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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

at <a href="https://salsa.debian.org/med-team/minimap2">Debian Med / minimap2</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/4e8c3e6fccfc387291ed10cd242bb73d9cbd05cf">4e8c3e6f</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-14T12:35:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches, dropping simde

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/f59569aed43480f538f7de7b5c0da39003504fe7">f59569ae</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-14T12:41:58+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add setuptools as a build-dep

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/1ca19dee9176426b9af9fd46229fea7b9422fea9">1ca19dee</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-14T12:47:02+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">collapse overlapping dh_auto_clean overrides

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/dcc5929a37635e276c038cff118a12ff388ddd81">dcc5929a</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-14T13:04:33+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#d4657693b4cbba1934a7abddc0a140b4505aebf7">

debian/patches/ar.patch

</a>

</li>

<li class="file-stats">

<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">

debian/patches/hardening.patch

</a>

</li>

<li class="file-stats">

<a href="#0152a445c5ca093e900d11b69b1be23f80f9d7db">

debian/patches/link_mappy_to_libminimap.patch

</a>

</li>

<li class="file-stats">

<a href="#d35b47736da2c4a1f6a0595ac0a6e0fc4759d32c">

debian/patches/python-sse4-arch.patch

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">

<span class="deleted-file">

−

debian/patches/simde

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">minimap2 (2.22+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">minimap2 (2.22+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>

</pre>

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2

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

2

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

</pre>

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

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

3

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

</pre>

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

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

4

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

</pre>

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

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

5

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * Fix watchfile to detect new versions on github</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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

5

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">  * Standards-Version: 4.6.0 (routine-update)</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * Use sensible file name for uscan downloads</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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

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

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Thu, 14 Oct 2021 08:51:33 +0200</span>

</pre>

</td>

</tr>

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

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  [ Michael R. Crusoe ]</span>

</pre>

</td>

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

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

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">  * Refresh patches, dropping simde</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  * Add setuptools as a build-dep</span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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"></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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"> -- Michael R. Crusoe <crusoe@debian.org>  Thu, 14 Oct 2021 12:59:39 +0200</span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">minimap2 (2.17+dfsg-12) unstable; urgency=medium</span>

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11

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

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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>

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

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">               python3-setuptools,</span>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               cython3,</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               python3-all-dev,</span>

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</li>

<li id="d4657693b4cbba1934a7abddc0a140b4505aebf7">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#d4657693b4cbba1934a7abddc0a140b4505aebf7"><strong>debian/patches/ar.patch</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,9 @@ Author: Steffen Moeller</td>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-03-15 04:06:20 +0100</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Descriptio: Fix ar call to support debugging symbols properly</span></span>

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/Makefile</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/Makefile</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">3</span>5,7 +<span class="idiff">3</span>5,8 @@</span><span class="idiff right"> minimap2-lite:example.o libminimap2.a</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">minimap2.orig</span>/Makefile</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">minimap2</span>/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -5<span class="idiff left">1</span>,7 +5<span class="idiff right">1</span>,8 @@</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">           $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> libminimap2.a:$(OBJS)</span>

</pre>

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<br>

</li>

<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,17 +2,17 @@ Author: Andreas Tille <tille@debian.org></td>

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<td class="old_line diff-line-num" 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="diff"><span class="p">Last-Update: Fri, 17 Aug 2018 11:04:09 +0200</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Propagate hardening options</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/Makefile</span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/Makefile</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">minimap2.orig</span>/Makefile</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">minimap2</span>/Makefile</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=           -g -Wall -O2 -Wc++-compat #-Wextra</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CPPFLAGS= -DHAVE_KALLOC</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+=         -g -Wall -O2 -Wc++-compat #-Wextra</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS+=       -DHAVE_KALLOC</span></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> OBJS=            kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o <span class="idiff left right">chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> <span class="idiff left right">PROG=             minimap2</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">33</span>,16 +<span class="idiff">33</span>,16 @@</span><span class="idiff right"> all:$(PROG)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> OBJS=            kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o <span class="idiff left right">\</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="diff"> <span class="idiff left right">                  lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="diff"><span class="p">@@ -<span class="idiff left">45</span>,16 +<span class="idiff right">45</span>,16 @@</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> extra:all $(PROG_EXTRA)</span>

