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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbbam">Debian Med / pbbam</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/25ba6fde382dd7980c9dbcb76f2fb98e7abc90d0">25ba6fde</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-10T09:47:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.19.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/dd9916acd3fa8cbbdbd6978165ecca6cd4b42a9c">dd9916ac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-10T09:47:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.19.0+dfsg'
Update to upstream version '0.19.0+dfsg'
with Debian dir 656052e8dac14b2e30c45eb0b1696ab0d376c2b4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/9d7f5f3347fff9ef6f4121ce907ef2728c8bf15b">9d7f5f33</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-10T09:47:18Z</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/pbbam/commit/593fd0e94f3f7cb9fc4e3c12dae1e113492ca7d4">593fd0e9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-10T10:03:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix samtools call in tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/a8f11402eca9dc629614eb938472f715aa392860">a8f11402</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-10T10:44:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump (fake) SOVERSION (=release version)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/c0a82780f2d3957725dbed2a13f87ba7faed6404">c0a82780</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-10T10:55:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#213872121f6ad280d08d4b11948914a21bd57a4d">
include/pbbam/BamWriter.h
</a>
</li>
<li class="file-stats">
<a href="#e05d4ab227d906896bf3f3542deee449cb8bf6b1">
include/pbbam/Compare.h
</a>
</li>
<li class="file-stats">
<a href="#13e6f05c8e887e418c96dbd9ea25d2567e409652">
include/pbbam/DataSet.h
</a>
</li>
<li class="file-stats">
<a href="#1e4911ad4aa317b1745074f1a0c4dfc639f0f991">
include/pbbam/DataSetTypes.h
</a>
</li>
<li class="file-stats">
<a href="#41cc8535cfb898a3bdd89449b8c1d14370328762">
include/pbbam/PbiFilterTypes.h
</a>
</li>
<li class="file-stats">
<a href="#95c79ed3d1b53d2962eb30ba93a760fe8ede024a">
include/pbbam/internal/PbiFilterTypes.inl
</a>
</li>
<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
</a>
</li>
<li class="file-stats">
<a href="#dc4d5d1220b0cd2b76cb436a076ddf99d8de0fdb">
scripts/ci/test.sh
</a>
</li>
<li class="file-stats">
<a href="#e0820644d18c5c08f877e2fdd356cbae7bc79dfc">
src/BamRecordImpl.cpp
</a>
</li>
<li class="file-stats">
<a href="#95114a6fbde6b3ead1127d4494372d6a91f30cea">
src/BamWriter.cpp
</a>
</li>
<li class="file-stats">
<a href="#584639dd9ffaa9227f61109731cb09c74ab4793f">
src/ChemistryTable.cpp
</a>
</li>
<li class="file-stats">
<a href="#227f5ff5f6801400bd559505c89b9ed57fb95601">
src/Compare.cpp
</a>
</li>
<li class="file-stats">
<a href="#f27e938fef11af21d17ab971101826251a9db705">
src/DataSet.cpp
</a>
</li>
<li class="file-stats">
<a href="#2924d26c2aef212f4282671a4301d3be92879c51">
src/DataSetTypes.cpp
</a>
</li>
<li class="file-stats">
<a href="#cdfa3536dcbcfe0ae4777ccc214b8f9199083a9f">
src/DataSetXsd.cpp
</a>
</li>
<li class="file-stats">
<a href="#58b7f0e1feb1ec8870c90e746592941feaae16e8">
src/FileProducer.h
</a>
</li>
<li class="file-stats">
<a href="#1996717698d7751cc78126e3ce12f1de57b1e566">
src/PbiFilter.cpp
</a>
</li>
<li class="file-stats">
<a href="#810ee2d4abdfb7b58a0e4890dcb9e1afc202c5c3">
src/PbiFilterTypes.cpp
</a>
</li>
<li class="file-stats">
<a href="#21a63d74511a44ba1fb2c2d37a812b57a0eec10a">
<span class="new-file">
+
tests/data/long-cigar-1.7.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#4b638936c81ded1d14a540297d3e74a211bf4a08">
<span class="deleted-file">
−
tests/data/long-cigar.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#af2b927c2ec3dd69e8b5addb910b2d1c766bea76">
tests/meson.build
</a>
</li>
<li class="file-stats">
<a href="#30d31f3c7bebba69a52a2cbbbac433fe1aaa2514">
tests/src/cram/pbbamify.t.in
</a>
</li>
<li class="file-stats">
<a href="#67c3d2c0ed79631940826d3634fa7f5a4e2a062e">
tests/src/test_BamWriter.cpp
</a>
</li>
<li class="file-stats">
<a href="#94cee03a39de65e3f51c168e5df3968e80341600">
tests/src/test_LongCigar.cpp
</a>
</li>
<li class="file-stats">
<a href="#94823b808e03917d439ba3f925435514840b570c">
tools/meson.build
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,11 @@ guarantees will be maintained within each major version series.</td>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Active</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="12" 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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.19.0] - 2018-09-11</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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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="LC14" class="line" lang="markdown"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Added</span></span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p"> -</span> TranscriptAlignmentSet to XML support</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.17.0] - 2018-03-18</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Added</span></span>
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<br>
</li>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -3,7 +3,7 @@</td>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">########################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>SET CMP0048 NEW<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># lets us set version in project()</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>PacBioBAM VERSION 0.1<span class="idiff left right">7</span>.0 LANGUAGES CXX C<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>PacBioBAM VERSION 0.1<span class="idiff left right">9</span>.0 LANGUAGES CXX C<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.0<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># project name & version</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pbbam (0.19.0+dfsg-1) unstable; 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fix samtools call in tests</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/control: Bump (fake) SOVERSION (=release version)</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"> -- Andreas Tille <tille@debian.org> Wed, 10 Oct 2018 12:45:02 +0200</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">pbbam (0.18.0+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#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">@@ -27,7 +27,7 @@ Package: pbbamtools</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> libpbbam0.1<span class="idiff left right">8</span>.0 (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> libpbbam0.1<span class="idiff left right">9</span>.0 (= ${binary:Version})</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Recommends: samtools</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Description: processing Pacific Biosciences binary alignment/map files</span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> The BAM format is a binary, compressed, record-oriented container format</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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="42" 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">@@ -42,7 +42,7 @@ Description: processing Pacific Biosciences binary alignment/map files</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> This package provides command-line utilities for working with PacBio BAM</span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> files.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">Package: libpbbam0.1<span class="idiff left right">8</span>.0</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Package: libpbbam0.1<span class="idiff left right">9</span>.0</span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Architecture: any</span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Multi-Arch: same</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Section: libs</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" 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="66" 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">@@ -66,7 +66,7 @@ Description: Pacific Biosciences binary alignment/map (BAM) library</td>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">Package: libpbbam-dev</span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">Depends: libpbbam0.1<span class="idiff left right">8</span>.0 (= ${binary:Version}),</span>
</pre>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Depends: libpbbam0.1<span class="idiff left right">9</span>.0 (= ${binary:Version}),</span>
</pre>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> libhts-dev,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="71" 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="LC71" class="line" lang="plaintext"> libssl-dev,</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> ${misc:Depends}</span>
</pre>
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<br>
</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,6 +56,7 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> -e 's|@PacBioBAM_VERSION@|$(DEB_VERSION_UPSTREAM)|g' \</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> -e 's|@GeneratedTestDataDir@|$(generated_data_dir)|g' \</span>
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<td class="diff-line-num old_line" data-linenumber="58" 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="LC58" class="line" lang="plaintext"> -e 's|+dfsg||g' -e 's|\(/build/$(DEB_SOURCE)-[0-9.]\+\)/|\1+dfsg/|' \</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> -e 's/$$SAMTOOLS/samtools/g' \</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> $< > $@</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">override_dh_install:</span>
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<li id="213872121f6ad280d08d4b11948914a21bd57a4d">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#213872121f6ad280d08d4b11948914a21bd57a4d"><strong>include/pbbam/BamWriter.h</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">@@ -87,14 +87,39 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">BinCalculation_OFF</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief The Config struct provides a "parameter object" for BamWriter</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// settings. This allows for writer configuration without having to</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// refer to ordering of parameters, default values, etc.</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Config</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">Config</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// zlib compression level</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">CompressionLevel</span> <span class="n" style="color: #333;">compressionLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DefaultCompression</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// The number of threads for compression. If set to 0, BamWriter will</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// attempt to determine a reasonable estimate. If set to 1, this will</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// force single-threaded execution. No checks are made against an upper limit.</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// If ON, ensures that proper BAI bin numbers are provided for all records.</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculation_ON</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// If true, write to <filename>.tmp, and rename to <filename> in dtor.</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// This allows downstream checks to see if BAM file may be truncated</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// due to early termination (e.g. a thrown exception). If false, write</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// directly to <filename>.</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useTempFile</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="LC115" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \name Constructors & Related Methods</span></span>
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92
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \{</span></span>
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93
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"></span>
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94
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Opens a %BAM file for writing & writes the header information.</span></span>
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95
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// The error status will be set if either operation fails.</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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98
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \note Set \p filename to "-" for stdout.</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] filename path to output %BAM file</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">@@ -111,13 +136,32 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// records written. This extra step may turned off when bin</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// numbers are not needed. Though if in doubt, keep the default.</span></span>
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113
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] useTempFile If true, write to <filename>.tmp, and rename</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// to <filename>. This provides for downstream</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// checks to see if BAM file may be truncated</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// due to early termination (a thrown exception).</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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114
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \throws std::runtmie_error if there was a problem opening the file for</span></span>
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115
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// writing or if an error occurred while writing the header</span></span>
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116
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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117
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">BamWriter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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118
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompressionLevel</span> <span class="n" style="color: #333;">compressionLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DefaultCompression</span><span class="p">,</span></span>
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119
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculation_ON</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculation_ON</span><span class="p">,</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useTempFile</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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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Opens a %BAM file for writing & writes the header information.</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] filename path to output %BAM file</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] header BamHeader object</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] config container for add'l configuration options</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \throws std::runtmie_error if there was a problem opening the file for</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// writing or if an error occurred while writing the header</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">BamWriter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Config</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">config</span><span class="p">);</span></span>
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121
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"></span>
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122
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Fully flushes all buffered data & closes file.</span></span>
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123
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">BamWriter</span><span class="p">()</span> <span class="n" style="color: #333;">override</span><span class="p">;</span></span>
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<li id="e05d4ab227d906896bf3f3542deee449cb8bf6b1">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#e05d4ab227d906896bf3f3542deee449cb8bf6b1"><strong>include/pbbam/Compare.h</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">@@ -434,6 +434,28 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \}</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">Check</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lhs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rhs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">cmp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">Compare</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">EQUAL</span><span class="o" style="font-weight: 600;">:</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">rhs</span><span class="p">;</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">Compare</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">LESS_THAN</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rhs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">Compare</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">rhs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">Compare</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">GREATER_THAN</span><span class="o" style="font-weight: 600;">:</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rhs</span><span class="p">;</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">Compare</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span><span class="o" style="font-weight: 600;">:</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">rhs</span><span class="p">;</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">Compare</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="o" style="font-weight: 600;">:</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">rhs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="c"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="c"> <span class="n" style="color: #333;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type requested"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="c"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace BAM</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#13e6f05c8e887e418c96dbd9ea25d2567e409652"><strong>include/pbbam/DataSet.h</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">@@ -46,7 +46,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">HDF_SUBREAD</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">REFERENCE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">SUBREAD</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">TRANSCRIPT</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">TRANSCRIPT</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">TRANSCRIPT_ALIGNMENT</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Converts printable dataset type to type enum.</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#1e4911ad4aa317b1745074f1a0c4dfc639f0f991"><strong>include/pbbam/DataSetTypes.h</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">@@ -861,6 +861,16 @@ public:</td>
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="c"> <span class="n" style="color: #333;">TranscriptSet</span><span class="p">();</span></span>
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862
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="c"><span class="p">};</span></span>
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// \brief The TranscriptAlignmentSet class represents a %TranscriptAlignmentSet</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// root element in DataSetXML.</span></span>
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">PBBAM_EXPORT</span> <span class="n" style="color: #333;">TranscriptAlignmentSet</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DataSetBase</span></span>
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="c"><span class="p">{</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Creates an empty TranscriptAlignmentSet dataset.</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"> <span class="n" style="color: #333;">TranscriptAlignmentSet</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"></span>
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="c"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace BAM</span></span>
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865
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="c"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace PacBio</span></span>
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="c"></span>
