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GitLab

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<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/421b9827590ee0f2d4b4925c7822d87b39bfbf96">421b9827</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-16T12:20:19+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/3cc895af4edfab54d50750ba8f7cf8970f63e894">3cc895af</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-16T12:30:40+02:00</i>

</div>

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

</pre>

</li>

</ul>

<h4>3 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<span class="new-file">

+

debian/patches/spelling.patch

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/infernal/compare/3fce8ef53b60465a9b9b2ee6e1266d2ba1fe548d...3cc895af4edfab54d50750ba8f7cf8970f63e894#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">infernal (1.1.2-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>

</pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">infernal (1.1.2-2) <span class="idiff left right">unstable</span>; urgency=medium</span>

</pre>

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2

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2

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

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

</pre>

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

3

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

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

</pre>

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

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * Add debian/TODO: remove code copy of hmmer</span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,8 +9,9 @@ infernal (1.1.2-2) UNRELEASED; urgency=medium</td>

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

9

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

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>

</pre>

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

10

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10

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Standards-Version: 4.1.5</span>

</pre>

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

11

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

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * Fix configure.ac to enable autoreconf</span>

</pre>

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

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

12

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

</pre>

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12

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13

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

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

</pre>

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  <span class="idiff left right">Wed, 18 Jan 2017 12:56:58 +01</span>00</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  <span class="idiff left right">Mon, 16 Jul 2018 12:20:32 +02</span>00</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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

</pre>

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15

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

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">infernal (1.1.2-1) unstable; urgency=medium</span>

</pre>

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16

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

17

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/infernal/compare/3fce8ef53b60465a9b9b2ee6e1266d2ba1fe548d...3cc895af4edfab54d50750ba8f7cf8970f63e894#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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1

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

</pre>

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2

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2

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

</pre>

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3

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

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4

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

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<br>

</li>

<li id="45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<a href="https://salsa.debian.org/med-team/infernal/compare/3fce8ef53b60465a9b9b2ee6e1266d2ba1fe548d...3cc895af4edfab54d50750ba8f7cf8970f63e894#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 16 Jul 2018 07:59:38 +0200</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Fix spelling</span>

</pre>

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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="gd" style="color: #000; background-color: #fdd;">--- a/src/cm_modelmaker.c</span></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;">+++ b/src/cm_modelmaker.c</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1373,7 +1373,7 @@ ConsensusModelmaker(const ESL_ALPHABET *</span></span>

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">   esl_wuss_nopseudo(ss_cons, ss_cons); /* remove pknots in place */</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">   ESL_ALLOC(ct, (clen+1) * sizeof(int));</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsisent in ConsensusModelMaker().");</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsistent in ConsensusModelMaker().");</span></span>

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

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff">   /* 2. Construct a guide tree. </span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">    *    This codes is borrowed from HandModelmaker(), where it</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/documentation/manpages/cmalign.man</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/documentation/manpages/cmalign.man</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -309,7 +309,7 @@ only cells within the bands need be allo</span></span>

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

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> Importantly, HMM banding sacrifices the guarantee of determining the</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> optimally accurarte or optimal alignment, which will be missed if it</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lies outside the bands. The tau paramater is the amount of probability</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lies outside the bands. The tau parameter is the amount of probability</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> mass considered negligible during HMM band calculation; lower values</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> of tau yield greater speedups but also a greater chance of missing the</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> optimal alignment. The default tau is 1E-7, determined empirically as</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -500,7 +500,7 @@ in previous versions of</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> .B --mapstr</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> Must be used in combination with </span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> .BI --mapali " <f>".</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Propogate structural information for any pseudoknots that exist in</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Propagate structural information for any pseudoknots that exist in</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> .I <f> </span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> to the output alignment. A similar option to this one was called</span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> .B --withstr </span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/documentation/manpages/cmcalibrate.man</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/documentation/manpages/cmcalibrate.man</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -51,7 +51,7 @@ Interface) can be also be used for paral</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> .B --mpi </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> option if Infernal was built with MPI enabled, but using more than 161</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> processors is not recommended because increasing past 161 won't</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-accelerate the calibration.  See the Installation seciton of the user</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+accelerate the calibration.  See the Installation section of the user</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> guide for more information.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/hmmer/src/p7_builder.c</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/hmmer/src/p7_builder.c</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -504,7 +504,7 @@ p7_Builder(P7_BUILDER *bld, ESL_MSA *msa</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff">  *            </span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">  * Args:      bld       - build configuration</span>

</pre>

</td>

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

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">  *            sq        - query sequence</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *            bg        - null model (needed to paramaterize insert emission probs)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *            bg        - null model (needed to parameterize insert emission probs)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff">  *            opt_hmm   - optRETURN: new HMM</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff">  *            opt_gm    - optRETURN: profile corresponding to <hmm></span>

</pre>

</td>

</tr>

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

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff">  *            opt_om    - optRETURN: optimized profile corresponding to <gm></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/documentation/manpages/cmscan.man</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/documentation/manpages/cmscan.man</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -746,7 +746,7 @@ option.</span></span>

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

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> .TP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> .BI --oskip " <f>"</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Omit any hit h from the tabular output file that satisifies the</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Omit any hit h from the tabular output file that satisfies the</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> following: another hit h2 overlaps with h and the E-value of h2 is</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> lower than that of h. Hit h will not appear in the tabular output</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> file, although it will still exist in the standard output. </span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/documentation/manpages/cmstat.man</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/documentation/manpages/cmstat.man</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -115,7 +115,7 @@ include Rfam GA, TC, and/or NC bit score</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> and/or</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> .B --cut_nc </span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> options can be used to display E-values that correspond to the bit</span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-score thresholds. Seperate bit scores or E-values will be displayed</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+score thresholds. Separate bit scores or E-values will be displayed</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> for each of the four possible CM search algorithm and model</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> configuration pairs: local Inside, local CYK, glocal Inside and glocal</span>

</pre>

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

79

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

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