</pre>

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<td class="old_line diff-line-num" 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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17

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

</pre>

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

18

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

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> minimap2:main.o libminimap2.a</span>

</pre>

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<br>

</li>

<li id="0152a445c5ca093e900d11b69b1be23f80f9d7db">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#0152a445c5ca093e900d11b69b1be23f80f9d7db"><strong>debian/patches/link_mappy_to_libminimap.patch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,9 +3,9 @@ Last-Update: Fri, 15 May 2020 14:00:54 +0200</td>

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3

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Add libminimap to Python library</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> FIXME: seems extra_link_args and extra_objects are ignored both</span>

</pre>

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5

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5

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC6" class="line" lang="diff">--- <span class="idiff left right">a</span>/setup.py</span>

</pre>

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

7

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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/setup.py</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC8" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">1</span>9,6 +<span class="idiff">1</span>9,8 @@</span><span class="idiff right"> import sys, platform</span></span>

</pre>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">minimap2.orig</span>/setup.py</span>

</pre>

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">minimap2</span>/setup.py</span></span>

</pre>

</td>

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

</td>

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

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -9,6 +9,8 @@</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> sys.path.append('python')</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> extra_compile_args = ['-DHAVE_KALLOC']</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="d35b47736da2c4a1f6a0595ac0a6e0fc4759d32c">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#d35b47736da2c4a1f6a0595ac0a6e0fc4759d32c"><strong>debian/patches/python-sse4-arch.patch</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,9 +3,9 @@ From: Michael Hudson-Doyle <michael.hudson@canonical.com></td>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/969596</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Description: Only pass -msse4.1 to the compiler on amd64</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">a</span>/setup.py</span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/setup.py</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">2</span>6,7 +<span class="idiff right">2</span>6,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">minimap2.orig</span>/setup.py</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">minimap2</span>/setup.py</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">1</span>6,7 +<span class="idiff right">1</span>6,7 @@</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> if platform.machine() in ["aarch64", "arm64"]:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff">  include_dirs.append("sse2neon/")</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">  extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])</span>

</pre>

</td>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening.patch</span>

</pre>

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2

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

2

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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

</pre>

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4

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3

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

</pre>

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5

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

</pre>

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<td class="old_line diff-line-num" 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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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">python-sse4-arch.patch</span></pre>

</td>

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</table>

<br>

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<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong>

deleted

</a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: Add support for more architectures</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3" class="line" lang="diff"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4" class="line" lang="diff">using the SIMD Everywhere library</span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- minimap2.orig/ksw2_extd2_sse.c</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/ksw2_extd2_sse.c</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -3,29 +3,19 @@</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC8" class="line" lang="diff"> #include <assert.h></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC9" class="line" lang="diff"> #include "ksw2.h"</span>

</pre>

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse4.1.h"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#undef __SSE4_1__</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<td class="old_line diff-line-num 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="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(SIMDE_SSE4_1_NATIVE)</span></span>

</pre>

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<td class="old_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">                             int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(SIMDE_SSE2_NATIVE)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> void ksw_extd2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

</pre>

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<td class="old_line diff-line-num 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">

32

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                            int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                  int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span></span>

</pre>

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                            int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                  int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

</pre>

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

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> #define __dp_code_block1 \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">  z = _mm_load_si128(&s[t]); \</span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -161,13 +151,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff">                          st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff">                          mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));</span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff">                          tmp = _mm_cmpeq_epi8(sq, st);</span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff">                          tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff">                          tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);</span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_or_si128(_mm_andnot_si128(tmp,  sc_mis_), _mm_and_si128(tmp,  sc_mch_));</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff">                          _mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);</span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff">                  }</span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff">          } else {</span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="p">@@ -184,7 +169,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff">                  for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff">                          __m128i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff">                          __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff">                          z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff">                          z = _mm_max_epi8(z, b);</span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff">                          z = _mm_max_epi8(z, a2);</span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="p">@@ -195,27 +179,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff">                          _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_max_epi8(b,  zero_), qe_));</span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff">                          _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, zero_), qe2_));</span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff">                          _mm_store_si128(&y2[t], _mm_sub_epi8(_mm_max_epi8(b2, zero_), qe2_));</span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a,  z);</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b,  z);</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a2, z);</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2));</span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b2, z);</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmplt_epi8(sc_mch_, z);</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         __dp_code_block2;</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a, zero_);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b, zero_);</span></span>

