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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-blastplus">Debian Med / ncbi-blastplus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/84d056974d84237de72ea2fb15bc1270b60841d0">84d05697</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T13:10:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improve reproducibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/91a3709182cd43b2175ccee75ceac2d7ddb8ef6a">91a37091</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T13:38:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix some spelling typos
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/804c97bf618f3b70ef8f81845a4418af2ec34651">804c97bf</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T13:38:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove some __FILE__ references
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/53531b4f8d95a56949ca6d88d8bc29be4ec3c4d5">53531b4f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T13:40:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/watch: use a secure URL
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/a3dd5f4948a32ad279c926691bf8c9b8df81232d">a3dd5f49</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T14:05:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more optional build-deps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/38e317d58229eb269acf177dd2e49473b540f4cd">38e317d5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T14:09:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reprobuild fixup
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/373bce9a1cb32b99e53140df887e12e4e11ab136">373bce9a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T19:21:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">delete spurious usr/bin/windowmasker_2.2.22_adapter.bak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/commit/1dc1e25c9484588b31f1c756ec26c7330fdf56e6">1dc1e25c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-04T20:05:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set up a HOME directory
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#6838b902f760d970d1188a57e8f64adbf75e7cf8">
<span class="new-file">
+
debian/patches/reprobuild
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
</span>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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 +15,11 @@ Build-Depends-Arch: 2to3,</td>
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15
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libmbedtls-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libpcre3-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> time,</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> procps,</span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> libbackward-cpp-dev,</span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> libdw-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> libmsgsl-dev</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git</span>
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<li id="6838b902f760d970d1188a57e8f64adbf75e7cf8">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6#6838b902f760d970d1188a57e8f64adbf75e7cf8"><strong>debian/patches/reprobuild</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: make the build more reproducible</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/build-system/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/build-system/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -2826,13 +2826,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> linux*)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> kver=`uname -r | sed -e 's/-.*//'`</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> libcver=`ldd --version | awk 'NR == 1 { print $NF }'`</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- verbose_host=$host_cpu-$host_vendor-linux$kver-gnu$libcver</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ verbose_host=$host_cpu-$host_vendor-linux-gnu$libcver</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> *) verbose_host=$host ;;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #### Overall configuration mode summary</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-signature_hostname=`(hostname || uname -n) 2>/dev/null \</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+signature_hostname=`echo debian_build 2>/dev/null \</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> | sed 's/\..*//; s/-/_/g; 1q'`</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> signature="${signature_compiler}_${signature_compiler_version}-${release_debug}${mt_sfx}${dll_sfx}${bit64_sfx}${prof_sfx}--${verbose_host}-${signature_hostname}"</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> AC_DEFINE_UNQUOTED(NCBI_SIGNATURE, "$signature",</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/algo/blast/core/blast_message.h</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/algo/blast/core/blast_message.h</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> /** Convenient define to call the function Blast_PerrorEx. */</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> #define Blast_PerrorWithLocation(msg, error_code, context) \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Blast_PerrorEx(msg, error_code, __FILE__, __LINE__, context)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Blast_PerrorEx(msg, error_code, "c++/include/algo/blast/core/blast_message.h", __LINE__, context)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> /** Extended version of Blast_Perror which includes parameters for the file</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> * name and line number where the error/warning occurred. This function should</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/connect/ncbi_util.h</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/connect/ncbi_util.h</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -113,7 +113,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> #define LOG_WRITE(lg, code, subcode, level, message) \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION, \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __FILE__, __LINE__, message, 0, 0)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "c++/include/connect/ncbi_util.h", __LINE__, message, 0, 0)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> #ifdef LOG_DATA</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> /* AIX's <pthread.h> defines LOG_DATA to be an integer constant;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -122,7 +122,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> #define LOG_DATA(lg, code, subcode, level, data, size, message) \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION, \</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;">- __FILE__, __LINE__, message, data, size)</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;">+ "c++/include/connect/ncbi_util.h", __LINE__, message, data, size)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> /** Default for THIS_MODULE.</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;">--- ncbi-blastplus.orig/c++/include/corelib/impl/ncbi_java.h</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/corelib/impl/ncbi_java.h</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> #define JAVA_ABORT(msg) \</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> { \</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- NcbiCerr << __FILE__ << ": " << NCBI_CURRENT_FUNCTION << ": " msg << endl; \</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ NcbiCerr << "c++/include/corelib/impl/ncbi_java.h" << ": " << NCBI_CURRENT_FUNCTION << ": " msg << endl; \</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> abort(); \</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"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/corelib/ncbidiag.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/corelib/ncbidiag.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -167,7 +167,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> /// @sa</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> /// CDiagCompileInfo</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> #define DIAG_COMPILE_INFO \</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;">- NCBI_NS_NCBI::CDiagCompileInfo(__FILE__, \</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;">+ NCBI_NS_NCBI::CDiagCompileInfo("c++/include/corelib/ncbidiag.hpp", \</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> __LINE__, \</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> NCBI_CURRENT_FUNCTION, \</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> NCBI_MAKE_MODULE(NCBI_MODULE))</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;">--- ncbi-blastplus.orig/c++/include/corelib/test_boost.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/corelib/test_boost.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -249,7 +249,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> boost::unit_test::make_test_case( \</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> &BOOST_AUTO_TC_INVOKER( test_name ), #test_name, \</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;">- __FILE__, __LINE__ ), \</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "c++/include/corelib/test_boost.hpp", __LINE__ ), \</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> ::NCBI_NS_NCBI::SNcbiTestTCTimeout< \</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> BOOST_AUTO_TC_UNIQUE_ID( test_name )>::instance()->value(), \</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> decorators ); \</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -1124,7 +1124,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> #define SEQDB_FILE_ASSERT(YESNO) \</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> do { \</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> if (! (YESNO)) { \</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SeqDB_FileIntegrityAssert(__FILE__, __LINE__, (#YESNO)); \</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SeqDB_FileIntegrityAssert("c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp", __LINE__, (#YESNO)); \</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> } \</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> } while(0)</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/util/ddump_viewer.