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<li id="41cc8535cfb898a3bdd89449b8c1d14370328762">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#41cc8535cfb898a3bdd89449b8c1d14370328762"><strong>include/pbbam/PbiFilterTypes.h</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">@@ -35,7 +35,7 @@ public:</td>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">FilterBase</span><span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">FilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">FilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">CompareHelper</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lhs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</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">@@ -54,7 +54,7 @@ struct BarcodeDataFilterBase : public FilterBase<T></td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">BarcodeDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">BarcodeDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">BarcodeDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">Accepts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PbiRawData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</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">@@ -69,7 +69,7 @@ struct BasicDataFilterBase : public FilterBase<T></td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">BasicDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">BasicDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">BasicDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">Accepts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PbiRawData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</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">@@ -84,7 +84,7 @@ struct MappedDataFilterBase : public FilterBase<T></td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">MappedDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">MappedDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">MappedDataFilterBase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">Accepts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PbiRawData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</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">@@ -201,7 +201,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist barcode IDs to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">PbiBarcodeFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">PbiBarcodeFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Performs the actual index lookup.</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">@@ -240,7 +240,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist barcode IDs to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">PbiBarcodeForwardFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">PbiBarcodeForwardFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// \brief The PbiBarcodeQualityFilter class provides a PbiFilter-compatible</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">@@ -288,7 +289,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist barcode IDs to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"> <span class="n" style="color: #333;">PbiBarcodeReverseFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c"> <span class="n" style="color: #333;">PbiBarcodeReverseFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// \brief The PbiBarcodesFilter class provides a PbiFilter-compatible filter on</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">@@ -411,7 +413,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \note There is no compare type parameter here, it is always</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Compare::EQUAL. Records will match movie name, exactly.</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">movieName</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="c"> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">movieName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Creates a 'whitelisted' movie name filter.</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</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">@@ -421,7 +423,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist movie names to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Performs the actual index lookup.</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">@@ -432,6 +435,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="c"> <span class="n" style="color: #333;">PbiFilter</span> <span class="n" style="color: #333;">compositeFilter_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// \brief The PbiNumDeletedBasesFilter class provides a PbiFilter-compatible</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">@@ -573,7 +577,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \note There is no compare type parameter here, it is always</span></span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Compare::EQUAL. Records will match query name, exactly.</span></span>
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="c"> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">qname</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="c"> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">qname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Creates a 'whitelisted' query name filter.</span></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</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">@@ -583,7 +587,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist query names to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="c"> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="c"> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c"> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">);</span></span>
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589
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">();</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">@@ -686,7 +691,7 @@ public:</td>
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691
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist read group IDs to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="c"> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="c"> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Creates a 'whitelisted' filter on read group printable IDs.</span></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</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">@@ -696,7 +701,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist read group ID strings to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="c"> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Creates a 'whitelisted' filter using read group objects.</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</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">@@ -706,7 +712,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist read group objects to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="c"> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ReadGroupInfo</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="c"> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ReadGroupInfo</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// \brief The PbiReferenceEndFilter class provides a PbiFilter-compatible</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">@@ -754,7 +761,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist reference IDs to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="c"> <span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">EQUAL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// \brief The PbiReferenceNameFilter class provides a PbiFilter-compatible</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">@@ -782,7 +789,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist reference names to compare on</span></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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785
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="c"> <span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="c"> <span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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786
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="c"></span>
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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788
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Performs the actual index lookup.</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">@@ -848,7 +856,39 @@ public:</td>
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \param[in] whitelist ZMW hole numbers to compare on</span></span>
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="c"> <span class="n" style="color: #333;">PbiZmwFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="c"> <span class="n" style="color: #333;">PbiZmwFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// ----------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// NOTE: modulo filtering only enabled for ZMW.</span></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// I need to generalize more if we're going to use</span></span>
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// this on more fields.</span></span>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// ----------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="c"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">FilterHash</span></span>
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"> <span class="n" style="color: #333;">UNSIGNED_LONG_CAST</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">BOOST_HASH_COMBINE</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">PbiZmwModuloFilter</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="c"> <span class="n" style="color: #333;">PbiZmwModuloFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">denominator</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FilterHash</span> <span class="n" style="color: #333;">hashtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FilterHash</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UNSIGNED_LONG_CAST</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// \brief Performs the actual index lookup.</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Most client code should not need to use this method directly.</span></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">Accepts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PbiRawData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">denominator_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="c"> <span class="n" style="color: #333;">FilterHash</span> <span class="n" style="color: #333;">hash_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="c"> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="c"><span class="p">};</span></span>
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893
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="c"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace BAM</span></span>
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<li id="95c79ed3d1b53d2962eb30ba93a760fe8ede024a">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#95c79ed3d1b53d2962eb30ba93a760fe8ede024a"><strong>include/pbbam/internal/PbiFilterTypes.inl</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">@@ -8,6 +8,8 @@</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">#include <cassert></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">#include <stdexcept></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">#include <boost/functional/hash/hash.hpp></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">namespace PacBio {</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">namespace BAM {</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></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">@@ -20,8 +22,9 @@ inline FilterBase<T>::FilterBase(T value, const Compare::Type cmp)</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">template <typename T></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">inline FilterBase<T>::FilterBase(std::vector<T> values)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">inline FilterBase<T>::FilterBase(std::vector<T> values<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> : multiValue_{std::move(values)}</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> , cmp_{cmp}</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">template<typename T></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">@@ -36,31 +39,38 @@ inline bool FilterBase<T>::CompareHelper(const T& lhs) const</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">template<typename T></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">inline bool FilterBase<T>::CompareMultiHelper(const T& lhs) const</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> // check provided value against all filter criteria,</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> // return true on any exact match</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> auto iter = multiValue_.get().cbegin();</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> const auto end = multiValue_.get().cend();</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> for (; iter != end; ++iter) {</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> if (*iter == lhs)</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> return true;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> if (cmp_ == Compare::EQUAL)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> // check provided value against all filter criteria,</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> // return true on any exact match</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> auto iter = multiValue_.get().cbegin();</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> const auto end = multiValue_.get().cend();</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> for (; iter != end; ++iter) {</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> if (*iter == lhs)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> return true;</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> return false; // no matches</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> else if (cmp_ == Compare::NOT_EQUAL)</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> // check provided value against all filter criteria,</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> // return true on any exact match</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> auto iter = multiValue_.get().cbegin();</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> const auto end = multiValue_.get().cend();</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> for (; iter != end; ++iter) {</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> if (*iter == lhs)</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> return false;</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> }</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> return true;</span>
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46
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> return false; // no matches</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> else</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> throw std::runtime_error{"unsupported compare type on multivalue filter"};</span>
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48
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">}</span>
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49
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"></span>
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50
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">template<typename T></span>
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51
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">inline bool FilterBase<T>::CompareSingleHelper(const T& lhs) const</span>
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52
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">{</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> switch(cmp_) {</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> case Compare::EQUAL: return lhs == value_;</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> case Compare::LESS_THAN: return lhs < value_;</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> case Compare::LESS_THAN_EQUAL: return lhs <= value_;</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> case Compare::GREATER_THAN: return lhs > value_;</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> case Compare::GREATER_THAN_EQUAL: return lhs >= value_;</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> case Compare::NOT_EQUAL: return lhs != value_;</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> default:</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> assert(false);</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> throw std::runtime_error{"unsupported compare type requested"};</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> }</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> return Compare::Check(lhs, value_, cmp_);</span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">}</span>
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65
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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66
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">template<></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" 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="100" 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">@@ -90,8 +100,8 @@ inline BarcodeDataFilterBase<T, field>::BarcodeDataFilterBase(T value, const Com</td>
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90
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">{ }</span>
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91
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"></span>
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92
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">template<typename T, PbiFile::BarcodeField field></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">inline BarcodeDataFilterBase<T, field>::BarcodeDataFilterBase(std::vector<T> values)</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> : FilterBase<T>{std::move(values)}</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">inline BarcodeDataFilterBase<T, field>::BarcodeDataFilterBase(std::vector<T> values<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> : FilterBase<T>{std::move(values)<span class="idiff left right">, cmp</span>}</span>
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95
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">{ }</span>
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96
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"></span>
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97
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">template<typename T, PbiFile::BarcodeField field></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" 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="127" 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">@@ -117,8 +127,8 @@ inline BasicDataFilterBase<T, field>::BasicDataFilterBase(T value, const Compare</td>
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117
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext">{ }</span>
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118
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="119" 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">
119
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext">template<typename T, PbiFile::BasicField field></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">inline BasicDataFilterBase<T, field>::BasicDataFilterBase(std::vector<T> values)</span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"> : FilterBase<T>{std::move(values)}</span>
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<td class="diff-line-num new old_line" data-linenumber="122" 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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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">inline BasicDataFilterBase<T, field>::BasicDataFilterBase(std::vector<T> values<span class="idiff left right">, const Compare::Type cmp</span>)</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> : FilterBase<T>{std::move(values)<span class="idiff left right">, cmp</span>}</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext">{ }</span>
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123
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"></span>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">template<typename T, PbiFile::BasicField field></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="169" 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">@@ -159,8 +169,8 @@ inline MappedDataFilterBase<T, field>::MappedDataFilterBase(T value, const Compa</td>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">template<typename T, PbiFile::MappedField field></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">inline MappedDataFilterBase<T, field>::MappedDataFilterBase(std::vector<T> values)</span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> : FilterBase<T>{std::move(values)}</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">inline MappedDataFilterBase<T, field>::MappedDataFilterBase(std::vector<T> values<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> : FilterBase<T>{std::move(values)<span class="idiff left right">, cmp</span>}</span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext">template<></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" 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="243" 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">@@ -233,9 +243,9 @@ inline PbiBarcodeFilter::PbiBarcodeFilter(const int16_t barcode, const Compare::</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext">inline PbiBarcodeFilter::PbiBarcodeFilter(std::vector<int16_t> whitelist)</span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext"> : compositeFilter_{ PbiFilter::Union({ PbiBarcodeForwardFilter{std::move(whitelist)},</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext"> PbiBarcodeReverseFilter{std::move(whitelist)}</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">inline PbiBarcodeFilter::PbiBarcodeFilter(std::vector<int16_t> whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> : compositeFilter_{ PbiFilter::Union({ PbiBarcodeForwardFilter{std::move(whitelist)<span class="idiff left right">, cmp</span>},</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> PbiBarcodeReverseFilter{std::move(whitelist)<span class="idiff left right">, cmp</span>}</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"> })</span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"> }</span>
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241
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<td class="diff-line-num new_line" data-linenumber="251" 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">
251
