id="LC777" class="line" lang="html">        cols, rows, begs, ends = chunk</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

</td>

<td class="diff-line-num new_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

</td>

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

<pre style="margin: 0;"> <span id="LC778" class="line" lang="html">        begWidth = maxlen(begs)</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="782" style="width: 35px; color: rgba(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="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -782,10 +784,10 @@ def writeHtml(opts, maf):</td>

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

<td class="diff-line-num old_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

</td>

<td class="diff-line-num new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

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

<pre style="margin: 0;"> <span id="LC784" class="line" lang="html">            spans = [htmlSpan(r, i) for i in classRuns]</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

</td>

<td class="diff-line-num new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

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

<pre style="margin: 0;"> <span id="LC785" class="line" lang="html">            spans = ''.join(spans)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

<td class="diff-line-num new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

</td>

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

<pre style="margin: 0;"> <span id="LC786" class="line" lang="html">            formatParams = nameWidth, n, begWidth, b, spans, endWidth, e</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="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

785

</td>

<td class="diff-line-num new_line old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC785" class="line" lang="html">            print<span class="idiff left right"> '%-*s %*s %s %*s' % formatParams</span></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="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

786

</td>

<td class="diff-line-num new_line old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC786" class="line" lang="html">        print<span class="idiff left right"> ' ' * nameWidth, ' ' * begWidth, matchSymbols</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

787

</td>

<td class="diff-line-num new_line old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC787" class="line" lang="html">        print</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="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

788

</td>

<td class="diff-line-num new_line old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC788" class="line" lang="html">    print<span class="idiff left"> '</span><span class="nt" style="color: navy;"><span class="idiff"></pre></span></span><span class="idiff right">'</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="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

<pre style="margin: 0;">+<span id="LC787" class="line" lang="html">            print<span class="idiff left right">('%-*s %*s %s %*s' % formatParams)</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="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

<pre style="margin: 0;">+<span id="LC788" class="line" lang="html">        print<span class="idiff left right">(' ' * nameWidth, ' ' * begWidth, matchSymbols)</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="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

<pre style="margin: 0;">+<span id="LC789" class="line" lang="html">        print<span class="idiff left right">()</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="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

<pre style="margin: 0;">+<span id="LC790" class="line" lang="html">    print<span class="idiff left">('</span><span class="nt" style="color: navy;"><span class="idiff"></pre></span></span><span class="idiff right">')</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

</td>

<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

</td>

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

<pre style="margin: 0;"> <span id="LC791" 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="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

</td>

<td class="diff-line-num new_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

</td>

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

<pre style="margin: 0;"> <span id="LC792" class="line" lang="html">def mafConvertToHtml(opts, lines):</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

</td>

<td class="diff-line-num new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

</td>

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

<pre style="margin: 0;"> <span id="LC793" class="line" lang="html">    for maf in mafInput(opts, lines):</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="841" style="width: 35px; color: rgba(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="843" style="width: 35px; color: rgba(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">@@ -841,7 +843,7 @@ def mafConvert(opts, args):</td>

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<td class="diff-line-num old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

</td>

<td class="diff-line-num new_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

843

</td>

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

<pre style="margin: 0;"> <span id="LC843" 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="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

</td>

<td class="diff-line-num new_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

844

</td>

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

<pre style="margin: 0;"> <span id="LC844" class="line" lang="html">    if not opts.noheader:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

843

</td>

<td class="diff-line-num new_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

845

</td>

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

<pre style="margin: 0;"> <span id="LC845" class="line" lang="html">        if isFormat(formatName, "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="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

844

</td>

<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC844" class="line" lang="html">            print<span class="idiff left"> "</span><span class="nt" style="color: navy;"><span class="idiff"></body></html></span></span><span class="idiff right">"</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="845" style="width: 35px; color: rgba(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="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

846

</td>

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

<pre style="margin: 0;">+<span id="LC846" class="line" lang="html">            print<span class="idiff left">("</span><span class="nt" style="color: navy;"><span class="idiff"></body></html></span></span><span class="idiff right">")</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