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/util/ddump_viewer.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> #define DEBUGDUMP_BPT(name,obj) \</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- do {CDebugDumpViewer().Bpt(name,&(obj),__FILE__,__LINE__);} while (0)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ do {CDebugDumpViewer().Bpt(name,&(obj),"c++/include/util/ddump_viewer.hpp",__LINE__);} while (0)</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> //---------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/util/static_set.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/util/static_set.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -886,17 +886,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> static const Type Var</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> #define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array) \</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ static const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__)</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> #define DEFINE_CLASS_STATIC_ARRAY_MAP(Type, Var, Array) \</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__)</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__)</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> #define DEFINE_STATIC_ARRAY_MAP_WITH_COPY(Type, Var, Array) \</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__, \</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ static const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__, \</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> NCBI_NS_NCBI::NStaticArray::eCopyWarn_hide)</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> #define DEFINE_CLASS_STATIC_ARRAY_MAP_WITH_COPY(Type, Var, Array) \</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__, \</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__, \</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> NCBI_NS_NCBI::NStaticArray::eCopyWarn_hide)</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/connect/mbedtls/mbedtls/debug.h</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/connect/mbedtls/mbedtls/debug.h</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -40,28 +40,28 @@</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> #define MBEDTLS_DEBUG_STRIP_PARENS( ... ) __VA_ARGS__</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> #define MBEDTLS_SSL_DEBUG_MSG( level, args ) \</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;">- mbedtls_debug_print_msg( ssl, level, __FILE__, __LINE__, \</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mbedtls_debug_print_msg( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, \</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> MBEDTLS_DEBUG_STRIP_PARENS args )</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> #define MBEDTLS_SSL_DEBUG_RET( level, text, ret ) \</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;">- mbedtls_debug_print_ret( ssl, level, __FILE__, __LINE__, text, ret )</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mbedtls_debug_print_ret( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, ret )</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> #define MBEDTLS_SSL_DEBUG_BUF( level, text, buf, len ) \</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mbedtls_debug_print_buf( ssl, level, __FILE__, __LINE__, text, buf, len )</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mbedtls_debug_print_buf( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, buf, len )</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> #if defined(MBEDTLS_BIGNUM_C)</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> #define MBEDTLS_SSL_DEBUG_MPI( level, text, X ) \</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;">- mbedtls_debug_print_mpi( ssl, level, __FILE__, __LINE__, text, X )</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mbedtls_debug_print_mpi( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X )</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> #if defined(MBEDTLS_ECP_C)</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> #define MBEDTLS_SSL_DEBUG_ECP( level, text, X ) \</span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mbedtls_debug_print_ecp( ssl, level, __FILE__, __LINE__, text, X )</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mbedtls_debug_print_ecp( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X )</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> #endif</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> #if defined(MBEDTLS_X509_CRT_PARSE_C)</span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> #define MBEDTLS_SSL_DEBUG_CRT( level, text, crt ) \</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mbedtls_debug_print_crt( ssl, level, __FILE__, __LINE__, text, crt )</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mbedtls_debug_print_crt( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, crt )</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> #endif</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> #else /* MBEDTLS_DEBUG_C */</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos_cxx.cpp</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/connect/ncbi_lbos_cxx.cpp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -145,7 +145,7 @@</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> {</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> /* Hostname should not be empty in any case */</span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> if (hostname.empty()) {</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> CLBOSException::eUnknown, </span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> "Internal error in LBOS Client IP Cache. Please contact developer",</span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> eLBOS_BadRequest);</span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="p">@@ -217,7 +217,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> if (lbos_answer != NULL) {</span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> message << " " << lbos_answer;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> CLBOSException::s_HTTPCodeToEnum(result),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> message.str(), result);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="p">@@ -248,7 +248,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> /* If we could not parse healthcheck URL, throw "Invalid Arguments" */</span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> if (cur_host.empty()) {</span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> ConnNetInfo_Destroy(healthcheck_info);</span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> CLBOSException::eInvalidArgs,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> NStr::IntToString(eLBOS_InvalidArgs),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> eLBOS_InvalidArgs);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="p">@@ -307,7 +307,7 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> port_int = NStr::StringToInt(port_str);</span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> }</span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> catch (...) {</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> CLBOSException::eInvalidArgs,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> "Could not parse port \"" + port_str + </span>
</pre>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> "\" in section \"" + reg_section + "\"",</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="p">@@ -315,7 +315,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> if (port_int < 1 || port_int > 65535)</span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> {</span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> CLBOSException::eInvalidArgs, </span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> "Invalid server port \"" + port_str + </span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> "\" in section \"" + reg_section + "\"",</span>
</pre>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="p">@@ -623,7 +623,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> /* Forbidden names for meta parameters */</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> if (name == "version" || name == "ip" || name == "port" || name == "check" </span>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC218" class="line" lang="diff"> || name == "format" || name == "name") {</span>
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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> CLBOSException::eInvalidArgs, </span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC222" class="line" lang="diff"> "This name cannot be used for metadata", </span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC223" class="line" lang="diff"> eLBOS_InvalidArgs);</span>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC224" class="line" lang="diff"><span class="p">@@ -679,7 +679,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> SetRate(NStr::StringToInt(rate));</span>