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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="LC251" class="line" lang="plaintext">{ }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" 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="259" 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">@@ -249,8 +259,8 @@ inline PbiBarcodeForwardFilter::PbiBarcodeForwardFilter(const int16_t bcFwdId, c</td>
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<td class="diff-line-num new_line" data-linenumber="259" 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="LC259" class="line" lang="plaintext"> : internal::BarcodeDataFilterBase<int16_t, PbiFile::BarcodeField::BC_FORWARD>{bcFwdId, cmp}</span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext">{ }</span>
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<td class="diff-line-num new_line" data-linenumber="261" 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="LC261" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="262" 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="LC252" class="line" lang="plaintext">inline PbiBarcodeForwardFilter::PbiBarcodeForwardFilter(std::vector<int16_t> whitelist)</span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="plaintext"> : internal::BarcodeDataFilterBase<int16_t, PbiFile::BarcodeField::BC_FORWARD>{std::move(whitelist)}</span>
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<td class="diff-line-num new old_line" data-linenumber="254" 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="plaintext">inline PbiBarcodeForwardFilter::PbiBarcodeForwardFilter(std::vector<int16_t> whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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<td class="diff-line-num new old_line" data-linenumber="254" 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="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">
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> : internal::BarcodeDataFilterBase<int16_t, PbiFile::BarcodeField::BC_FORWARD>{std::move(whitelist)<span class="idiff left right">, cmp</span>}</span>
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<td class="diff-line-num old_line" data-linenumber="254" 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="LC264" class="line" lang="plaintext">{ }</span>
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<td class="diff-line-num new_line" data-linenumber="265" 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="LC265" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="266" 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="LC266" class="line" lang="plaintext">// PbiBarcodeQualityFilter</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" 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="275" 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">@@ -265,8 +275,8 @@ inline PbiBarcodeReverseFilter::PbiBarcodeReverseFilter(const int16_t bcRevId, c</td>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"> : internal::BarcodeDataFilterBase<int16_t, PbiFile::BarcodeField::BC_REVERSE>{bcRevId, cmp}</span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="268" 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="278" 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="LC268" class="line" lang="plaintext">inline PbiBarcodeReverseFilter::PbiBarcodeReverseFilter(std::vector<int16_t> whitelist)</span>
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<td class="diff-line-num old old_line" data-linenumber="269" 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="LC269" class="line" lang="plaintext"> : internal::BarcodeDataFilterBase<int16_t, PbiFile::BarcodeField::BC_REVERSE>{std::move(whitelist)}</span>
</pre>
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<td class="diff-line-num new old_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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<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="plaintext">inline PbiBarcodeReverseFilter::PbiBarcodeReverseFilter(std::vector<int16_t> whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
</pre>
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<td class="diff-line-num new old_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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<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="plaintext"> : internal::BarcodeDataFilterBase<int16_t, PbiFile::BarcodeField::BC_REVERSE>{std::move(whitelist)<span class="idiff left right">, cmp</span>}</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="270" 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="LC280" class="line" lang="plaintext">{ }</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="281" 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="LC281" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="272" 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="282" 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="LC282" class="line" lang="plaintext">// PbiBarcodesFilter</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="308" 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="318" 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">@@ -308,7 +318,12 @@ inline PbiMapQualityFilter::PbiMapQualityFilter(const uint8_t mapQual, const Com</td>
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<td class="diff-line-num old_line" data-linenumber="308" 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="LC318" class="line" lang="plaintext">// PbiMovieNameFilter</span>
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309
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="plaintext"></span>
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310
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="plaintext">inline bool PbiMovieNameFilter::Accepts(const PbiRawData& idx, const size_t row) const</span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="plaintext">{ return compositeFilter_.Accepts(idx, row); }</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">{</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> const bool found = compositeFilter_.Accepts(idx, row);</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"> if (cmp_ == Compare::EQUAL) return found;</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> else if (cmp_ == Compare::NOT_EQUAL) return !found;</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> else throw std::runtime_error{"unsupported compare type on movie name filter"};</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">}</span>
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312
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="plaintext"></span>
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313
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext">// PbiNumDeletedBasesFilter</span>
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314
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" 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="387" 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">@@ -372,20 +387,20 @@ inline PbiReadGroupFilter::PbiReadGroupFilter(const ReadGroupInfo& rg, const Com</td>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="plaintext"> : PbiReadGroupFilter{rg.Id(), cmp}</span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="plaintext"></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="plaintext">inline PbiReadGroupFilter::PbiReadGroupFilter(std::vector<int32_t> whitelist)</span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::RG_ID>{std::move(whitelist)}</span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">inline PbiReadGroupFilter::PbiReadGroupFilter(std::vector<int32_t> whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::RG_ID>{std::move(whitelist)<span class="idiff left right">, cmp</span>}</span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="plaintext"></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="plaintext">inline PbiReadGroupFilter::PbiReadGroupFilter(const std::vector<std::string>& whitelist)</span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::RG_ID>{std::vector<int32_t>{}}</span>
</pre>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">inline PbiReadGroupFilter::PbiReadGroupFilter(const std::vector<std::string>& whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::RG_ID>{std::vector<int32_t>{}<span class="idiff left right">, cmp</span>}</span>
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381
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="plaintext">{</span>
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382
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"> multiValue_->reserve(whitelist.size());</span>
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383
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext"> for (const auto& rg : whitelist)</span>
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384
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext"> multiValue_->push_back(ReadGroupInfo::IdToInt(rg));</span>
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385
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="plaintext">}</span>
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386
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="plaintext"></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="plaintext">inline PbiReadGroupFilter::PbiReadGroupFilter(const std::vector<ReadGroupInfo>& whitelist)</span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::RG_ID>{std::vector<int32_t>{}}</span>
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<td class="diff-line-num new old_line" data-linenumber="389" 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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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">inline PbiReadGroupFilter::PbiReadGroupFilter(const std::vector<ReadGroupInfo>& whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::RG_ID>{std::vector<int32_t>{}<span class="idiff left right">, cmp</span>}</span>
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389
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext">{</span>
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390
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"> multiValue_->reserve(whitelist.size());</span>
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391
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<td class="diff-line-num new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext"> for (const auto& rg : whitelist)</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="404" 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="419" 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">@@ -404,8 +419,8 @@ inline PbiReferenceIdFilter::PbiReferenceIdFilter(const int32_t tId, const Compa</td>
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404
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="plaintext"> : internal::MappedDataFilterBase<int32_t, PbiFile::MappedField::T_ID>{tId, cmp}</span>
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405
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext">{ }</span>
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406
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext"></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="plaintext">inline PbiReferenceIdFilter::PbiReferenceIdFilter(std::vector<int32_t> whitelist)</span>
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<td class="diff-line-num old old_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="plaintext"> : internal::MappedDataFilterBase<int32_t, PbiFile::MappedField::T_ID>{std::move(whitelist)}</span>
</pre>
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<td class="diff-line-num new old_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">
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">inline PbiReferenceIdFilter::PbiReferenceIdFilter(std::vector<int32_t> whitelist<span class="idiff left right">, const Compare::Type cmp</span>)</span>
</pre>
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<td class="diff-line-num new old_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">
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext"> : internal::MappedDataFilterBase<int32_t, PbiFile::MappedField::T_ID>{std::move(whitelist)<span class="idiff left right">, cmp</span>}</span>
</pre>
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409
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext">{ }</span>
</pre>
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410
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="plaintext"></span>
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411
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="plaintext">// PbiReferenceStartFilter</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">@@ -420,9 +435,70 @@ inline PbiZmwFilter::PbiZmwFilter(const int32_t zmw, const Compare::Type cmp)</td>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::ZMW>{zmw, cmp}</span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="plaintext">inline PbiZmwFilter::PbiZmwFilter(std::vector<int32_t> whitelist)</span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::ZMW>{std::move(whitelist)}</span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">inline PbiZmwFilter::PbiZmwFilter(std::vector<int32_t> whitelist, const Compare::Type cmp)</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext"> : internal::BasicDataFilterBase<int32_t, PbiFile::BasicField::ZMW>{std::move(whitelist), cmp}</span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext">// PbiZmwModuloFilter</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext">inline PbiZmwModuloFilter::PbiZmwModuloFilter(</span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext"> const uint32_t denominator,</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> const uint32_t value,</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext"> const FilterHash hashType,</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext"> const Compare::Type cmp)</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext"> : denominator_{denominator}</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext"> , value_{value}</span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext"> , hash_{hashType}</span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext"> , cmp_{cmp}</span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="plaintext">{ }</span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">inline uint32_t UnsignedLongIntCast(const int32_t zm)</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"> return static_cast<uint32_t>(zm);</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">}</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext">inline uint32_t BoostHashCombine(const int32_t zm)</span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> constexpr static const uint16_t mask = 0xFFFF;</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext"> const uint16_t upper = (zm >> 16) & mask;</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext"> const uint16_t lower = zm & mask;</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext"> // FIXME: discrepancies with Python API. Will return to nail down.</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext"> size_t seed = 0;</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext"> boost::hash_combine(seed, upper);</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext"> boost::hash_combine(seed, lower);</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext"> return static_cast<uint32_t>(seed);</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">}</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext">inline bool PbiZmwModuloFilter::Accepts(const PbiRawData& idx,</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext"> const size_t row) const</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> const auto zm = idx.BasicData().holeNumber_.at(row);</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"> uint32_t hashValue;</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> switch(hash_)</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> {</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"> case FilterHash::UNSIGNED_LONG_CAST :</span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext"> {</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext"> hashValue = UnsignedLongIntCast(zm);</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"> break;</span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext"> }</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext"> case FilterHash::BOOST_HASH_COMBINE :</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext"> hashValue = BoostHashCombine(zm);</span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext"> break;</span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"> default:</span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> throw std::runtime_error{"unsupported filter hash type"};</span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext"> }</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> const auto modResult = hashValue % denominator_;</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> return Compare::Check(modResult, value_, cmp_);</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext">}</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"></span>
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427
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="plaintext">} // namespace BAM</span>
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428
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="plaintext">} // namespace PacBio</span></pre>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</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">project(</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> 'PacBioBAM',</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> 'cpp',</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> version : '0.1<span class="idiff left right">8</span>.0',</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> version : '0.1<span class="idiff left right">9</span>.0',</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> default_options : [</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> 'buildtype=release',</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> 'warning_level=3',</span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#dc4d5d1220b0cd2b76cb436a076ddf99d8de0fdb"><strong>scripts/ci/test.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,4 +5,26 @@ set -vex</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># TEST #</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">########</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">type </span>module <span class="o" style="font-weight: 600;">></span>& /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Note: htslib v1.7 added native long CIGAR support. pbbam "spoofs" it </span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># when running <1.7. So we'll always check the default htslib for </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># general test success/fail, and then check pre-/post-v1.7 explicitly</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># to ensure we pass in either context (detectable at runtime).</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># default htslib</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">ninja <span class="nt" style="color: navy;">-C</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CURRENT_BUILD_DIR</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: teal;">build</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-v</span> <span class="nb" style="color: #0086b3;">test</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># explicit htslib v1.6</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">module unload htslib</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">module load htslib/1.6</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell">ninja <span class="nt" style="color: navy;">-C</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CURRENT_BUILD_DIR</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: teal;">build</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-v</span> <span class="nb" style="color: #0086b3;">test</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># explicit htslib v1.7</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">module unload htslib</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">module load htslib/1.7</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">ninja <span class="nt" style="color: navy;">-C</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CURRENT_BUILD_DIR</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: teal;">build</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-v</span> <span class="nb" style="color: #0086b3;">test</span><span class="se" style="color: #d14;">\</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># restore default</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">module unload htslib</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">module load htslib</span></pre>
