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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/primer3">Debian Med / primer3</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/primer3/commit/388a46142b9008b225f412358edd3090b6bcd99a">388a4614</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-21T09:19:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/primer3/commit/3993096e6a7fc2c4694bb616c4dcfe1230ed5476">3993096e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-21T09:21:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/primer3/commit/804a5d02253b12f387632a4b41ea668089cd452d">804a5d02</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-21T09:21:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/primer3/commit/4afea24e8a55fdbd28c497cc18d8d7ee11b5320c">4afea24e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-21T09:39:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Doc was moved to src, settings files were moved as well
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/primer3/commit/32549cc5825d06321a38d868b88770e3155afdfc">32549cc5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-21T09:48:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
</a>
</li>
<li class="file-stats">
<a href="#e9b81568d556ec514ae9dc37a9850816b04209cc">
debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
</a>
</li>
<li class="file-stats">
<a href="#f2c5cd6b02ff8ee04b1776fdbebb9f7ec35b0176">
debian/primer3.docs
</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/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">primer3 (2.4.0-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">primer3 (2.4.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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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"> * New upstream version</span>
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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"> * Secure URI in watch file</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.3</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 21 Feb 2018 09:<span class="idiff left right">01:27</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 21 Feb 2018 09:<span class="idiff left right">21:42</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">primer3 (2.3.7-5) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,8 @@ Uploaders: Steffen Moeller <moeller@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>)</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1</span>)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/primer3.git</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/primer3.git</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://primer3.sourceforge.net</span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ Description: Propagate hardening options</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> # Note, for profiling, use</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </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;">@@ -1<span class="idiff left right">63,7 +163</span>,7 @@ $(NTTHAL_EXE): thal_main.o thal.o</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;">@@ -1<span class="idiff left right">75,7 +175</span>,7 @@ $(NTTHAL_EXE): thal_main.o thal.o</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)</span>
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<li id="e9b81568d556ec514ae9dc37a9850816b04209cc">
<a href="https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc#e9b81568d556ec514ae9dc37a9850816b04209cc"><strong>debian/patches/primer_thermodynamic_parameters_path_2_etc.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Description: Configuration in /etc</td>
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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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/primer3_boulder_main.c</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/primer3_boulder_main.c</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5<span class="idiff left right">05,18 +505</span>,18 @@ read_thermodynamic_parameters()</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5<span class="idiff left right">39,18 +539</span>,18 @@ read_thermodynamic_parameters()</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> return;</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"> #else</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,7 @@ Description: Configuration in /etc</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n");</span>
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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/src/release_notes.txt</span></span>
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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/src/release_notes.txt</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">18,9 +218</span>,9 @@ defaults. The default is --default_vers</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">72,9 +272</span>,9 @@ defaults. The default is --default_vers</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> 1.5 IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1,</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> This tag specifies the path to the directory that contains all the</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,26 +58,23 @@ Description: Configuration in /etc</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> there is only one default location: .\primer3_config\. If the the</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> parameter files are not in one these locations, be sure to set</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> PRIMER_THERMODYNAMIC_PARAMETERS_PATH</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/primer3_manual.htm</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/primer3_manual.htm</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -229,9 +229,9 @@ defaults. The default is --default_vers</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> 2.5. IMPORTANT: because <a href="#PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT">PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT</a>=1,</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a> must point to the right location.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/primer3_manual.htm</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -222,7 +222,7 @@ defaults. The default is --default_vers</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> This tag specifies the path to the directory that contains all the</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parameter files used by the thermodynamic approach. In Linux, there</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parameter files used by the thermodynamic approach. In Debian, there</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> parameter files used by the thermodynamic approach. In Linux, there</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> are two *default* locations that are tested if this tag is not</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-defined: ./primer3_config/ and /opt/primer3_config/. For Windows,</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+defined: ./primer3_config/ and /etc/primer3_config/. For Windows,</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> there is only one default location: .\primer3_config\. If the the</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> parameter files are not in one these locations, be sure to set</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a>.<br></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">452,7 +245</span>2,7 @@ the propensity of oligos to anneal to un</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">082,7 +208</span>2,7 @@ the propensity of oligos to anneal to un</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> <p>This tag specifies the path to the directory that contains all the</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> parameter files used by the thermodynamic approach. In Linux, there are two</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> default locations that are tested if this tag is not defined:<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> default locations that are tested if this tag is not defined:</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;">-<i>./primer3_config/</i> and <i>/opt/primer3_config/</i>.</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<i>./primer3_config/</i> and <i>/etc/primer3_config/</i>.</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> For Windows, there is only one default location: <i>.\primer3_config\</i>.</p></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> </span></pre>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> <span class="idiff left right"><h3><a name="PRIMER_MAX_SELF_ANY">PRIMER_MAX_SELF_ANY (decimal, 9999.99; default 8.00)</a></h3></span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> <span class="idiff left right"><p>PRIMER_MAX_SELF_ANY describes the tendency of a primer to bind to</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">primer3_manual.htm</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">src/</span>primer3_manual.htm</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">src/release_notes.txt</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/primer3/compare/65e8ca5fa33ed6974ecc1a75b01c1d4f940852a5...32549cc5825d06321a38d868b88770e3155afdfc#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ override_dh_installexamples:</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> mkdir -p $(sampledir)/src;</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> cp -aR ./test/* $(sampledir)/test;</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> cp -aR ./src/humrep_and_simple.txt $(sampledir)/src;</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> cp primer*.txt $(sampledir)/;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> cp <span class="idiff left right">-a settings_files/</span>primer*.txt $(sampledir)/;</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> chmod -x $(sampledir)/test/thal*;</span>
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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(sampledir)/test/long_seq_tm_test.pl ;</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(sampledir)/test/vgrep.pl ;</span></pre>
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