845

</td>

<td class="diff-line-num new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

</td>

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

<pre style="margin: 0;"> <span id="LC847" class="line" lang="html"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

</td>

<td class="diff-line-num new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

</td>

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

<pre style="margin: 0;"> <span id="LC848" class="line" lang="html">if __name__ == "__main__":</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

</td>

<td class="diff-line-num new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

849

</td>

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

<pre style="margin: 0;"> <span id="LC849" class="line" lang="html">    signal.signal(signal.SIGPIPE, signal.SIG_DFL)  # avoid silly error message</span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -882,6 +884,6 @@ if __name__ == "__main__":</td>

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

<td class="diff-line-num old_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

</td>

<td class="diff-line-num new_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

</td>

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

<pre style="margin: 0;"> <span id="LC884" class="line" lang="html">        <span class="na" style="color: teal;">op</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">error</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: teal;">need</span> <span class="na" style="color: teal;">file</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">not</span> <span class="na" style="color: teal;">pipe</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="na" style="color: teal;">with</span> <span class="na" style="color: teal;">option</span> <span class="na" style="color: teal;">-d</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

</td>

<td class="diff-line-num new_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

</td>

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

<pre style="margin: 0;"> <span id="LC885" 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="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

</td>

<td class="diff-line-num new_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

886

</td>

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

<pre style="margin: 0;"> <span id="LC886" class="line" lang="html">    <span class="na" style="color: teal;">try:</span> <span class="na" style="color: teal;">mafConvert</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: teal;">args</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

885

</td>

<td class="diff-line-num new_line old" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC885" class="line" lang="html">    <span class="na" style="color: teal;">except</span> <span class="na" style="color: teal;">Exception</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">,</span></span> <span class="na" style="color: teal;">e:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="886" style="width: 35px; color: rgba(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="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

887

</td>

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

<pre style="margin: 0;">+<span id="LC887" class="line" lang="html">    <span class="na" style="color: teal;">except</span> <span class="na" style="color: teal;">Exception</span><span class="idiff left"> </span><span class="na" style="color: teal;"><span class="idiff right">as</span></span> <span class="na" style="color: teal;">e:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

886

</td>

<td class="diff-line-num new_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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

<pre style="margin: 0;"> <span id="LC888" class="line" lang="html">        <span class="na" style="color: teal;">prog =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">os.path.basename(sys.argv[0])</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

</td>

<td class="diff-line-num new_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

</td>

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

<pre style="margin: 0;"> <span id="LC889" class="line" lang="html">        <span class="na" style="color: teal;">sys</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">exit</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">prog</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: teal;">:</span> <span class="na" style="color: teal;">error:</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: teal;">str</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="c647c36ae9d03ba272edef63f9a8da1d719e4c7d">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#c647c36ae9d03ba272edef63f9a8da1d719e4c7d"><strong>scripts/maf-join</strong></a>

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<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,8 @@</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># WARNING: Alignment columns with a gap in the top genome are joined</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># arbitrarily!!!</span></span>

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

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<pre style="margin: 0;">+<span id="LC13" 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>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">fileinput</span><span class="p">,</span> <span class="n" style="color: #333;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span></span>

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIGPIPE</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIG_DFL</span><span class="p">)</span>  <span class="c" style="color: #998; font-style: italic;"># stop spurious error message</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">        <span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrSize</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">        <span class="n" style="color: #333;">widths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">maxLen</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'a'</span></span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'a'</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">columns</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">            <span class="n" style="color: #333;">widthsAndFields</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">widths</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">            <span class="n" style="color: #333;">field0</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%-*</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">widthsAndFields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span>  <span class="c" style="color: #998; font-style: italic;"># left-justify</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC79" class="line" lang="python">            <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">widthsAndFields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]]</span>  <span class="c" style="color: #998; font-style: italic;"># right-justify</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'s'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">field0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">' '</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fields</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'s'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">field0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">' '</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">        <span class="n" style="color: #333;">pad</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;">join</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">widths</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 new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prob</span><span class="p">:</span></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="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'p'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pad</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(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="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC82" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span>  <span class="c" style="color: #998; font-style: italic;"># blank line afterwards</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="83" style="width: 35px; color: rgba(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="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'p'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pad</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="83" style="width: 35px; color: rgba(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="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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