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<li id="e0820644d18c5c08f877e2fdd356cbae7bc79dfc">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#e0820644d18c5c08f877e2fdd356cbae7bc79dfc"><strong>src/BamRecordImpl.cpp</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">@@ -12,19 +12,46 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdlib></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstring></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <tuple></span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <utility></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/hts_endian.h></span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "pbbam/BamTagCodec.h"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BamRecordTags.h"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "MemoryUtils.h"</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "<span class="idiff left right">pbbam/BamTagCodec</span>.h"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "<span class="idiff left right">StringUtils</span>.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">PacBio</span> <span class="p">{</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">BAM</span> <span class="p">{</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="p">{</span></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">DoesHtslibSupportLongCigar</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">htsVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_version</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// remove any "-<blah>" for non-release versions</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">versionBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">htsVersion</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">versionBase</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"invalid htslib version format: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">htsVersion</span><span class="p">};</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// grab major/minor version numbers</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">versionParts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">versionBase</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">);</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">versionParts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"invalid htslib version format: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">htsVersion</span><span class="p">};</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check against v1.7</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">versionMajor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">versionParts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">versionMinor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">versionParts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v17_major</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v17_minor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tie</span><span class="p">(</span><span class="n" style="color: #333;">versionMajor</span><span class="p">,</span> <span class="n" style="color: #333;">versionMinor</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tie</span><span class="p">(</span><span class="n" style="color: #333;">v17_major</span><span class="p">,</span> <span class="n" style="color: #333;">v17_minor</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_native_long_cigar_support</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DoesHtslibSupportLongCigar</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="n" style="color: #333;">Cigar</span> <span class="nf" style="color: #900; font-weight: 600;">FetchRawCigar</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"><span class="p">{</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">Cigar</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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>
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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">@@ -148,27 +175,21 @@ bool BamRecordImpl::AddTagImpl(const std::string& tagName, const Tag& value,</td>
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148
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"><span class="n" style="color: #333;">Cigar</span> <span class="n" style="color: #333;">BamRecordImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CigarData</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d_</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">();</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">HasLongCigar</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">))</span> <span class="p">{</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">has_native_long_cigar_support</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">HasLongCigar</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fetch long CIGAR from tag</span></span>
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<td class="diff-line-num old_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cigarTag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TagValue</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">);</span></span>
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154
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cigarTagValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigarTag</span><span class="p">.</span><span class="n" style="color: #333;">ToUInt32Array</span><span class="p">();</span></span>
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155
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FetchRawCigar</span><span class="p">(</span><span class="n" style="color: #333;">cigarTagValue</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">cigarTagValue</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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156
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fetch <span class="idiff left right">normal, short </span>CIGAR from the standard location</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fetch CIGAR from the standard location</span></span>
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158
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FetchRawCigar</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_cigar</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">),</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span><span class="p">);</span></span>
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159
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="p">}</span></span>
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160
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"><span class="p">}</span></span>
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161
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"></span>
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162
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"><span class="n" style="color: #333;">BamRecordImpl</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BamRecordImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CigarData</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Cigar</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cigar</span><span class="p">)</span></span>
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163
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"><span class="p">{</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set normal, "short" CIGAR and remove CG tag if present.</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">65536</span><span class="p">)</span> <span class="p">{</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">SetCigarData</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">))</span> <span class="n" style="color: #333;">RemoveTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">);</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set long CIGAR data</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if long CIGAR, using htslib version < 1.7, set it "manually"</span></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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">has_native_long_cigar_support</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">65536</span><span class="p">)</span> <span class="p">{</span></span>
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172
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add the 'fake' CIGAR in normal place.</span></span>
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173
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">Cigar</span> <span class="n" style="color: #333;">fake</span><span class="p">;</span></span>
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174
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">fake</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">CigarOperationType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SOFT_CLIP</span><span class="p">,</span> <span class="n" style="color: #333;">SequenceLength</span><span class="p">());</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">@@ -190,6 +211,12 @@ BamRecordImpl& BamRecordImpl::CigarData(const Cigar& cigar)</td>
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190
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">AddTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">,</span> <span class="n" style="color: #333;">Tag</span><span class="p">{</span><span class="n" style="color: #333;">cigarData</span><span class="p">});</span></span>
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191
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="p">}</span></span>
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192
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// otherwise (v1.7+ or short CIGAR), use standard APIs</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">))</span> <span class="n" style="color: #333;">RemoveTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">SetCigarData</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"></span>
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193
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"><span class="p">}</span></span>
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195
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"></span>
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<li id="95114a6fbde6b3ead1127d4494372d6a91f30cea">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#95114a6fbde6b3ead1127d4494372d6a91f30cea"><strong>src/BamWriter.cpp</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">@@ -25,12 +25,13 @@ namespace PacBio {</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">BAM</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">internal</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BamWriterPrivate</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">public</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">internal</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">FileProducer</span></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BamWriterPrivate</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriterPrivate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rawHeader</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompressionLevel</span> <span class="n" style="color: #333;">compressionLevel</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numThreads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useTempFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamRecord</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">record</span><span class="p">);</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">@@ -41,21 +42,23 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">calculateBins_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">samFile</span><span class="p">,</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HtslibFileDeleter</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">file_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">header_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileProducer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fileProducer_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="n" style="color: #333;">BamWriterPrivate</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamWriterPrivate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rawHeader</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompressionLevel</span> <span class="n" style="color: #333;">compressionLevel</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numThreads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileProducer</span><span class="p">{</span><span class="n" style="color: #333;">filename</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="p">,</span> <span class="n" style="color: #333;">calculateBins_</span><span class="p">{</span><span class="n" style="color: #333;">binCalculationMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculation_ON</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="p">,</span> <span class="n" style="color: #333;">header_</span><span class="p">{</span><span class="n" style="color: #333;">rawHeader</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useTempFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">calculateBins_</span><span class="p">{</span><span class="n" style="color: #333;">binCalculationMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BinCalculation_ON</span><span class="p">},</span> <span class="n" style="color: #333;">header_</span><span class="p">{</span><span class="n" style="color: #333;">rawHeader</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">header_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"null header"</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">useTempFile</span><span class="p">)</span> <span class="n" style="color: #333;">fileProducer_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileProducer</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// open file</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">usingFilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">TempFilename</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">usingFilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fileProducer_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fileProducer_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">TempFilename</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"wb"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">compressionLevel</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">(</span><span class="n" style="color: #333;">sam_open</span><span class="p">(</span><span class="n" style="color: #333;">usingFilename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">mode</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()));</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">file_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"could not open file for writing"</span><span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" 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>
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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">@@ -123,7 +126,7 @@ inline void BamWriterPrivate::Write(const BamRecordImpl& recordImpl)</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamWriter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompressionLevel</span> <span class="n" style="color: #333;">compressionLevel</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numThreads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BinCalculationMode</span> <span class="n" style="color: #333;">binCalculationMode</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">useTempFile</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">IRecordWriter</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if PBBAM_AUTOVALIDATE</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">@@ -131,7 +134,18 @@ BamWriter::BamWriter(const std::string& filename, const BamHeader& header,</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">d_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamWriterPrivate</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamHeaderMemory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MakeRawHeader</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">),</span> <span class="n" style="color: #333;">compressionLevel</span><span class="p">,</span> <span class="n" style="color: #333;">numThreads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">binCalculationMode</span><span class="p">,</span> <span class="n" style="color: #333;">useTempFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"><span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamWriter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Config</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">BamWriter</span><span class="p">{</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">compressionLevel</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">numThreads</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">binCalculationMode</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">useTempFile</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"><span class="p">{</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"><span class="p">}</span></span>
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136
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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137
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"><span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">BamWriter</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#584639dd9ffaa9227f61109731cb09c74ab4793f"><strong>src/ChemistryTable.cpp</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">@@ -16,6 +16,8 @@ namespace PacBio {</td>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">BAM</span> <span class="p">{</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">internal</span> <span class="p">{</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// clang-format off</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"></span>
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19
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChemistryTable</span> <span class="n" style="color: #333;">BuiltInChemistryTable</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></span>
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21
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// BindingKit, SequencingKit, BasecallerVersion, Chemistry</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" 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>
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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">@@ -72,23 +74,21 @@ extern const ChemistryTable BuiltInChemistryTable = {</td>
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72
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-365-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"100-861-800"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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73
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-365-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-093-700"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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74
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet"); S/P2-C2</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-365-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-309-500"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet (4 rxn)"); S/P2-C2</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-365-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-309-400"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel; Sequel® Binding Kit 2.1; S/P2-C2</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-365-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-309-500"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span> <span class="c1" style="color: #998; font-style: italic;">// Sequel® Sequencing Plate 2.1 Silwet (8 rxn)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-365-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-309-400"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span> <span class="c1" style="color: #998; font-style: italic;">// Sequel® Sequencing Plate 2.1 Silwet (4 rxn)</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet - prototype parts"); S/P2-C2</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-490-800"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-490-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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82
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<td class="diff-line-num new_line old" data-linenumber="81" 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="LC82" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet (4 rxn) - prototype parts"); S/P2-C2</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-490-800"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-491-000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet - prototype parts"); S/P2-C2</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-500-400"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-490-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet (4 rxn) - prototype parts"); S/P2-C2</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-500-400"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-491-000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="89" 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="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel; Sequel® Binding Kit 3.0; S/P3-C3</span></span>
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<td class="diff-line-num new old_line" data-linenumber="89" 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="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-500-400"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-427-500"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P3-C3/5.0"</span><span class="p">}},</span> <span class="c1" style="color: #998; font-style: italic;">// Sequel® Sequencing Plate 3.0 (8 rxn)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-500-400"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-427-800"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P3-C3/5.0"</span><span class="p">}},</span> <span class="c1" style="color: #998; font-style: italic;">// Sequel® Sequencing Plate 3.0 (4 rxn)</span></span>
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89
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.0.1 ChemRel; Sequel® Dev Binding Kit; S/P2-C2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-490-800"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-490-900"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span> <span class="c1" style="color: #998; font-style: italic;">// Sequel® Dev Sequencing Plate (4 rxn)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="p">{{</span><span class="s" style="color: #d14;">"101-490-800"</span><span class="p">,</span> <span class="s" style="color: #d14;">"101-491-000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S/P2-C2/5.0"</span><span class="p">}},</span> <span class="c1" style="color: #998; font-style: italic;">// Sequel® Dev Sequencing Plate (8 rxn)</span></span>