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC226" class="line" lang="diff"> } </span>
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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC227" class="line" lang="diff"> catch (const CStringException&) {</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="228" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="229" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> CLBOSException::eInvalidArgs,</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> "Could not parse string value for SetRate",</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> eLBOS_InvalidArgs);</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="p">@@ -706,7 +706,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> return NStr::StringToDouble(rate);</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> catch (const CStringException&) {</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> CLBOSException::eInvalidArgs,</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> "Value in \"rate\" meta parameter cannot "</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> "be represented as an integer",</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="p">@@ -718,7 +718,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> void LBOS::CMetaData::SetType(const string& host_type)</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> if (host_type.find_first_of(" \t\n\v\f\r") != string::npos) {</span>
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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> CLBOSException::eInvalidArgs,</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> "This convenience function throws on whitespace characters "</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> "in \"type\" meta parameter. If you know what you are doing, "</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="p">@@ -759,7 +759,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> SetType("");</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> default:</span>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> CLBOSException::eInvalidArgs, "Unknown EHostType "</span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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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="LC258" class="line" lang="diff"> "value. If you are sure that a correct value is "</span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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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="LC259" class="line" lang="diff"> "used, please tell the developer about this issue", </span>
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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="p">@@ -793,7 +793,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC261" class="line" lang="diff"> SetType("FIREWALL");</span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC262" class="line" lang="diff"> break;</span>
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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> default:</span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> CLBOSException::eInvalidArgs, "Unknown ESERV_Type "</span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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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="LC267" class="line" lang="diff"> "value. If you are sure that a correct value is "</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC268" class="line" lang="diff"> "used, please tell the developer about this issue", </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC269" class="line" lang="diff"><span class="p">@@ -824,7 +824,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC270" class="line" lang="diff"> SetType("");</span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> break;</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> default:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> CLBOSException::eInvalidArgs, "Unknown EHostType "</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> "value. If you are sure that a correct value is "</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> "used, please tell the developer about this issue",</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="p">@@ -870,7 +870,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> void LBOS::CMetaData::SetExtra(const string& extra)</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> if (extra.find_first_of(" \t\n\v\f\r") != string::npos) {</span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> CLBOSException::eInvalidArgs,</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> "This convenience function throws on whitespace characters "</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> "in \"extra\" meta parameter. If you know what you are doing, "</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/connect/ncbi_monkey.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/connect/ncbi_monkey.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="p">@@ -83,7 +83,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC290" class="line" lang="diff"> const string kSeedField = "seed";</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> #define PARAM_TWICE_EXCEPTION(param) \</span>
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__), \</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__), \</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs, \</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> string("Parameter \"" param "\" is set " \</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> "twice in [") + GetSection() + "]" + \</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="p">@@ -371,7 +371,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> case eMonkey_Send:</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> return "write";</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> default:</span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> string("Unknown EMonkeyActionType value"));</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> }</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="p">@@ -390,7 +390,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> case eMonkey_Connect:</span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> return "connect()";</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> default:</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> string("Unknown EMonkeyActionType value"));</span>
</pre>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> }</span>
</pre>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="p">@@ -467,7 +467,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> {</span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC318" class="line" lang="diff"> if (m_RunPos.find(sock) == m_RunPos.end()) {</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> throw CMonkeyException(</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC323" class="line" lang="diff"> "The socket provided has not been registered with current rule");</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> }</span>
</pre>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="p">@@ -511,7 +511,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> m_ReturnStatus = eIO_Closed;</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> } else if (eIOStatus == "eio_invalidarg") {</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> throw CMonkeyException(</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> string("Unsupported 'return_status': ") + eIOStatus_in);</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> } else if (eIOStatus == "eio_interrupt") {</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="p">@@ -526,7 +526,7 @@</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> m_ReturnStatus = eIO_NotSupported;</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> } else {</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> throw CMonkeyException(</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> string("Could not parse 'return_status': ") + eIOStatus_in);</span>
</pre>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="p">@@ -543,7 +543,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> split it on commas*/</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> vector<string> runs_list = s_Monkey_Split(runs, ',');</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> if (runs_list.size() == 0)</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
