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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/commit/aac8545bd1c18af9d611d759ae96392cb762a690">aac8545b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-10T06:24:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.9.2+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/commit/c4b84d6ac2d5c08273a5d90d830c69601f257b25">c4b84d6a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-10T06:24:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.9.2+dfsg'
Update to upstream version '2.9.2+dfsg'
with Debian dir cd68f85f63957545b375597d898edcbdd78808c0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/commit/774651a2ac215e2ecadc85be57202c82b042ea62">774651a2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-10T06:24:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/commit/fd914b2778858642ba4626cd005f6d490546683d">fd914b27</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-10T06:25:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
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</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#c9512c0b1798e84b5d6a945ad880784dab140a53">
build/Makefile.vers
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#4705a68e02a22c6bfea0273af010dd42e1861b4a">
shared/toolkit.vers
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<li class="file-stats">
<a href="#5cd76f234790117309267153be422c6d4e826541">
shared/toolkit.vers.h
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<li class="file-stats">
<a href="#17c0dcfb431c244d45baad5c1d64a5077181102e">
tools/bam-loader/loader-imp.c
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># NCBI External Developer Release:</span></span>
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.9.2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**July 23, 2018**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**kfg, vfs**</span>: Introduced enhanced handling of download-only NGC files that lack read/decrypt permissions</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.9.1-2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**July 17, 2018**</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**bam-load**</span>: fixed a bug preventing early termination on error</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.9.1-1</span></span>
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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="markdown"><span class="gs" style="font-weight: 600;">**June 26, 2018**</span></span>
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<li id="c9512c0b1798e84b5d6a945ad880784dab140a53">
<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#c9512c0b1798e84b5d6a945ad880784dab140a53"><strong>build/Makefile.vers</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,4 +23,4 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># ===========================================================================</span></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="make"></span>
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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># SRA-TOOLS and library version</span></span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="nv" style="color: teal;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.9.<span class="idiff left right">1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="nv" style="color: teal;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.9.<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sra-sdk (2.9.2+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 10 Sep 2018 08:24:17 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">sra-sdk (2.9.1-1+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libmagic-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libxml2-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sra-sdk</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sra-sdk.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/ncbi/sra-tools/</span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#4705a68e02a22c6bfea0273af010dd42e1861b4a"><strong>shared/toolkit.vers</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.9.<span class="idiff left right">1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.9.<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#5cd76f234790117309267153be422c6d4e826541"><strong>shared/toolkit.vers.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x0209000<span class="idiff left right">1</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x0209000<span class="idiff left right">2</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/compare/fd79fe1ba99baf455b9332bffd7903242384a7d6...fd914b2778858642ba4626cd005f6d490546683d#17c0dcfb431c244d45baad5c1d64a5077181102e"><strong>tools/bam-loader/loader-imp.c</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">@@ -2622,6 +2622,8 @@ WRITE_ALIGNMENT:</td>
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<pre style="margin: 0;"> <span id="LC2622" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2623" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="2624" style="width: 35px; color: rgba(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="LC2624" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">had_sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2625" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC2626" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2627" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2628" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bamread_thread</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bamq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2629" class="line" lang="c"> <span class="n" style="color: #333;">KQueueSeal</span><span class="p">(</span><span class="n" style="color: #333;">bamq</span><span class="p">);</span></span>
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