<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span>  <span class="c" style="color: #998; font-style: italic;"># blank line afterwards</span></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="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"></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="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="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">topSeqBeg</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">):</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">beg</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">topSeqEnd</span><span class="p">(</span><span class="n" style="color: #333;">maf</span><span class="p">):</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="350d50b528bcd24a057c181965b2a50120bca4c7">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#350d50b528bcd24a057c181965b2a50120bca4c7"><strong>scripts/maf-swap</strong></a>

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<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">@@ -9,11 +9,13 @@</td>

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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">

9

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

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

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Seems to work with Python 2.x, x>=4</span></span>

</pre>

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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="python"></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="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="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 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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">fileinput</span><span class="p">,</span> <span class="n" style="color: #333;">itertools</span><span class="p">,</span> <span class="n" style="color: #333;">optparse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>

</pre>

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<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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filterComments</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>

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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="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">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">):</span> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">):</span> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">i</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafInput</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,8 +121,8 @@ def mafSwap(opts, args):</td>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">        <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">stop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">stop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">start</span><span class="p">]</span></span>

</pre>

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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="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;">isCanonicalStrand</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]):</span></span>

</pre>

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<td class="diff-line-num 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="123" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC123" class="line" lang="python">            <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flippedMaf</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="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="124" style="width: 35px; color: rgba(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="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC123" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span>  <span class="c" style="color: #998; font-style: italic;"># blank line after each alignment</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">

</td>

<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></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">

</td>

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

<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span>  <span class="c" style="color: #998; font-style: italic;"># blank line after each alignment</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"></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="127" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC127" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></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="128" style="width: 35px; color: rgba(0,0,0,0.3); 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="python">    <span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIGPIPE</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIG_DFL</span><span class="p">)</span>  <span class="c" style="color: #998; font-style: italic;"># avoid silly error message</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,6 +137,6 @@ if __name__ == "__main__":</td>

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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num 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">

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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="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="n" style="color: #333;">mafSwap</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>

</pre>

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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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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC139" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyboardInterrupt</span><span class="p">:</span> <span class="k" style="font-weight: 600;">pass</span>  <span class="c" style="color: #998; font-style: italic;"># avoid silly error message</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(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="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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="140" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC140" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">        <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": error: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span></pre>

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<br>

</li>

<li id="4b7be8c3b80efc62977b307791d1a304c23e1fa4">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,15 +41,14 @@ static char parseOutputFormat( const char* text ){</td>

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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="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="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="p">}</span></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">

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

</pre>

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parseScoreOrPercent</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</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="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">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parseScoreAndSuffix</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffix</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="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">