</pre>

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<td class="old_line diff-line-num 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="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_and_si128(tmp, b),  qe_));</span></span>

</pre>

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<td class="old_line diff-line-num 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">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a2, zero_);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_and_si128(tmp, a2), qe2_));</span></span>

</pre>

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<td class="old_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b2, zero_);</span></span>

</pre>

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<td class="old_line diff-line-num 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">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&y2[t], _mm_sub_epi8(_mm_and_si128(tmp, b2), qe2_));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff">          } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>

</pre>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff">                  __m128i *pr = p + (size_t)r * n_col_ - st_;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="p">@@ -223,7 +186,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff">                  for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff">                          __m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff">                          __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff">                          d = _mm_and_si128(_mm_cmpgt_epi8(a, z), _mm_set1_epi8(1));       // d = a  > z? 1 : 0</span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(2), _mm_cmpgt_epi8(b,  z)); // d = b  > z? 2 : d</span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="p">@@ -233,22 +195,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(4), _mm_cmpgt_epi8(b2, z)); // d = a2 > z? 3 : d</span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff">                                 z = _mm_max_epi8(z, b2);</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC105" class="line" lang="diff">                                 z = _mm_min_epi8(z, sc_mch_);</span>

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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>

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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a,  z);</span></span>

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<td class="old_line diff-line-num 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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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_and_si128(tmp, _mm_set1_epi8(1));</span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b,  z);</span></span>

</pre>

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<td class="old_line diff-line-num 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="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(2)));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a2, z);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(3)));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b2, z);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(4)));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmplt_epi8(sc_mch_, z);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a, zero_);</span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="p">@@ -270,7 +216,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff">                                 __m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff">                                 d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), _mm_set1_epi8(1));    // d = z > a?  0 : 1</span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(2), d, _mm_cmpgt_epi8(z, b));  // d = z > b?  d : 2</span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="p">@@ -280,22 +225,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(4), d, _mm_cmpgt_epi8(z, b2)); // d = z > b2? d : 4</span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff">                                 z = _mm_max_epi8(z, b2);</span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff">                                 z = _mm_min_epi8(z, sc_mch_);</span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a);</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_andnot_si128(tmp, _mm_set1_epi8(1));</span></span>

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<td class="old_line diff-line-num 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="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a));</span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, b);</span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(2)));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a2);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(3)));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a2));</span></span>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, b2);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(4)));</span></span>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b2));</span></span>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmplt_epi8(sc_mch_, z);</span></span>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(zero_, a);</span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_andnot_si128(tmp, a),  qe_));</span>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="p">@@ -330,13 +259,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff">                                         _mm_storeu_si128((__m128i*)&H[t], H1);</span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff">                                         t_ = _mm_set1_epi32(t);</span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff">                                         tmp = _mm_cmpgt_epi32(H1, max_H_);</span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff">                                         max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff">                                         max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));</span></span>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));</span></span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff">                                 }</span>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)HH, max_H_);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)tt, max_t_);</span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="p">@@ -391,4 +315,3 @@</span></span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff">                 kfree(km, mem2); kfree(km, off);</span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"> }</span>

</pre>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- minimap2.orig/ksw2_exts2_sse.c</span></span>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/ksw2_exts2_sse.c</span></span>

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="p">@@ -3,29 +3,19 @@</span></span>

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"> #include <assert.h></span>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"> #include "ksw2.h"</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC180" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>