</pre>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> string("Parameter \"runs\" is empty in [")</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> + m_Section + "]" +</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="p">@@ -573,7 +573,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> if (m_RunMode == eMonkey_RunProbability) {</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> if (*run.rbegin() != '%') {</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> throw CMonkeyException(</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> "Value is not percentage: " + run +</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> ", values have to be either only percentages or "</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="p">@@ -593,7 +593,7 @@</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> size_t last_step = m_Runs.size();</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> if (last_step == 0 && step != 1) {</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> throw CMonkeyException(</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> "In the string of runs: " + runs + " the first "</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> "element MUST set value for the first run");</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="p">@@ -610,7 +610,7 @@</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> assert(run_format == eMonkey_RunSequence);</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> if (*run.rbegin() == '%') {</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> throw CMonkeyException(</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> string("Value is percentage: ") + run +</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> string(", values have to be either only percentages or "</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="p">@@ -619,7 +619,7 @@</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> int val = NStr::StringToInt(run);</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> if (m_Runs.size() > 0 && val <= *m_Runs.rbegin()) {</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> throw CMonkeyException(</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> string("\"runs\" should contain values in "</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> "increasing order"));</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="p">@@ -815,7 +815,7 @@</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> string value = name_value[1];</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> if (name == "allow") {</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> if (allow_set) {</span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> NULL, </span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> CMonkeyException::e_MonkeyInvalidArgs,</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> string("Parameter \"allow\" is set "</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="p">@@ -827,7 +827,7 @@</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> }</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> }</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> if (!allow_set)</span>
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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> string("Parameter \"allow\" not set in [")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> + GetSection() + "]" +</span>
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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="p">@@ -902,7 +902,7 @@</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> string value = name_value[1];</span>
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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> if (name == "ignore") {</span>
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<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> if (ignore_set) {</span>
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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> NULL,</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> CMonkeyException::e_MonkeyInvalidArgs,</span>
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<td class="diff-line-num new new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> string("Parameter \"ignore\" is set "</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="p">@@ -914,7 +914,7 @@</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> }</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> }</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> if (!ignore_set) {</span>
</pre>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
</pre>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> string("Parameter \"ignore\" not set in [")</span>
</pre>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> + GetSection() + "]" +</span>
</pre>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="p">@@ -1032,7 +1032,7 @@</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> ".*" , "");</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC426" class="line" lang="diff"> if (filtered.find_first_of("[]()+^?{}$.*\\") != string::npos) {</span>
</pre>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> throw CMonkeyException(</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
</pre>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> NULL,</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> CMonkeyException::e_MonkeyInvalidArgs,</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> exception_message);</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="p">@@ -1051,7 +1051,7 @@</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> }</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> else {</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> throw CMonkeyException(</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> NULL,</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> CMonkeyException::e_MonkeyInvalidArgs,</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> exception_message);</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="p">@@ -1179,7 +1179,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> ss << "Probability below zero for write rule in plan " << m_Name</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> << ". Check config!";</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> throw CMonkeyException(</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs, </span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> ss.str());</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> }</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="p">@@ -1221,7 +1221,7 @@</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> stringstream ss;</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> ss << "Probability below zero for write rule in plan " << m_Name</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> << ". Check config!";</span>
</pre>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> ss.str());</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"> }</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="p">@@ -1270,7 +1270,7 @@</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> stringstream ss;</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> ss << "Probability below zero for write rule in plan " << m_Name</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> << ". Check config!";</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> ss.str());</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> }</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="p">@@ -1313,7 +1313,7 @@</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> ss << "Probability below zero for write rule in plan " << m_Name</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> << ". Check config!";</span>
</pre>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> throw CMonkeyException(</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs, </span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> ss.str());</span>
</pre>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> }</span>
</pre>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="p">@@ -1372,7 +1372,7 @@</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> {</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> if (sm_HookSwitch == NULL) {</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> throw CMonkeyException(</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> "Launch CONNECT_Init() before initializing CMonkey instance");</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> }</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="p">@@ -1458,7 +1458,7 @@</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> prob = (int)(NStr::StringToDouble(prob_str) * 100);</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> }</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> if (prob < 0 || prob > 100) {</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> NULL,</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> CMonkeyException::e_MonkeyInvalidArgs,</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> "Parameter \"probability\"=" + prob_str</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="p">@@ -1469,7 +1469,7 @@</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> m_Probability = (unsigned short)prob;</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> }</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> catch (const CStringException&) {</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> "Parameter \"probability\"=" + prob_str</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> + " for section [" + monkey_section</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="p">@@ -1757,7 +1757,7 @@</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> << " has been already registered in CMonkey and cannot be used again";</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> if (m_RegisteredTokens.find(token) != m_RegisteredTokens.end()) {</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> throw CMonkeyException(</span>