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90
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"><span class="p">};</span></span>
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91
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// clang-format on</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="n" style="color: #333;">ChemistryTable</span> <span class="nf" style="color: #900; font-weight: 600;">ChemistryTableFromXml</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mappingXml</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">FileUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Exists</span><span class="p">(</span><span class="n" style="color: #333;">mappingXml</span><span class="p">))</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#227f5ff5f6801400bd559505c89b9ed57fb95601"><strong>src/Compare.cpp</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">@@ -41,31 +41,33 @@ struct CompareTypeHash</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">opToTypeMap</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// basic operators plus some permissiveness for other representations</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"=="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"eq"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"!="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"ne"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"lt"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"lte"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"gt"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"gte"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"&"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CONTAINS</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"~"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_CONTAINS</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"=="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"eq"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"in"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"!="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"ne"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"not_in"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"lt"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"lte"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"<="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"gt"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"gte"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">">="</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN_EQUAL</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"&"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CONTAINS</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"~"</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_CONTAINS</span> <span class="p">}</span></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="p">};</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">,</span> <span class="n" style="color: #333;">CompareTypeHash</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">typeAliases</span> <span class="o" style="font-weight: 600;">=</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::EQUAL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"=="</span><span class="p">,</span> <span class="s" style="color: #d14;">"eq"</span> <span class="idiff left right"> </span><span class="p">}</span> <span class="p">},</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::NOT_EQUAL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"!="</span><span class="p">,</span> <span class="s" style="color: #d14;">"ne"</span> <span class="idiff left right"> </span><span class="p">}</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::EQUAL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"=="</span><span class="p">,</span> <span class="s" style="color: #d14;">"eq"</span> <span class="p">}</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::NOT_EQUAL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"!="</span><span class="p">,</span> <span class="s" style="color: #d14;">"ne"</span> <span class="p">}</span> <span class="p">},</span></span>
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69
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::LESS_THAN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lt"</span> <span class="p">}</span> <span class="p">},</span></span>
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70
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LESS_THAN_EQUAL</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::LESS_THAN_EQUAL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<="</span><span class="p">,</span> <span class="s" style="color: #d14;">"lte"</span> <span class="p">}</span> <span class="p">},</span></span>
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71
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GREATER_THAN</span><span class="p">,</span> <span class="n" style="color: #333;">TypeAlias</span><span class="p">{</span> <span class="s" style="color: #d14;">"Compare::GREATER_THAN"</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gt"</span> <span class="p">}</span> <span class="p">},</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#f27e938fef11af21d17ab971101826251a9db705"><strong>src/DataSet.cpp</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">@@ -93,6 +93,9 @@ DataSet::DataSet(const DataSet::TypeEnum type)</td>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">DataSet</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">TRANSCRIPT</span><span class="o" style="font-weight: 600;">:</span></span>
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94
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">d_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TranscriptSet</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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95
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">DataSet</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">TRANSCRIPT_ALIGNMENT</span><span class="o" style="font-weight: 600;">:</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">d_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TranscriptAlignmentSet</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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96
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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97
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported dataset type"</span><span class="p">};</span></span>
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98
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="229" 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="232" 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">@@ -229,6 +232,7 @@ DataSet::TypeEnum DataSet::NameToType(const std::string& typeName)</td>
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229
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">lookup</span><span class="p">[</span><span class="s" style="color: #d14;">"ReferenceSet"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataSet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">REFERENCE</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">lookup</span><span class="p">[</span><span class="s" style="color: #d14;">"SubreadSet"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataSet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SUBREAD</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">lookup</span><span class="p">[</span><span class="s" style="color: #d14;">"TranscriptSet"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataSet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TRANSCRIPT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">lookup</span><span class="p">[</span><span class="s" style="color: #d14;">"TranscriptAlignmentSet"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataSet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TRANSCRIPT_ALIGNMENT</span><span class="p">;</span></span>
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232
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="p">}</span></span>
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233
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lookup</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">typeName</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// throws if unknown typename</span></span>
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234
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" 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="297" 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">@@ -293,6 +297,8 @@ std::string DataSet::TypeToName(const DataSet::TypeEnum& type)</td>
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293
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"SubreadSet"</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">DataSet</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">TRANSCRIPT</span><span class="o" style="font-weight: 600;">:</span></span>
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295
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"TranscriptSet"</span><span class="p">;</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">DataSet</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">TRANSCRIPT_ALIGNMENT</span><span class="o" style="font-weight: 600;">:</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"TranscriptAlignmentSet"</span><span class="p">;</span></span>
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296
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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297
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported dataset type"</span><span class="p">};</span></span>
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298
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="2924d26c2aef212f4282671a4301d3be92879c51">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#2924d26c2aef212f4282671a4301d3be92879c51"><strong>src/DataSetTypes.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="157" 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">@@ -157,6 +157,8 @@ std::shared_ptr<DataSetBase> DataSetBase::Create(const std::string& typeName)</td>
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157
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">typeName</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"HdfSubreadSet"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_shared</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">HdfSubreadSet</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">typeName</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"ReferenceSet"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_shared</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ReferenceSet</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">typeName</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"TranscriptSet"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_shared</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TranscriptSet</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">typeName</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"TranscriptAlignmentSet"</span><span class="p">))</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_shared</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TranscriptAlignmentSet</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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160
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// unknown typename</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported dataset type"</span><span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="437" 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="439" 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">@@ -437,5 +439,15 @@ TranscriptSet::TranscriptSet()</td>
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437
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"><span class="p">{</span></span>
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438
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440
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"><span class="p">}</span></span>
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439
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -------------------</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// TranscriptAlignmentSet</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -------------------</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"><span class="n" style="color: #333;">TranscriptAlignmentSet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TranscriptAlignmentSet</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">DataSetBase</span><span class="p">(</span><span class="s" style="color: #d14;">"PacBio.DataSet.TranscriptAlignmentSet"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TranscriptAlignmentSet"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">XsdType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DATASETS</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"></span>
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace BAM</span></span>
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441
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace PacBio</span></span></pre>
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<li id="cdfa3536dcbcfe0ae4777ccc214b8f9199083a9f">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#cdfa3536dcbcfe0ae4777ccc214b8f9199083a9f"><strong>src/DataSetXsd.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" 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="103" 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">@@ -103,6 +103,7 @@ static const auto elementRegistry = std::unordered_map<std::string, XsdType></td>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"SummaryStats"</span><span class="p">,</span> <span class="n" style="color: #333;">XsdType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DATASETS</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"TotalLength"</span><span class="p">,</span> <span class="n" style="color: #333;">XsdType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DATASETS</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"TranscriptSet"</span><span class="p">,</span> <span class="n" style="color: #333;">XsdType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DATASETS</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"TranscriptAlignmentSet"</span><span class="p">,</span><span class="n" style="color: #333;">XsdType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DATASETS</span> <span class="p">},</span></span>
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106
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 'pbmeta' elements</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<li id="58b7f0e1feb1ec8870c90e746592941feaae16e8">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#58b7f0e1feb1ec8870c90e746592941feaae16e8"><strong>src/FileProducer.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ namespace internal {</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">FileProducer</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="n" style="color: #333;">p<span class="idiff left right">rotected</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="n" style="color: #333;">p<span class="idiff left right">ublic</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> <span class="n" style="color: #333;">FileProducer</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Initializes FileProducer with specified target filename. Temp filename is</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">@@ -42,9 +42,8 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FileProducer</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"><span class="n" style="color: #333;">p<span class="idiff left right">rotected</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="n" style="color: #333;">p<span class="idiff left right">ublic</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">TargetFilename</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">targetFilename_</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">TempFilename</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tempFilename_</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<li id="1996717698d7751cc78126e3ce12f1de57b1e566">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#1996717698d7751cc78126e3ce12f1de57b1e566"><strong>src/PbiFilter.cpp</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">@@ -21,6 +21,7 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/algorithm/string/trim.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/numeric/conversion/cast.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "FileUtils.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "StringUtils.h"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "pbbam/PbiFilterTypes.h"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></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">@@ -202,8 +203,31 @@ static PbiFilter CreateLocalContextFilter(const std::string& value, const Compar</td>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiFilter</span><span class="p">{</span><span class="n" style="color: #333;">PbiLocalContextFilter</span><span class="p">{</span><span class="n" style="color: #333;">filterValue</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">}};</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">Create<span class="idiff left">QueryNamesFilterFromFile</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DataSet</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dataset</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">Create<span class="idiff left">MovieNameFilter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">compareType</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"empty value for movie property"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isBracketed</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isList</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on movie property"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">CreateQueryNamesFilterFromFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dataset</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on query name property"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// resolve file from dataset, value</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">resolvedFilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataset</span><span class="p">.</span><span class="n" style="color: #333;">ResolvePath</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" 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>
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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">@@ -211,12 +235,102 @@ static PbiFilter CreateQueryNamesFilterFromFile(const std::string& value, const</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">(</span><span class="n" style="color: #333;">resolvedFilename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">whitelist</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">whitelist</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">whitelist</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">compareType</span></span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">Create<span class="idiff left">ZmwFilter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">value</span></span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">Create<span class="idiff left">QueryNameFilter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DataSet</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dataset</span></span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"empty value for query name property"</span><span class="p">};</span></span>
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219
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// try possible filename first</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">resolvedFilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataset</span><span class="p">.</span><span class="n" style="color: #333;">ResolvePath</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Exists</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateQueryNamesFilterFromFile</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">dataset</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// otherwise "normal" qname (single, or list)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isBracketed</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isList</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on query name property"</span><span class="p">};</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"><span class="p">}</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">CreateReadGroupFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"><span class="p">{</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"empty value for read group property"</span><span class="p">};</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isBracketed</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isList</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on read group property"</span><span class="p">};</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">{</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"><span class="p">}</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">CreateReferenceIdFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"><span class="p">{</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"empty value for reference ID property"</span><span class="p">};</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isBracketed</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="p">}</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isList</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on reference name ID property"</span><span class="p">};</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ids</span><span class="p">;</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">ids</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tokens</span><span class="p">)</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">ids</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)));</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">{</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"><span class="p">}</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">CreateReferenceNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"><span class="p">{</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"empty value for reference name property"</span><span class="p">};</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isBracketed</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isList</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on reference name property"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">{</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">CreateZmwFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"empty value for ZMW filter property"</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isBracketed</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="235" 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="349" 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">@@ -235,10 +349,38 @@ static PbiFilter CreateZmwFilter(std::string value, const Compare::Type compareT</td>