</pre>

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<td class="old_line diff-line-num 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="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse4.1.h"</span></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#undef __SSE4_1__</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(SIMDE_SSE4_1_NATIVE)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC197" class="line" lang="diff"> void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC198" class="line" lang="diff">                                    int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(SIMDE_SSE2_NATIVE)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC201" class="line" lang="diff"> void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC202" class="line" lang="diff">                                    int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"> #else</span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"> void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff">                                    int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"> {</span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"> #define __dp_code_block1 \</span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff">         z = _mm_load_si128(&s[t]); \</span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="p">@@ -194,13 +184,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff">                                 st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff">                                 mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));</span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff">                                 tmp = _mm_cmpeq_epi8(sq, st);</span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);</span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(tmp,  sc_mis_), _mm_and_si128(tmp,  sc_mch_));</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));</span></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff">                 } else {</span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"><span class="p">@@ -217,7 +202,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff">                                 __m128i z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff">                                 z = _mm_max_epi8(z, b);</span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff">                                 z = _mm_max_epi8(z, a2a);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"><span class="p">@@ -226,23 +210,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff">                                 _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_max_epi8(b,  zero_), qe_));</span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff">                                 tmp = _mm_load_si128(&donor[t]);</span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff">                                 _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, tmp), q2_));</span>

</pre>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a,  z);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b,  z);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a2a, z);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                __dp_code_block2;</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a, zero_);</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b, zero_);</span></span>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_and_si128(tmp, b),  qe_));</span></span>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_load_si128(&donor[t]); // TODO: check if this is correct</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a2, tmp);</span></span>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(tmp, tmp), _mm_and_si128(tmp, a2));</span></span>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&x2[t], _mm_sub_epi8(tmp, q2_));</span></span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff">                 } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff">                         __m128i *pr = p + r * n_col_ - st_;</span>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="p">@@ -250,24 +217,12 @@</span></span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff">                                 __m128i d, z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp, tmp2;</span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff">                                 d = _mm_and_si128(_mm_cmpgt_epi8(a, z), _mm_set1_epi8(1));       // d = a  > z? 1 : 0</span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(2), _mm_cmpgt_epi8(b,  z)); // d = b  > z? 2 : d</span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff">                                 z = _mm_max_epi8(z, b);</span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(3), _mm_cmpgt_epi8(a2a, z)); // d = a2 > z? 3 : d</span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff">                                 z = _mm_max_epi8(z, a2a);</span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a,  z);</span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_and_si128(tmp, _mm_set1_epi8(1));</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b,  z);</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(2)));</span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a2a, z);</span></span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(3)));</span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a));</span></span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a, zero_);</span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span>

</pre>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff"><span class="p">@@ -278,11 +233,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff">                                 tmp2 = _mm_load_si128(&donor[t]);</span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a2, tmp2);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="diff">                                 tmp2 = _mm_max_epi8(a2, tmp2);</span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp2 = _mm_or_si128(_mm_andnot_si128(tmp, tmp2), _mm_and_si128(tmp, a2));</span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff">                                 _mm_store_si128(&x2[t], _mm_sub_epi8(tmp2, q2_));</span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff">                                 d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x20)));</span>