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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">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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="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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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC46" 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;">istringstream</span> <span class="n" style="color: #333;">iss</span><span class="p">(</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_line old" 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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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"bad value: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'%'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"bad value: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp">    <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;">x</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// negative value indicates percentage (kludge)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC47" 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;">istringstream</span> <span class="n" style="color: #333;">i</span><span class="p">(</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="52" style="width: 35px; color: rgba(0,0,0,0.3); 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">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</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;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</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;">c</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;">c</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="52" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp">    <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"bad value: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">  <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></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">@@ -78,9 +77,11 @@ LastalArguments::LastalArguments() :</td>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp">  <span class="n" style="color: #333;">gapPairCost</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// this means: OFF</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">  <span class="n" style="color: #333;">frameshiftCost</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// this means: ordinary, non-translated alignment</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">  <span class="n" style="color: #333;">matrixFile</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropGapped</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">100</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on minScoreGapped & maxDropGapless</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropGapped</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on maxDropFinal</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropGappedSuffix</span><span class="p">(</span><span class="sc" style="color: #d14;">'%'</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropGapless</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on the score matrix</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropFinal</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on maxDropGapped</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropFinal</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on minScoreGapped</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">  <span class="n" style="color: #333;">maxDropFinalSuffix</span><span class="p">(</span><span class="sc" style="color: #d14;">'%'</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">  <span class="n" style="color: #333;">inputFormat</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;">fasta</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">  <span class="n" style="color: #333;">minHitDepth</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">  <span class="n" style="color: #333;">maxHitDepth</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,9 +129,9 @@ Score options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC129" 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="LC130" 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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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="s" style="color: #d14;">-F: frameshift cost (off)</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="LC131" class="line" lang="cpp"><span class="s" style="color: #d14;">-x: maximum score drop for <span class="idiff left right">gapped alignments (e-1</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="LC132" class="line" lang="cpp"><span class="s" style="color: #d14;">-x: maximum score drop for <span class="idiff left right">preliminary gapped alignments (z</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="LC133" class="line" lang="cpp"><span class="s" style="color: #d14;">-y: maximum score drop for gapless alignments (min[t*10, x])</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="LC133" class="line" lang="cpp"><span class="s" style="color: #d14;">-z: maximum score drop for final gapped alignments (<span class="idiff left right">x</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="LC134" class="line" lang="cpp"><span class="s" style="color: #d14;">-z: maximum score drop for final gapped alignments (<span class="idiff left right">e-1</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="LC135" class="line" lang="cpp"><span class="s" style="color: #d14;">-d: minimum score for gapless alignments (min[e, t*ln(1000*refSize/n)])</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="s" style="color: #d14;">-e: minimum score for gapped alignments</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="LC137" class="line" lang="cpp"><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">@@ -234,15 +235,14 @@ LAST home page: http://last.cbrc.jp/\n\</td>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">frameshiftCost</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;">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="LC236" 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="LC237" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp">      <span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseScore<span class="idiff left">OrPercent</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">optarg</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">      <span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseScore<span class="idiff left">AndSuffix</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">optarg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxDropGappedSuffix</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC240" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'y'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC241" class="line" lang="cpp">      <span class="n" style="color: #333;">unstringify</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropGapless</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC242" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropGapless</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;">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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC243" 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="LC244" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'z'</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">      <span class="n" style="color: #333;">unstringify</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropFinal</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="LC245" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropFinal</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;">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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC245" class="line" lang="cpp">      <span class="n" style="color: #333;">maxDropFinal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseScoreAndSuffix</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropFinalSuffix</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC246" 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="LC247" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">      <span class="n" style="color: #333;">unstringify</span><span class="p">(</span> <span class="n" style="color: #333;">minScoreGapless</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="523" style="width: 35px; color: rgba(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="523" style="width: 35px; color: rgba(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">@@ -523,6 +523,10 @@ void LastalArguments::setDefaultsFromAlphabet( bool isDna, bool isProtein,</td>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC525" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); 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="526" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC526" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">percent</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">percentage</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="526" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC527" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LastalArguments</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setDefaultsFromMatrix</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minScore</span> <span class="p">){</span></span>

</pre>

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531

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<pre style="margin: 0;"> <span id="LC531" 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;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">minScoreGapped</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;">minScoreGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minScoreGapless</span><span class="p">;</span></span>

</pre>

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528

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">minScoreGapped</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 unfold js-unfold old_line" data-linenumber="536" style="width: 35px; color: rgba(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="540" style="width: 35px; color: rgba(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">@@ -536,11 +540,19 @@ To proceed without E-values, set a score threshold with option -e.");</td>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"></span>

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541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lambda</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); 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="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

539

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<td class="diff-line-num new_line old" data-linenumber="543" style="width: 35px; color: rgba(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="LC539" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropGapped</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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540