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235
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiZmwFilter</span><span class="p">{</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">compareType</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">CreateZmwModuloFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Property</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">property</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">HasAttribute</span><span class="p">(</span><span class="s" style="color: #d14;">"Modulo"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">HasAttribute</span><span class="p">(</span><span class="s" style="color: #d14;">"Hash"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Name</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"zm"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"Modulo filter not supported on property: "</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="p">}</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">hashType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="s" style="color: #d14;">"Hash"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FilterHash</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hashType</span><span class="p">]()</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">algorithm</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_lower_copy</span><span class="p">(</span><span class="n" style="color: #333;">hashType</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"uint32cast"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FilterHash</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UNSIGNED_LONG_CAST</span><span class="p">;</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">algorithm</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_lower_copy</span><span class="p">(</span><span class="n" style="color: #333;">hashType</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"boosthashcombine"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FilterHash</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BOOST_HASH_COMBINE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsuppoerted hash type: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hashType</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="p">}();</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="s" style="color: #d14;">"Modulo"</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Value</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiZmwModuloFilter</span><span class="p">{</span> <span class="n" style="color: #333;">denom</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">hash</span><span class="p">,</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span> <span class="p">};</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"></span>
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238
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PbiFilter</span> <span class="nf" style="color: #900; font-weight: 600;">FromDataSetProperty</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Property</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">property</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dataset</span><span class="p">)</span></span>
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239
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"><span class="p">{</span></span>
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240
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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241
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Value</span><span class="p">();</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Name</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"zm"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">HasAttribute</span><span class="p">(</span><span class="s" style="color: #d14;">"Modulo"</span><span class="p">))</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateZmwModuloFilter</span><span class="p">(</span><span class="n" style="color: #333;">property</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">compareType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TypeFromOperator</span><span class="p">(</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Operator</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BuiltIn</span> <span class="n" style="color: #333;">builtInCode</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">builtInLookup</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">algorithm</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_lower_copy</span><span class="p">(</span><span class="n" style="color: #333;">property</span><span class="p">.</span><span class="n" style="color: #333;">Name</span><span class="p">()));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="252" 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="394" 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">@@ -252,16 +394,11 @@ static PbiFilter FromDataSetProperty(const Property& property, const DataSet& da</td>
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252
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">AlignedStartFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiAlignedStartFilter</span><span class="p">{</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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253
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<td class="diff-line-num new_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">BarcodeQualityFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiBarcodeQualityFilter</span><span class="p">{</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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254
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">IdentityFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiIdentityFilter</span><span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stof</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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255
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<td class="diff-line-num new_line old" data-linenumber="397" 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="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">MovieNameFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">{</span> <span class="n" style="color: #333;">value</span> <span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="256" 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">
256
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<td class="diff-line-num new_line" data-linenumber="397" 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">
397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryEndFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryEndFilter</span><span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="257" 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">
257
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<td class="diff-line-num new_line" data-linenumber="398" 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">
398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryLengthFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryLengthFilter</span><span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="258" 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">
258
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<td class="diff-line-num new_line old" data-linenumber="399" 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="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryNameFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">{</span> <span class="n" style="color: #333;">value</span> <span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryStartFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiQueryStartFilter</span><span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="260" 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">
260
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<td class="diff-line-num new_line" data-linenumber="400" 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">
400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReadAccuracyFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReadAccuracyFilter</span><span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stof</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReadGroupFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReadGroupFilter</span><span class="p">{</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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262
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<td class="diff-line-num new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReferenceEndFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceEndFilter</span><span class="p">{</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReferenceIdFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="264" 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">
264
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<td class="diff-line-num new_line old" data-linenumber="402" 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="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReferenceNameFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">{</span> <span class="n" style="color: #333;">value</span> <span class="p">};</span></span>
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265
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReferenceStartFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PbiReferenceStartFilter</span><span class="p">{</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">compareType</span> <span class="p">};</span></span>
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266
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"></span>
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267
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (maybe) list-value filters</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" 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="406" 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">@@ -269,10 +406,15 @@ static PbiFilter FromDataSetProperty(const Property& property, const DataSet& da</td>
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269
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">BarcodeForwardFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateBarcodeForwardFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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270
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">BarcodeReverseFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateBarcodeReverseFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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271
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<td class="diff-line-num new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">LocalContextFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateLocalContextFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></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="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">MovieNameFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateMovieNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></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="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryNameFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateQueryNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">dataset</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</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="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReadGroupFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateReadGroupFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReferenceIdFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateReferenceIdFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ReferenceNameFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateReferenceNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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272
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ZmwFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateZmwFilter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">compareType</span><span class="p">);</span></span>
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273
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"></span>
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274
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// other built-ins</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryNamesFromFileFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateQueryNamesFilterFromFile</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">dataset</span><span class="p"><span class="idiff left">);</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// compareType ignored</span></span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BuiltIn</span><span class="p">:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">QueryNamesFromFileFilter</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CreateQueryNamesFilterFromFile</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">dataset</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">compareType</span></span><span class="p"><span class="idiff right">);</span></span></span>
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276
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"></span>
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277
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span> <span class="o" style="font-weight: 600;">:</span></span>
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278
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">""</span><span class="p">};</span></span>
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<li id="810ee2d4abdfb7b58a0e4890dcb9e1afc202c5c3">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#810ee2d4abdfb7b58a0e4890dcb9e1afc202c5c3"><strong>src/PbiFilterTypes.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" 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">@@ -127,13 +127,15 @@ bool PbiIdentityFilter::Accepts(const PbiRawData& idx, const size_t row) const</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"></span>
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128
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// PbiMovieNameFilter</span></span>
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129
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">movieName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">movieName</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cmp</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">compositeFilter_</span><span class="p">{</span><span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filterFromMovieName</span><span class="p">(</span><span class="n" style="color: #333;">movieName</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)}</span> <span class="c1" style="color: #998; font-style: italic;">// include CCS</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="p">,</span> <span class="n" style="color: #333;">cmp_</span><span class="p">{</span><span class="n" style="color: #333;">cmp</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">compositeFilter_</span><span class="p">{</span><span class="n" style="color: #333;">PbiFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UNION</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiMovieNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">compositeFilter_</span><span class="p">{</span><span class="n" style="color: #333;">PbiFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UNION</span><span class="p">},</span> <span class="n" style="color: #333;">cmp_</span><span class="p">{</span><span class="n" style="color: #333;">cmp</span><span class="p">}</span></span>
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137
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"><span class="p">{</span></span>
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138
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">movieName</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">whitelist</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">compositeFilter_</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">internal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filterFromMovieName</span><span class="p">(</span><span class="n" style="color: #333;">movieName</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// include CCS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" 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>
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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">@@ -162,7 +164,9 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">RgIdLookup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">ZmwLookupPtr</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">cmp_</span><span class="p">{</span><span class="n" style="color: #333;">cmp</span><span class="p">}</span></span>
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166
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="p">{</span></span>
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167
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">queryName</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">whitelist</span><span class="p">)</span> <span class="p">{</span></span>
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168
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" 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="181" 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">@@ -177,7 +181,10 @@ public:</td>
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span></span>
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179
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="p">{</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="n" style="color: #333;">lookup_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lookup_</span><span class="p">;</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">lookup_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lookup_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">cmp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cmp_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Accepts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PbiRawData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" 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="208" 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">@@ -201,7 +208,14 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">qStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basicData</span><span class="p">.</span><span class="n" style="color: #333;">qStart_</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">qEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basicData</span><span class="p">.</span><span class="n" style="color: #333;">qEnd_</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">);</span></span>
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203
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">queryInterval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">qStart</span><span class="p">,</span> <span class="n" style="color: #333;">qEnd</span><span class="p">);</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">queryIntervals</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">queryInterval</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">queryIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryIntervals</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">queryInterval</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">queryIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmp_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">found</span><span class="p">;</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmp_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NOT_EQUAL</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found</span><span class="p">;</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"unsupported compare type on query name filter"</span><span class="p">};</span></span>
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205