</pre>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff">                                 _mm_store_si128(&pr[t], d);</span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff"><span class="p">@@ -293,24 +244,12 @@</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff">                                 __m128i d, z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp, tmp2;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff">                                 __dp_code_block1;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff">                                 d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), _mm_set1_epi8(1));    // d = z > a?  0 : 1</span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC302" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(2), d, _mm_cmpgt_epi8(z, b));  // d = z > b?  d : 2</span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff">                                 z = _mm_max_epi8(z, b);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(3), d, _mm_cmpgt_epi8(z, a2a)); // d = z > a2? d : 3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff">                                 z = _mm_max_epi8(z, a2a);</span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a);</span></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_andnot_si128(tmp, _mm_set1_epi8(1));</span></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a));</span></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, b);</span></span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(2)));</span></span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b));</span></span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a2a);</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(3)));</span></span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a2a));</span></span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(zero_, a);</span>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_andnot_si128(tmp, a),  qe_));</span>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"><span class="p">@@ -321,11 +260,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff">                                 tmp2 = _mm_load_si128(&donor[t]);</span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(tmp2, a2);</span>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff">                                 tmp2 = _mm_max_epi8(tmp2, a2);</span>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp2 = _mm_or_si128(_mm_andnot_si128(tmp, a2), _mm_and_si128(tmp, tmp2));</span></span>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff">                                 _mm_store_si128(&x2[t], _mm_sub_epi8(tmp2, q2_));</span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff">                                 d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0</span>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff">                                 _mm_store_si128(&pr[t], d);</span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"><span class="p">@@ -349,13 +284,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff">                                         _mm_storeu_si128((__m128i*)&H[t], H1);</span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff">                                         t_ = _mm_set1_epi32(t);</span>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff">                                         tmp = _mm_cmpgt_epi32(H1, max_H_);</span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff">                                         max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff">                                         max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));</span></span>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));</span></span>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff">                                 }</span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)HH, max_H_);</span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)tt, max_t_);</span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"><span class="p">@@ -406,4 +336,3 @@</span></span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="diff">                 kfree(km, mem2); kfree(km, off);</span>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- minimap2.orig/ksw2_extz2_sse.c</span></span>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/ksw2_extz2_sse.c</span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"><span class="p">@@ -2,26 +2,16 @@</span></span>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"> #include <assert.h></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff"> #include "ksw2.h"</span>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse4.1.h"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#undef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(SIMDE_SSE4_1_NATIVE)</span></span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"> void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(SIMDE_SSE2_NATIVE)</span></span>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="diff"> void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="diff"> #else</span>

</pre>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="diff"> void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="diff"> {</span>

</pre>

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="diff"> #define __dp_code_block1 \</span>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff">         z = _mm_add_epi8(_mm_load_si128(&s[t]), qe2_); \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="diff"><span class="p">@@ -129,13 +119,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="diff">                                 st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="diff">                                 mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));</span>

</pre>

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="diff">                                 tmp = _mm_cmpeq_epi8(sq, st);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);</span>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(tmp,  sc_mis_), _mm_and_si128(tmp,  sc_mch_));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="diff">                         }</span>

</pre>

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="diff">                 } else {</span>

</pre>

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"><span class="p">@@ -151,22 +136,10 @@</span></span>

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

</pre>

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff">                                 __m128i z, a, b, xt1, vt1, ut, tmp;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff">                                 __dp_code_block1;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);                          // z = z > a? z : a (signed)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_));  // z = z > 0? z : 0;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_max_epu8(z, a);                          // z = max(z, a); this works because both are non-negative</span></span>

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff">                                 _mm_store_si128(&x[t], _mm_max_epi8(a, zero_));</span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="diff">                                 _mm_store_si128(&y[t], _mm_max_epi8(b, zero_));</span>

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<pre style="margin: 0;">-<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a, zero_);</span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&x[t], _mm_and_si128(a, tmp));</span></span>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b, zero_);</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&y[t], _mm_and_si128(b, tmp));</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff">                 } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff">                         __m128i *pr = p + (size_t)r * n_col_ - st_;</span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="diff"><span class="p">@@ -175,16 +148,9 @@</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff">                                 __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="diff">                                 d = _mm_and_si128(_mm_cmpgt_epi8(a, z), flag1_); // d = a > z? 1 : 0</span>

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<pre style="margin: 0;">-<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);                          // z = z > a? z : a (signed)</span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(b, z);</span>

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, flag2_, tmp);             // d = b > z? 2 : d</span>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_));  // z = z > 0? z : 0;</span></span>

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_max_epu8(z, a);                          // z = max(z, a); this works because both are non-negative</span></span>

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b, z);</span></span>

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, flag2_)); // d = b > z? 2 : d; emulating blendv</span></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a, zero_);</span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="diff">                                 _mm_store_si128(&x[t], _mm_and_si128(tmp, a));</span>

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<pre style="margin: 0;">-<span id="LC439" class="line" lang="diff"><span class="p">@@ -201,16 +167,9 @@</span></span>

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<pre style="margin: 0;">-<span id="LC440" class="line" lang="diff">                                 __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="diff">                                 d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), flag1_); // d = z > a? 0 : 1</span>