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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxDropGapped</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC541" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropGapped</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;">max</span><span class="p">(</span> <span class="n" style="color: #333;">minScoreGapped</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropGapped</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;">max</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropGapped</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropGapless</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC543" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">percent</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percent</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">defaultMaxScoreDrop</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;">max</span><span class="p">(</span><span class="n" style="color: #333;">minScoreGapped</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp">  <span class="n" style="color: #333;">defaultMaxScoreDrop</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;">max</span><span class="p">(</span><span class="n" style="color: #333;">defaultMaxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropGapless</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxDropFinalSuffix</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'%'</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropFinal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">percent</span><span class="p">(</span><span class="n" style="color: #333;">defaultMaxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropFinal</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC548" 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;">maxDropFinalSuffix</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropFinal</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;">min</span><span class="p">(</span><span class="n" style="color: #333;">minGapCost</span><span class="p">(</span><span class="n" style="color: #333;">maxDropFinal</span><span class="p">),</span> <span class="n" style="color: #333;">defaultMaxScoreDrop</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp">  <span class="p">}</span></span>

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551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxDropGappedSuffix</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'%'</span><span class="p">)</span> <span class="p">{</span></span>

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553

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">percent</span><span class="p">(</span><span class="n" style="color: #333;">maxDropFinal</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropGapped</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC554" 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;">maxDropGappedSuffix</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">)</span> <span class="p">{</span></span>

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555

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropGapped</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;">min</span><span class="p">(</span><span class="n" style="color: #333;">minGapCost</span><span class="p">(</span><span class="n" style="color: #333;">maxDropGapped</span><span class="p">),</span> <span class="n" style="color: #333;">maxDropFinal</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropGapless</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">){</span>  <span class="c1" style="color: #998; font-style: italic;">// should it depend on temperature or lambda?</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="548" style="width: 35px; color: rgba(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">@@ -548,8 +560,6 @@ To proceed without E-values, set a score threshold with option -e.");</td>

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548

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span>                  <span class="n" style="color: #333;">maxDropGapless</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span> <span class="mf" style="color: #099;">10.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">0.5</span> <span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC561" class="line" lang="cpp">    <span class="n" style="color: #333;">maxDropGapless</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;">min</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropGapless</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropGapped</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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551

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<td class="diff-line-num new_line old" data-linenumber="563" style="width: 35px; color: rgba(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="LC551" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC552" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">maxDropFinal</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;">maxDropFinal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxDropGapped</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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554

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC565" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">LastalArguments</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calcMinScoreGapless</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">numLettersInReference</span><span class="p">,</span></span>

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<br>

</li>

<li id="c41d15f61c8e13ecbdb96a800b59fc069d2c6695">

<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#c41d15f61c8e13ecbdb96a800b59fc069d2c6695"><strong>src/LastalArguments.hh</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,6 +56,11 @@ struct LastalArguments{</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// how many strands are we scanning (1 or 2)?</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numOfStrands</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

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

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<td class="diff-line-num new old_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="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minGapCost</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapLength</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC60" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">gapExistCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gapLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gapExtendCost</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">               <span class="n" style="color: #333;">insExistCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gapLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insExtendCost</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC63" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC64" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// options:</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outputFormat</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outputType</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -80,8 +85,10 @@ struct LastalArguments{</td>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC86" 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;">matrixFile</span><span class="p">;</span></span>

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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="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">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDropGapped</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); 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="88" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC88" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">maxDropGappedSuffix</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDropGapless</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDropFinal</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">maxDropFinalSuffix</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC92" 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;">inputFormat</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">minHitDepth</span><span class="p">;</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxHitDepth</span><span class="p">;</span></span>

</pre>

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<a href="https://salsa.debian.org/med-team/last-align/compare/e2061edc0f126034f89e1bf00ed3aad468447d23...54f0b1f06cf4f118ee23f5da391f6776a40cbc36#69737f84c540417aafef4e696f66adcc9f92fa66"><strong>src/version.hh</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"93<span class="idiff left right">2</span>"</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"93<span class="idiff left right">8</span>"</span></span></pre>

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