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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;">- CDiagCompileInfo(__FILE__, __LINE__),</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> NULL, CMonkeyException::e_MonkeyInvalidArgs,</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> ss.str());</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> }</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/connect/ncbi_priv.h</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/connect/ncbi_priv.h</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="p">@@ -223,7 +223,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> _mess.level = _xx_level; \</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> _mess.module = THIS_MODULE; \</span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> _mess.func = CORE_CURRENT_FUNCTION; \</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _mess.file = __FILE__; \</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _mess.file = "c++/src/connect/ncbi_priv.h"; \</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> _mess.line = __LINE__; \</span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> _mess.raw_data = (_raw_data); \</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> _mess.raw_size = (_raw_size); \</span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objects/seqfeat/BioSource.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objects/seqfeat/BioSource.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="p">@@ -938,7 +938,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> typedef CStaticArraySet<const char*, PNocase_CStr> TCIgnoreCaseQualsSet;</span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static const TCIgnoreCaseQualsSet s_IgnoreCaseQualsSet(s_IgnoreCaseQuals, sizeof(s_IgnoreCaseQuals), __FILE__, __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static const TCIgnoreCaseQualsSet s_IgnoreCaseQualsSet(s_IgnoreCaseQuals, sizeof(s_IgnoreCaseQuals), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> bool s_MayIgnoreCase(const string& value)</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> { </span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="p">@@ -960,7 +960,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> typedef CStaticArraySet<const char*, PNocase_CStr> TCTaxNameElementQualsSet;</span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static const TCTaxNameElementQualsSet s_TaxNameElementQualsSet(s_TaxNameElementQuals, sizeof(s_TaxNameElementQuals), __FILE__, __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static const TCTaxNameElementQualsSet s_TaxNameElementQualsSet(s_TaxNameElementQuals, sizeof(s_TaxNameElementQuals), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> bool s_IsTaxNameElement(const string& value)</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> { </span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="p">@@ -1364,7 +1364,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> typedef CStaticArraySet<const char*, PNocase_CStr> TCStopWordStrSet;</span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static const TCStopWordStrSet s_StopWordsSet(s_StopWords, sizeof(s_StopWords), __FILE__, __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static const TCStopWordStrSet s_StopWordsSet(s_StopWords, sizeof(s_StopWords), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> bool CBioSource::IsStopWord(const string& value)</span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objects/seqfeat/SubSource.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objects/seqfeat/SubSource.cpp</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="p">@@ -3043,7 +3043,7 @@</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> "Zimbabwe"</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> };</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> typedef CStaticArraySet<const char*, PCase_CStr> TCStrSet;</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), __FILE__, __LINE__);</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), "c++/src/objects/seqfeat/SubSource.cpp", __LINE__);</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> </span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> // former legal country names, must be in alphabetical order (case sensitive)</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> static const char* const s_Former_Countries[] = {</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="p">@@ -3061,7 +3061,7 @@</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> "Yugoslavia",</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> "Zaire"</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static const TCStrSet s_Former_CountriesSet(s_Former_Countries, sizeof(s_Former_Countries), __FILE__, __LINE__);</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static const TCStrSet s_Former_CountriesSet(s_Former_Countries, sizeof(s_Former_Countries), "c++/src/objects/seqfeat/SubSource.cpp", __LINE__);</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> </span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> bool CCountries::IsValid(const string& country)</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> {</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/serial/datatool/classstr.cpp</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/serial/datatool/classstr.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="p">@@ -850,7 +850,7 @@</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> " if (!CanGet"<< mem_cName<<"()) {\n"</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> " ThrowUnassigned("<<member_index;</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> #if 0</span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- code.Methods(inl) << ", __FILE__, __LINE__";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ code.Methods(inl) << ", "c++/src/serial/datatool/classstr.cpp", __LINE__";</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> #endif</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> code.Methods(inl) << ");\n"</span>
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<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> " }\n";</span>
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<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/serial/serialobject.cpp</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/serial/serialobject.cpp</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="p">@@ -295,7 +295,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> // set temporary diag compile info to use argument file name and line</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> #undef DIAG_COMPILE_INFO</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> #define DIAG_COMPILE_INFO \</span>
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<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- NCBI_NS_NCBI::CDiagCompileInfo(file_name? file_name: __FILE__, \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ NCBI_NS_NCBI::CDiagCompileInfo(file_name? file_name: "c++/src/serial/serialobject.cpp", \</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> file_line? file_line: __LINE__, \</span>
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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> NCBI_CURRENT_FUNCTION, \</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> NCBI_MAKE_MODULE(NCBI_MODULE))</span>
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<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="p">@@ -303,7 +303,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> // restore original diag compile info definition</span>
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<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> #undef DIAG_COMPILE_INFO</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> #define DIAG_COMPILE_INFO \</span>
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<td class="diff-line-num new new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- NCBI_NS_NCBI::CDiagCompileInfo(__FILE__, \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ NCBI_NS_NCBI::CDiagCompileInfo("c++/src/serial/serialobject.cpp", \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> __LINE__, \</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> NCBI_CURRENT_FUNCTION, \</span>
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<td class="diff-line-num new new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> NCBI_MAKE_MODULE(NCBI_MODULE))</span>
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<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mdb.c</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mdb.c</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="p">@@ -1523,7 +1523,7 @@</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> #ifndef NDEBUG</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> # define mdb_assert0(env, expr, expr_txt) ((expr) ? (void)0 : \</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mdb_assert_fail(env, expr_txt, mdb_func_, __FILE__, __LINE__))</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mdb_assert_fail(env, expr_txt, mdb_func_, "c++/src/util/lmdb/mdb.c", __LINE__))</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> </span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> static void ESECT</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> mdb_assert_fail(MDB_env *env, const char *expr_txt,</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest.c</span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mtest.c</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)</span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \</span>