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<pre style="margin: 0;">-<span id="LC443" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);                          // z = z > a? z : a (signed)</span>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(z, b);</span>

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="diff">                                 d = _mm_blendv_epi8(flag2_, d, tmp);             // d = z > b? d : 2</span>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>

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<pre style="margin: 0;">-<span id="LC448" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_));  // z = z > 0? z : 0;</span></span>

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<pre style="margin: 0;">-<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_max_epu8(z, a);                          // z = max(z, a); this works because both are non-negative</span></span>

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, b);</span></span>

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<pre style="margin: 0;">-<span id="LC451" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_andnot_si128(tmp, flag2_), _mm_and_si128(tmp, d)); // d = z > b? d : 2; emulating blendv</span></span>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC453" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(zero_, a);</span>

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<pre style="margin: 0;">-<span id="LC455" class="line" lang="diff">                                 _mm_store_si128(&x[t], _mm_andnot_si128(tmp, a));</span>

</pre>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="diff"><span class="p">@@ -241,13 +200,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC457" class="line" lang="diff">                                         _mm_storeu_si128((__m128i*)&H[t], H1);</span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="diff">                                         t_ = _mm_set1_epi32(t);</span>

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="diff">                                         tmp = _mm_cmpgt_epi32(H1, max_H_);</span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="diff">                                         max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="diff">                                         max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));</span></span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));</span></span>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="diff">                                 }</span>

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<pre style="margin: 0;">-<span id="LC468" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)HH, max_H_);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)tt, max_t_);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC470" class="line" lang="diff"><span class="p">@@ -302,4 +256,3 @@</span></span>

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<pre style="margin: 0;">-<span id="LC471" class="line" lang="diff">                 kfree(km, mem2); kfree(km, off);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="diff">         }</span>

</pre>

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<pre style="margin: 0;">-<span id="LC473" class="line" lang="diff"> }</span>

</pre>

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<pre style="margin: 0;">-<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

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<pre style="margin: 0;">-<span id="LC475" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- minimap2.orig/ksw2_ll_sse.c</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/ksw2_ll_sse.c</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC477" class="line" lang="diff"><span class="p">@@ -1,7 +1,8 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC478" class="line" lang="diff"> #include <stdlib.h></span>

</pre>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="diff"> #include <stdint.h></span>

</pre>

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<pre style="margin: 0;">-<span id="LC480" class="line" lang="diff"> #include <string.h></span>

</pre>

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<pre style="margin: 0;">-<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse2.h"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC484" class="line" lang="diff"> #include "ksw2.h"</span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC486" class="line" lang="diff"> #ifdef __GNUC__</span>

</pre>

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<pre style="margin: 0;">-<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- minimap2.orig/Makefile</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/Makefile</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="diff"><span class="p">@@ -6,21 +6,17 @@</span></span>

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="diff"> PROG_EXTRA=     sdust minimap2-lite</span>

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<td class="old_line diff-line-num old" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC491" class="line" lang="diff"> LIBS=           -lm -lz -lpthread</span>

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

493

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<pre style="margin: 0;">-<span id="LC493" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq ($(arm_neon),) # if arm_neon is not defined</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq ($(sse2only),) # if sse2only is not defined</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC495" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifneq ($(amd64),)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC498" class="line" lang="diff">         OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

499

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else                # if sse2only is defined</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else ifneq ($(i386),)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        OBJS+=ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o</span></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

504

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC504" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else                            # if arm_neon is defined</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

505

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

506

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

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<pre style="margin: 0;">-<span id="LC506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    INCLUDES+=-Isse2neon</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

507

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq ($(aarch64),)      #if aarch64 is not defined</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

508

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

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<pre style="margin: 0;">-<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char</span></span>

</pre>

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509

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<pre style="margin: 0;">-<span id="LC509" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else                            #if aarch64 is defined</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

510

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

</td>

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

<pre style="margin: 0;">-<span id="LC510" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

511

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

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

<pre style="margin: 0;">-<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifneq ($(aarch64),)     #if aarch64 is defined</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

512

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC512" class="line" lang="diff">         CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