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">CandidateRgIds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">movieName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">RecordType</span> <span class="n" style="color: #333;">type</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="295" 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="309" 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">@@ -295,16 +309,18 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"><span class="k" style="font-weight: 600;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">RgIdLookup</span> <span class="n" style="color: #333;">lookup_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">qname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">qname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Compare</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Type</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cmp</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">d_</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">{</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qname</span><span class="p">})}</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">{</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qname</span><span class="p">}<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cmp</span></span><span class="p">)}</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"><span class="p">}</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp"><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">)</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">d_</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">whitelist</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">d_</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_unique</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PbiQueryNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiQueryNameFilterPrivate</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">whitelist</span><span class="p">,</span> <span class="n" style="color: #333;">cmp</span><span class="p">)}</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="333" 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>
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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">@@ -333,8 +349,9 @@ PbiReferenceNameFilter::PbiReferenceNameFilter(std::string rname, Compare::Type</td>
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"><span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rnameWhitelist_</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">whitelist</span><span class="p">)},</span> <span class="n" style="color: #333;">cmp_</span><span class="p">{</span><span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EQUAL</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"><span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbiReferenceNameFilter</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">whitelist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Compare</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">cmp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rnameWhitelist_</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">whitelist</span><span class="p">)},</span> <span class="n" style="color: #333;">cmp_</span><span class="p">{</span><span class="n" style="color: #333;">cmp</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"></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">@@ -358,9 +375,10 @@ void PbiReferenceNameFilter::Initialize(const PbiRawData& idx) const</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// multi-value whitelist</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">s<span class="idiff left">ubFilter_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PbiFilter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">PbiFilter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">UNION</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ids</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rnameWhitelist_</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">subFilter_</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">{</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">ReferenceId</span><span class="p">(</span><span class="n" style="color: #333;">rname</span><span class="p">)});</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">ids</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">ReferenceId</span><span class="p">(</span><span class="n" style="color: #333;">rname</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">subFilter_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PbiReferenceIdFilter</span><span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">),</span> <span class="n" style="color: #333;">cmp_</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized_</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="LC384" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#21a63d74511a44ba1fb2c2d37a812b57a0eec10a"><strong>tests/data/long-cigar-1.7.bam</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">@@ -44,18 +44,27 @@ custom_target('pbbam_generate_data',</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> build_by_default : true,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> install : false)</span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">pbbamify_synthetic_dataset = configure_file(</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> input : files('data/pbbamify/synthetic_movie_all.subreadset.xml.in'),</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> output : 'synthetic_movie_all.subreadset.xml',</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> configuration : pbbam_PbbamTestData_h_config)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">#########</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"># tests #</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">#########</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">test(</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> 'pbbam unit tests',</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> 'pbbam formatting check',</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> pbbam_clang_formatter,</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> args : [</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> '--all'],</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> workdir : meson.source_root())</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">test(</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> 'pbbam gtest unittests',</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> pbbam_test,</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> args : [</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> '--gtest_output=xml:' + join_paths(meson.build_root(), 'pbbam-<span class="idiff left right">unit-</span>tests.xml')],</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> '--gtest_output=xml:' + join_paths(meson.build_root(), 'pbbam-<span class="idiff left right">gtest-unit</span>tests.xml')],</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> env : [</span>
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53
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> 'ARGS=-V',</span>
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54
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> 'VERBOSE=1'])</span></pre>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">test('pbbam formatting check', pbbam_clang_formatter, args : ['--all'], workdir : meson.source_root())</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">pbbamify_synthetic_dataset = configure_file(</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> input : files('data/pbbamify/synthetic_movie_all.subreadset.xml.in'),</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> output : 'synthetic_movie_all.subreadset.xml',</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> configuration : pbbam_PbbamTestData_h_config)</span></pre>
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<li id="30d31f3c7bebba69a52a2cbbbac433fe1aaa2514">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#30d31f3c7bebba69a52a2cbbbac433fe1aaa2514"><strong>tests/src/cram/pbbamify.t.in</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">@@ -8,7 +8,7 @@ Setup:</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Forward alignments with and without user specified tags, one alignment with undefined mapq, some alignments with basic CIGAR operations, 2 alignemtns with hard clipping, and several invalid alignments (1 without a seq field and 1 not present in the dataset) which should be skipped:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | <span class="idiff left right">samtools</span> view -h</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | <span class="idiff left right">$SAMTOOLS</span> view -h</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> [Warning] No records found for query 'synthetic_movie_1/10/0_100'. Skipping.</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> [Warning] Sequence 'synthetic_movie_1/1/0_100' (length 90) is not of the same length as the PacBio BAM sequence (length 100)! Skipping.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> [Warning] Found 1 alignments without a seq field which were not converted (most likely secondary alignments).</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">@@ -34,7 +34,7 @@ Forward alignments with and without user specified tags, one alignment with unde</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t8S1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I1=6S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc)</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Reverse alignments: 2 primary alignments and 7 secondary, 6 alignments with extended CIGAR and 2 with basic CIGAR strings, 1 alignment with undefined (255) mapq, 2 alignments with hard clipping, 1 alignment with user defined tag. All alignments have a read group assigned which is different than the dataset.</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | <span class="idiff left right">samtools</span> view -h</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | <span class="idiff left right">$SAMTOOLS</span> view -h</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> [INFO] Done processing 9 alignments in 0 min.</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" 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="55" 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">@@ -55,7 +55,7 @@ Reverse alignments: 2 primary alignments and 7 secondary, 6 alignments with exte</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">CCS read:</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="58" 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="LC58" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | <span class="idiff left right">samtools</span> view -h</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | <span class="idiff left right">$SAMTOOLS</span> view -h</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="59" 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="LC59" class="line" lang="plaintext"> [INFO] Done processing 1 alignments in 0 min.</span>
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<td class="diff-line-num old_line" data-linenumber="60" 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="LC60" class="line" lang="plaintext"> @HD\tVN:1.5\tSO:unknown\tpb:3.0.1 (esc)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="61" 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="LC61" class="line" lang="plaintext"> @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" 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="66" 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">@@ -66,7 +66,7 @@ CCS read:</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">No verbose output:</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | <span class="idiff left right">samtools</span> view -h</span>
</pre>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | <span class="idiff left right">$SAMTOOLS</span> view -h</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc)</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">@@ -89,7 +89,7 @@ No verbose output:</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">Test on a dataset, input contains alignments from all subread sets.</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa $GENERATEDDATADIR/synthetic_movie_all.subreadset.xml | <span class="idiff left right">samtools</span> view -h</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa $GENERATEDDATADIR/synthetic_movie_all.subreadset.xml | <span class="idiff left right">$SAMTOOLS</span> view -h</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> [Warning] No records found for query 'synthetic_movie_1/10/0_100'. Skipping.</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> [Warning] Sequence 'synthetic_movie_1/1/0_100' (length 90) is not of the same length as the PacBio BAM sequence (length 100)! Skipping.</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> [Warning] Found 1 alignments without a seq field which were not converted (most likely secondary alignments).</span>
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<li id="67c3d2c0ed79631940826d3634fa7f5a4e2a062e">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#67c3d2c0ed79631940826d3634fa7f5a4e2a062e"><strong>tests/src/test_BamWriter.cpp</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">@@ -15,7 +15,11 @@</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">PacBio</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">BamWriterTest</span><span class="p">,</span> <span class="n" style="color: #333;">SingleWrite_UserRecord</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// clang-format off</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">BamWriterTests</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">checkSingleRecord</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useTempFile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="p">{</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fullName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test/100/0_5"</span><span class="p">;</span></span>
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21
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">rgId</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"6002b307"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="62" 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">@@ -58,7 +62,9 @@ TEST(BamWriterTest, SingleWrite_UserRecord)</td>
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58
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">generatedBamFn</span> <span class="o" style="font-weight: 600;">=</span></span>
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59
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">PbbamTestsConfig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GeneratedData_Dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/bamwriter_generated.bam"</span><span class="p">;</span></span>
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60
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="p">{</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriter</span> <span class="n" style="color: #333;">writer</span><span class="p">(</span><span class="n" style="color: #333;">generatedBamFn</span><span class="p">,</span> <span class="n" style="color: #333;">inputHeader</span><span class="p">);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Config</span> <span class="n" style="color: #333;">config</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">useTempFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">useTempFile</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriter</span> <span class="n" style="color: #333;">writer</span><span class="p">(</span><span class="n" style="color: #333;">generatedBamFn</span><span class="p">,</span> <span class="n" style="color: #333;">inputHeader</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">);</span></span>
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62
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">Write</span><span class="p">(</span><span class="n" style="color: #333;">bamRecord</span><span class="p">);</span></span>
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63
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="p">}</span></span>
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64
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" 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="97" 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">@@ -91,3 +97,17 @@ TEST(BamWriterTest, SingleWrite_UserRecord)</td>
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91
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// clean up</span></span>
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92
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">generatedBamFn</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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93
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="p">}</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace BamWriterTests</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">BamWriterTest</span><span class="p">,</span> <span class="n" style="color: #333;">SingleWrite_UserRecord_WithTempFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"><span class="p">{</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriterTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">checkSingleRecord</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"><span class="p">}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">BamWriterTest</span><span class="p">,</span> <span class="n" style="color: #333;">SingleWrite_UserRecord_NoTempFile</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"><span class="p">{</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriterTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">checkSingleRecord</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"><span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// clang-format on</span></span></pre>
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<li id="94cee03a39de65e3f51c168e5df3968e80341600">
<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#94cee03a39de65e3f51c168e5df3968e80341600"><strong>tests/src/test_LongCigar.cpp</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">@@ -2,6 +2,7 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <tuple></span></span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gtest/gtest.h></span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"></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">@@ -10,6 +11,9 @@</td>
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10
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <pbbam/BamReader.h></span></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <pbbam/BamWriter.h></span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../../src/MemoryUtils.h"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../../src/StringUtils.h"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>
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13
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">BamReader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamReader</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">BamRecord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamRecord</span><span class="p">;</span></span>
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15
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">BamWriter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamWriter</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -18,15 +22,42 @@ using CigarOp = PacBio::BAM::CigarOperation;</td>
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18
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CigarOperationType</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">Tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Tag</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// clang-format off</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">LongCigarTests</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">DoesHtslibSupportLongCigar</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">htsVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_version</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// remove any "-<blah>" for non-release versions</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">versionBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">htsVersion</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">versionBase</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"invalid htslib version format: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">htsVersion</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// grab major/minor version numbers</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">versionParts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">versionBase</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">versionParts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">{</span><span class="s" style="color: #d14;">"invalid htslib version format: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">htsVersion</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check against v1.7</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">versionMajor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">versionParts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">versionMinor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">versionParts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v17_major</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v17_minor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tie</span><span class="p">(</span><span class="n" style="color: #333;">versionMajor</span><span class="p">,</span> <span class="n" style="color: #333;">versionMinor</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tie</span><span class="p">(</span><span class="n" style="color: #333;">v17_major</span><span class="p">,</span> <span class="n" style="color: #333;">v17_minor</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_native_long_cigar_support</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DoesHtslibSupportLongCigar</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>
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23