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<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest.c", __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> int main(int argc,char * argv[])</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> {</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest2.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mtest2.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC629" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest2.c", __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> </span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> int main(int argc,char * argv[])</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> {</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest3.c</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mtest3.c</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"> #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest3.c", __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> </span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> int main(int argc,char * argv[])</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> {</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest4.c</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mtest4.c</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))</span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \</span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest4.c", __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"> </span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> int main(int argc,char * argv[])</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> {</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest5.c</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mtest5.c</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest5.c", __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"> </span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> int main(int argc,char * argv[])</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> {</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest6.c</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/lmdb/mtest6.c</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest6.c", __LINE__, msg, mdb_strerror(rc)), abort()))</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> </span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> char dkbuf[1024];</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> </span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/regexp/pcre_scanner_unittest.cc</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/regexp/pcre_scanner_unittest.cc</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> #define CHECK_EQ(a, b) do { \</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> if ( (a) != (b) ) { \</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"> fprintf(stderr, "%s:%d: Check failed because %s != %s\n", \</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __FILE__, __LINE__, #a, #b); \</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "c++/src/util/regexp/pcre_scanner_unittest.cc", __LINE__, #a, #b); \</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> exit(1); \</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"> } \</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> } while (0)</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/regexp/pcre_stringpiece_unittest.cc</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/regexp/pcre_stringpiece_unittest.cc</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> #define CHECK(condition) do { \</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> if (!(condition)) { \</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"> fprintf(stderr, "%s:%d: Check failed: %s\n", \</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __FILE__, __LINE__, #condition); \</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "c++/src/util/regexp/pcre_stringpiece_unittest.cc", __LINE__, #condition); \</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> exit(1); \</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> } \</span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> } while (0)</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/static_set.cpp</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/static_set.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="p">@@ -87,7 +87,7 @@</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> TParamStaticArrayCopyWarning::GetDefault()) ) {</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> // report incorrect usage</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> CDiagCompileInfo diag_compile_info</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (file? file: __FILE__,</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (file? file: "c++/src/util/static_set.cpp",</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> file? line: __LINE__,</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> NCBI_CURRENT_FUNCTION,</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"> NCBI_MAKE_MODULE(NCBI_MODULE));</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="p">@@ -122,7 +122,7 @@</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> if ( TParamStaticArrayUnsafeTypeWarning::GetDefault() ) {</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> // report incorrect usage</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> CDiagCompileInfo diag_compile_info</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (file? file: __FILE__,</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (file? file: "c++/src/util/static_set.cpp",</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> file? line: __LINE__,</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> NCBI_CURRENT_FUNCTION,</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> NCBI_MAKE_MODULE(NCBI_MODULE));</span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="p">@@ -145,7 +145,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"> {</span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> { // report incorrect usage</span>
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> CDiagCompileInfo diag_compile_info</span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (file? file: __FILE__,</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (file? file: "c++/src/util/static_set.cpp",</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> file? line: __LINE__,</span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> NCBI_CURRENT_FUNCTION,</span>
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"> NCBI_MAKE_MODULE(NCBI_MODULE));</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -11,3 +11,5 @@ suppress_gnutls_version_check</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">optionally_keep_sequence</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">fix_unit_tests</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">system_mbedtls_only</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">reprobuild</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">spelling</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Spelling fixes</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/include/objtools/alnmgr/seqids_extractor.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/include/objtools/alnmgr/seqids_extractor.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -232,7 +232,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> else if (*id_vec[i] != *id) {</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> string err("Inconsistent Seq-ids found in seg ");</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> err += NStr::NumericToString(i) +</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;">- ". Excpected " + id_vec[i]->AsString() +</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;">+ ". Expected " + id_vec[i]->AsString() +</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> ", encountered " + id->AsString() + ".";</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> NCBI_THROW(CAlnException, eInvalidSeqId, err);</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"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/algo/blast/api/blast_setup_cxx.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/algo/blast/api/blast_setup_cxx.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -784,7 +784,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if(warning != kEmptyStr){</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> warning += ": ";</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"><span class="gd" style="color: #000; background-color: #fdd;">- warning += "Subject sequence contians no data";</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ warning += "Subject sequence contains no data";</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> ERR_POST(Warning << warning);</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> continue;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/algo/winmask/seq_masker_ostat_factory.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/algo/winmask/seq_masker_ostat_factory.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -75,7 +75,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> else NCBI_THROW( CSeqMaskerOstatFactoryException,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> eBadName,</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;">- "unkown unit counts format" );</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;">+ "unknown unit counts format" );</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> catch( CException & e ) {</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -113,7 +113,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> else NCBI_THROW( CSeqMaskerOstatFactoryException,</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> eBadName,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "unkown unit counts format" );</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "unknown unit counts format" );</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> catch( CException & e ) {</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/app/blastdb/blastdbcheck.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/app/blastdb/blastdbcheck.