513

</td>

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

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

<pre style="margin: 0;">-<span id="LC513" class="line" lang="diff"> endif</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

514

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

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

<pre style="margin: 0;">-<span id="LC514" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

515

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

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

<pre style="margin: 0;">-<span id="LC515" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

516

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC516" class="line" lang="diff"> .PHONY:all extra clean depend</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

517

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

</td>

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

<pre style="margin: 0;">-<span id="LC517" class="line" lang="diff"> .SUFFIXES:.c .o</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

518

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

</td>

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

<pre style="margin: 0;">-<span id="LC518" class="line" lang="diff"><span class="p">@@ -46,7 +42,7 @@</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

519

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

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

<pre style="margin: 0;">-<span id="LC519" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

520

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC520" class="line" lang="diff"> # SSE-specific targets on x86/x86_64</span>

</pre>

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521

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

</td>

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

<pre style="margin: 0;">-<span id="LC521" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

522

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)</span></span>

</pre>

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<td class="old_line diff-line-num 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">

523

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifneq ($(amd64),)   # if amd64 is not defined, compile this target with the default setting (i.e. no -msse2)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

524

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC524" class="line" lang="diff"> ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

525

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC525" class="line" lang="diff">                 $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@</span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

526

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

</td>

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

<pre style="margin: 0;">-<span id="LC526" class="line" lang="diff"> endif</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

527

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC527" class="line" lang="diff"><span class="p">@@ -72,17 +68,6 @@</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

528

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC528" class="line" lang="diff"> ksw2_dispatch.o:ksw2_dispatch.c ksw2.h</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

529

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

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

<pre style="margin: 0;">-<span id="LC529" class="line" lang="diff">                 $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

530

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

531

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# NEON-specific targets on ARM</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

532

</td>

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

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

<pre style="margin: 0;">-<span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

533

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC533" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h</span></span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

534

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC534" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@</span></span>

</pre>

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535

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC535" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

536

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<pre style="margin: 0;">-<span id="LC536" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

537

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC537" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

538

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC538" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

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

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

<pre style="margin: 0;">-<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h</span></span>

</pre>

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

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

541

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

542

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC542" class="line" lang="diff"> # other non-file targets</span>

</pre>

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<td class="old_line diff-line-num 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">

543

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC543" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

544

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

</td>

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

<pre style="margin: 0;">-<span id="LC544" class="line" lang="diff"> clean:</span></pre>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/minimap2/-/compare/b58b74db97f2a93f8802202caa21f2da0bd3b590...dcc5929a37635e276c038cff118a12ff388ddd81#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># from minimap 1</span>

</pre>

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

5

</td>

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">#export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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

</td>

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

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/architecture.mk</span>

</pre>

</td>

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

7

</td>

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP</span>

</pre>

</td>

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

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

</td>

<td class="new_line diff-line-num new" 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">export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP<span class="idiff left right"> -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES</span></span>

</pre>

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<td class="old_line diff-line-num" 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

</td>

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

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

</pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">RANLIB ?= ranlib</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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

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

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,9 @@ RANLIB ?= ranlib</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="plaintext">override_dh_auto_clean:</span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">     dh_auto_clean</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">     cd tex && make clean</span>

</pre>

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

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">     rm -f MT-human.mmi</span>

</pre>

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

18

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf</span>

</pre>

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

</td>

<td class="new_line diff-line-num new" 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">     rm -f libminimap2.a</span>

</pre>

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

17

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<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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

18

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<td class="new_line diff-line-num" 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="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH_CPU),amd64))</span>

</pre>

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

22

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">build_vars += amd64=1</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,11 +50,5 @@ override_dh_strip:</td>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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

</pre>

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

48

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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">     $(RANLIB) $(CURDIR)/debian/libminimap2-dev/usr/lib/libminimap2.a</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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

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

</pre>

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

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

</pre>

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

51

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

52

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

<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">     rm -f MT-human.mmi</span>

</pre>

</td>

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

53

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<td class="new_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">     rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">     rm -f libminimap2.a</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">override_dh_installman:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">     dh_installman --language=C</span></pre>

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