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// BAM record in this file has its CIGAR data in the new "CG" tag</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">LongCigarBam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbbamTestsConfig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Data_Dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/long-cigar.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">LongCigarBam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbbamTestsConfig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Data_Dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/long-cigar<span class="idiff left right">-1.7</span>.bam"</span><span class="p">;</span></span>
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25
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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26
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">LongCigarOut</span> <span class="o" style="font-weight: 600;">=</span></span>
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27
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">PacBio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BAM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PbbamTestsConfig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GeneratedData_Dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/long-cigar-generated.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">66000</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">72091</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">BamRecord</span> <span class="nf" style="color: #900; font-weight: 600;">ReadLongCigarRecord</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="p">{</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">@@ -37,90 +68,58 @@ static BamRecord ReadLongCigarRecord(const std::string& fn)</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">SetLongCigar</span><span class="p">(</span><span class="n" style="color: #333;">BamRecord</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">Cigar</span> <span class="n" style="color: #333;">cigar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">numOps</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numOps</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CigarOperationType</span> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">CigarOperationType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SEQUENCE_MATCH</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">CigarOperationType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INSERTION</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CigarOp</span><span class="p">(</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">CigarData</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">CheckLongCigar</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Cigar</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cigar</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">ASSERT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">numOps</span><span class="p">,</span> <span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOps</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CigarOp</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">Length</span><span class="p">());</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CigarOperationType</span> <span class="n" style="color: #333;">expectedType</span> <span class="o" style="font-weight: 600;">=</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">CigarOperationType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SEQUENCE_MATCH</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">CigarOperationType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INSERTION</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">expectedType</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">Type</span><span class="p">());</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"><span class="p">}</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">CheckLongCigarTag</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Tag</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cigarTag</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="p">{</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">ASSERT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">cigarTag</span><span class="p">.</span><span class="n" style="color: #333;">IsUInt32Array</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">tagArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigarTag</span><span class="p">.</span><span class="n" style="color: #333;">ToUInt32Array</span><span class="p">();</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">ASSERT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">numOps</span><span class="p">,</span> <span class="n" style="color: #333;">tagArray</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOps</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tagArray</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">expectedLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">expectedType</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">BAM_CEQUAL</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">BAM_CINS</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">expectedType</span><span class="p">,</span> <span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">expectedLength</span><span class="p">,</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace LongCigarTests</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTest</span><span class="p">,</span> <span class="n" style="color: #333;">ReadAndFetchLongCigar</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadLongCigarRecord</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongCigarBam</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// public API</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">();</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="mi" style="color: #099;">66000</span><span class="p">,</span> <span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO: come back & check raw data once we have 'private access wrapper'</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// but we're looking good</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numOps</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">has_native_long_cigar_support</span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_FALSE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
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94
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="p">}</span></span>
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95
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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96
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTest</span><span class="p">,</span> <span class="n" style="color: #333;">EditLongCigar</span><span class="p">)</span></span>
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97
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="p">{</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">SCOPED_TRACE</span><span class="p">(</span><span class="s" style="color: #d14;">"EditLongCigar"</span><span class="p">);</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"></span>
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100
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadLongCigarRecord</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongCigarBam</span><span class="p">);</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">LongCigarTests</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">SetLongCigar</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">b</span></span><span class="p">);</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">b</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Impl</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">CigarData</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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102
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">recordCigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cigarTag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">TagValue</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CheckLongCigar</span><span class="p">(</span><span class="n" style="color: #333;">recordCigar</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CheckLongCigarTag</span><span class="p">(</span><span class="n" style="color: #333;">cigarTag</span><span class="p">);</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numOps</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">has_native_long_cigar_support</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="107" 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="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_FALSE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="107" 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="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new old_line" data-linenumber="107" 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="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</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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<td class="diff-line-num new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="108" 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">
108
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<td class="diff-line-num new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTest</span><span class="p">,</span> <span class="n" style="color: #333;">WriteLongCigar</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="110" 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">
110
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<td class="diff-line-num new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="111" 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">
111
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<td class="diff-line-num new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">SCOPED_TRACE</span><span class="p">(</span><span class="s" style="color: #d14;">"WriteLongCigar"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="112" 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">
112
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<td class="diff-line-num new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// write record with our custom long CIGAR</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="114" 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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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="p">{</span> <span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// edit & write</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="114" 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">
114
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<td class="diff-line-num new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadLongCigarRecord</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongCigarBam</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="115" 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">
115
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<td class="diff-line-num new_line old" data-linenumber="102" 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="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SetLongCigar</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="116" 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="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">CigarData</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numOps</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">has_native_long_cigar_support</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="116" 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="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_FALSE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="116" 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="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></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="cpp"> <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"></span>
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116
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">BamWriter</span> <span class="n" style="color: #333;">writer</span><span class="p">{</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongCigarOut</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">header_</span><span class="p">};</span></span>
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117
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">Write</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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118
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// read back in to check</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// read back in</span></span>
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120
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadLongCigarRecord</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongCigarOut</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">recordCigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">();</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cigarTag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">TagValue</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CheckLongCigar</span><span class="p">(</span><span class="n" style="color: #333;">recordCigar</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CheckLongCigarTag</span><span class="p">(</span><span class="n" style="color: #333;">cigarTag</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numOps</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">CigarData</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">LongCigarTests</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">has_native_long_cigar_support</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_FALSE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">Impl</span><span class="p">().</span><span class="n" style="color: #333;">HasTag</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">));</span></span>
</pre>
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125
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<td class="diff-line-num new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="p">}</span></span>
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126
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"><span class="p">}</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// clang-format on</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/a90e83c9fdcbcd2415303185465e50926c78680e...c0a82780f2d3957725dbed2a13f87ba7faed6404#94823b808e03917d439ba3f925435514840b570c"><strong>tools/meson.build</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">@@ -12,10 +12,6 @@ pbbam_Bam2SamVersion_h = configure_file(</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> output : 'Bam2SamVersion.h',</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> configuration : pbbam_Bam2SamVersion_h_config)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">if pbbam_htslib_dep.found()</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> pbbam_htslib_libdir = pbbam_htslib_dep.get_pkgconfig_variable('libdir')</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">pbbam_bam2sam_cpp_sources = [pbbam_Bam2SamVersion_h]</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">pbbam_bam2sam_cpp_sources += files([</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> 'common/OptionParser.cpp',</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +24,6 @@ pbbam_bam2sam = executable(</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> dependencies : [pbbam_htslib_dep, pbbam_thread_dep, pbbam_zlib_dep],</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> include_directories : [pbbam_include_directories, include_directories('bam2sam')],</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> install : get_option('build-tools'),</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> build_rpath : pbbam_htslib_libdir,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> cpp_args : pbbam_warning_flags)</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"># tests</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">@@ -42,7 +37,7 @@ if get_option('tests')</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> 'bam2sam_CramTests',</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> pbbam_cram_script,</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> args : [</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">blasr</span>-cram-bam2sam.xml'),</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">pbbam</span>-cram-bam2sam.xml'),</span>
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46
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> '--verbose'] + [</span>
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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
47
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> bam2sam_t],</span>
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48
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> timeout : 1800)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="114" 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">@@ -119,7 +114,7 @@ if get_option('tests')</td>
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119
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> 'pbindexdump_CramTests',</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> pbbam_cram_script,</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> args : [</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">blasr</span>-cram-pbindexdump.xml'),</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">pbbam</span>-cram-pbindexdump.xml'),</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> '--verbose'] + [</span>
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<td class="diff-line-num old_line" data-linenumber="124" 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="LC119" class="line" lang="plaintext"> pbindexdump_json_t,</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> pbindexdump_cpp_t],</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" 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="173" 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">@@ -178,7 +173,7 @@ if get_option('tests') and not get_option('auto-validate')</td>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"> 'pbmerge_CramTests',</span>
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<td class="diff-line-num old_line" data-linenumber="179" 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="LC174" class="line" lang="plaintext"> pbbam_cram_script,</span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext"> args : [</span>
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<td class="diff-line-num old old_line" data-linenumber="181" 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="LC181" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">blasr</span>-cram-pbmerge.xml'),</span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">pbbam</span>-cram-pbmerge.xml'),</span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> '--verbose'] + [</span>
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<td class="diff-line-num old_line" data-linenumber="183" 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="LC178" class="line" lang="plaintext"> pbmerge_pacbio_ordering_t,</span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"> pbmerge_aligned_ordering_t,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" 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="219" 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">@@ -224,6 +219,8 @@ pbbam_pbbamify = executable(</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"># tests</span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">if get_option('tests')</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> pbbam_test_samtools = find_program('samtools', required : true)</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"></span>
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227
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext"> pbbamify_t = configure_file(</span>
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228
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="plaintext"> input : pbbam_cram_pbbamify_t_in,</span>
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229
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext"> output : 'pbbamify.t',</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" 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="230" 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">@@ -233,11 +230,10 @@ if get_option('tests')</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="plaintext"> 'pbbamify_CramTests',</span>
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<td class="diff-line-num old_line" data-linenumber="234" 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="LC231" class="line" lang="plaintext"> pbbam_cram_script,</span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="plaintext"> args : [</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">blasr</span>-cram-pbbamify.xml'),</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), '<span class="idiff left right">pbbam</span>-cram-pbbamify.xml'),</span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="plaintext"> '--verbose'] + [</span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext"> pbbamify_t],</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> env : [</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> 'SAMTOOLS=' + pbbam_test_samtools.path()],</span>
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<td class="diff-line-num old_line" data-linenumber="239" 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="LC238" class="line" lang="plaintext"> timeout : 1800)</span>
</pre>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="plaintext">endif</span></pre>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="plaintext">### Tests will be added later.</span></pre>
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