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -232,7 +232,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> "Require that all sequences in the database have taxid set.");</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> arg_desc->AddFlag</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;">- ("cdd_delta", "Do aditional tests for a CDD database for DELTA-BLAST");</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ("cdd_delta", "Do additional tests for a CDD database for DELTA-BLAST");</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> // Setup arg.descriptions for this application</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> SetupArgDescriptions(arg_desc.release());</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/app/blastdb/makeprofiledb.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/app/blastdb/makeprofiledb.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -546,13 +546,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength()))</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"><span class="gd" style="color: #000; background-color: #fdd;">- string err = filename + " contians no bioseq data";</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ string err = filename + " contains no bioseq data";</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> NCBI_THROW(CInputException, eInvalidInput, err);</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> }</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if(!pssm.IsSetNumRows() || !pssm.IsSetNumColumns())</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> {</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- string err = filename + " contians no info on num of columns or num of rows";</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ string err = filename + " contains no info on num of columns or num of rows";</span></span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> NCBI_THROW(CInputException, eInvalidInput, err);</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> }</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -605,13 +605,13 @@</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> if(sm_invalid == sm)</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> {</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- string err = filename + " contians no pssm or residue frequencies";</span></span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ string err = filename + " contains no pssm or residue frequencies";</span></span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> NCBI_THROW(CInputException, eInvalidInput, err);</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> }</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> }</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> else</span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> {</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- string err = filename + " contians no scoremat";</span></span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ string err = filename + " contains no scoremat";</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> NCBI_THROW(CInputException, eInvalidInput, err);</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> }</span>
</pre>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -1563,7 +1563,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> *m_LogFile << filename +</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- " was excluded: it conatins an invalid CD \n";</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ " was excluded: it contains an invalid CD \n";</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> return false;</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos.c</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/connect/ncbi_lbos.c</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -951,7 +951,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> sizeof(char) * (strlen(buf) + 1))) ) </span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> CORE_LOG(eLOG_Warning, "s_LBOS_UrlReadAll: Buffer shrink error, using "</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "original stirng");</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "original string");</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> buf = realloc_result;</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> }</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;">--- ncbi-blastplus.orig/c++/src/objects/seqalign/Dense_seg.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objects/seqalign/Dense_seg.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -988,7 +988,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> NCBI_THROW(CSeqalignException, eInvalidInputData,</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> "CDense_seg::RemapToLoc():"</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- " The strand should be the same accross"</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ " The strand should be the same across"</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> " the input seq-loc");</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> }</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objects/seqalign/Seq_align.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objects/seqalign/Seq_align.cpp</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="p">@@ -872,7 +872,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> if (dim != ss.GetDim() || row != dim) {</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> NCBI_THROW(CSeqalignException, eInvalidInputAlignment,</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> "CreateDensegFromStdseg(): "</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Inconsistent dimentions!");</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "Inconsistent dimensions!");</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> if (widths_determined[seg]) {</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.inc</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.inc</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="p">@@ -661,7 +661,7 @@</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> "BPS\ts\tCalifornia Department of Food and Agriculture\t\t\t",</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> "BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t",</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> "BR<BEL>\ts\tBotanic Garden Meise\t\t\t",</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-"BR<BRA>\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\t\t\t",</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+"BR<BRA>\tc\tJohanna Dobereiner Biological Resource Center (CRB-JD)\t\t\t",</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> "BRA\ts\tSlovak National Museum, Botany Department\t\t\t",</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> "BRAD\ts\tUniversity of Bradford, Biology Department\t\t\t",</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> "BRC\ts\tBotanical Record Club\t\t\t",</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.txt</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.txt</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="p">@@ -628,7 +628,7 @@</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> BPS s California Department of Food and Agriculture </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> BPU s Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology </span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> BR<BEL> s Botanic Garden Meise </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BR<BRA> c Johanna Dobereiner Biological Resouce Center (CRB-JD) </span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+BR<BRA> c Johanna Dobereiner Biological Resource Center (CRB-JD) </span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> BRA s Slovak National Museum, Botany Department </span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> BRAD s University of Bradford, Biology Department </span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> BRC s Botanical Record Club </span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objmgr/util/sequence.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objmgr/util/sequence.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="p">@@ -274,7 +274,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> if ( best_feats.empty() ) {</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> NCBI_THROW_FMT(CObjMgrException, eFindFailed,</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> "GetProteinName("<<GetId(seq, eGetId_Best)<<"): "</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "the sequence does't have prot feature");</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "the sequence doesn't have prot feature");</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> if ( best_feats.size() > 1 ) {</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> NCBI_THROW_FMT(CObjMgrException, eFindConflict,</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objtools/align_format/taxFormat.cpp</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objtools/align_format/taxFormat.cpp</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -587,7 +587,7 @@</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> } </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> }</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> if (!tax_load_ok) {</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- NCBI_THROW(CException, eUnknown,"Taxonomic load was not successfull.");</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ NCBI_THROW(CException, eUnknown,"Taxonomic load was not successful.");</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> m_TaxTreeLoaded = true;</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objtools/format/flat_file_config.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objtools/format/flat_file_config.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -614,7 +614,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> // from</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> arg_desc->AddOptionalKey("from", "From",</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Begining of shown range", CArgDescriptions::eInteger);</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "Beginning of shown range", CArgDescriptions::eInteger);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> // to</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> arg_desc->AddOptionalKey("to", "To",</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_converter.cpp</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objtools/readers/agp_converter.cpp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="p">@@ -728,7 +728,7 @@</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo());</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> submit_block_writer.Flush();</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> seq_sub_header_strm << "," << endl;</span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq_sub_header_strm << "data entrys {" << endl;</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_sub_header_strm << "data entries {" << endl;</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> </span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> out_sObjectOpeningString = seq_sub_header_strm.str();</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> out_sObjectClosingString = "} }" + out_sObjectClosingString;</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_util.cpp</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objtools/readers/agp_util.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="p">@@ -67,7 +67,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> "object_beg != previous object_end + 1",</span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> "no valid AGP lines",</span>
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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "consequtive gaps lines with the same type and linkage",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "consecutive gaps lines with the same type and linkage",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC206" class="line" lang="diff"> "in \"Scaffold from component\" file, invalid scaffold-breaking gap",</span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="p">@@ -88,7 +88,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> // Content Warnings</span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> "gap at the end of object (OK if X is the circular chromosome/plasmid)",</span>
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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC212" class="line" lang="diff"> "gap at the beginning of object ",</span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "two consequtive gap lines (e.g. a gap at the end of "</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "two consecutive gap lines (e.g. a gap at the end of "</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> "a scaffold, two non scaffold-breaking gaps, ...)",</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> "no components in object",</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> "the span overlaps a previous span for this component",</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_validate_reader.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/objtools/readers/agp_validate_reader.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="p">@@ -295,7 +295,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> int prev_comp_file=spans.rbegin()->file_num;</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> int prev_comp_line=spans.rbegin()->line_num;</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> if(prev_comp_file < m_last_scaf_start_file || prev_comp_line < m_last_scaf_start_line) {</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sameComId_otherScaf="; previous occurance at ";</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sameComId_otherScaf="; previous occurrence at ";</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> if(prev_comp_file && prev_comp_file!=m_AgpErr->GetFileNum()) {</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> sameComId_otherScaf += m_AgpErr->GetFile(prev_comp_file);</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> sameComId_otherScaf += ":";</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ncbi-blastplus.orig/c++/src/util/compress/api/compress.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ncbi-blastplus/c++/src/util/compress/api/compress.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="p">@@ -160,7 +160,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) {</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> os.write(buf.get(), nread);</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> if ( !os.good() ) {</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SetError(-1, "Error writing to ouput file");</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SetError(-1, "Error writing to output file");</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> return false;</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6#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">@@ -4,6 +4,8 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Uncomment this to turn on verbose mode.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#export DH_VERBOSE=1</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CURDIR)</span>/fakehome</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">NUMJOBS</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"> <span class="nv" style="color: #008080;">NUMJOBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">patsubst</span> <span class="nv" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">=</span>%,%,<span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">filter</span> <span class="nv" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">=</span>%,<span class="nv" style="color: #008080;">$(DEB_BUILD_OPTIONS)</span><span class="nf" style="color: #900; font-weight: 600;">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +64,7 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make"><span class="nl">override_dh_auto_configure-indep</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"><span class="nl">override_dh_auto_configure-arch</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PREBUILT_DATATOOL_EXE)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(HOME)</span></span>
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65
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>c++ <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">CONFIG_SHELL</span><span class="o" style="font-weight: 600;">=</span>/bin/bash <span class="se" style="color: #d14;">\</span></span>
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66
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"> ./configure <span class="nv" style="color: #008080;">$(DEB_CONFIGURE_EXTRA_FLAGS)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-n</span> +0 config.log BUILD/status/config.log<span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1<span class="o" style="font-weight: 600;">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +105,7 @@ override_dh_install-arch:</td>
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102
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/windowmasker_2.2.22_adapter</span>
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103
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="make"> 2to3 <span class="nt" style="color: #000080;">-w</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/windowmasker_2.2.22_adapter</span>
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104
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="make"> <span class="nb" style="color: #0086b3;">chmod</span> +x <span class="nv" style="color: #008080;">$(instroot)</span>/bin/windowmasker_2.2.22_adapter</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/windowmasker_2.2.22_adapter.py</span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/windowmasker_2.2.22_adapter.py<span class="k" style="font-weight: 600;"><span class="idiff left right">*</span></span></span>
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106
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Clean up tests, demos, and internal build tools</span></span>
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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-f</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(instroot)/bin/*test*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(instroot)/bin/seqdb_demo</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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108
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(instroot)/bin/datatool</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(instroot)/bin/run_with_lock</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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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">version=3</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">opts=<span class="idiff left right">pasv,</span>filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right">ftp</span>://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts=filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right">https</span>://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate</span></pre>
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