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<h3>
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libmaus2">Debian Med / libmaus2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0">f487c237</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2022-02-24T20:33:22+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.810+ds</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#a7f99236fa7771d4b1dc4f0025a0b2881dbb3a8f">
src/libmaus2/suffixsort/BwtMergeBlockSortResult.hpp
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<li class="file-stats">
<a href="#23edc13602cd8272402debc0ba8dce317b5e3c23">
src/libmaus2/suffixsort/BwtMergeTempFileNameSet.hpp
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<li class="file-stats">
<a href="#6bce6ba7853cfde7990a59364860c00fbb2922a5">
src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
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<li class="file-stats">
<a href="#544bbc78e83add663505786a84e9c3021c826425">
src/libmaus2/suffixsort/bwtb3m/MergeStrategyBaseBlock.hpp
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<li class="file-stats">
<a href="#abc051354cc3c15fdf03d1a3a92187108d6dc32c">
src/libmaus2/suffixsort/bwtb3m/MergeStrategyBlock.hpp
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<li class="file-stats">
<a href="#d74d3fb91360d8a835161a332cb5e683eef62bbb">
src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeBlock.hpp
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<li class="file-stats">
<a href="#f5317e989ea71106d5c87c33e735f9a00a3f4d6c">
src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequest.hpp
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<li class="file-stats">
<a href="#1b92add32e64064816c27ce5d24c732587fa9d20">
src/libmaus2/suffixsort/bwtb3m/MergeTree.hpp
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libmaus2 (2.0.810-1) 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"> * Apply some improvements in BWT construction</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 16 Feb 2022 14:51:33 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">libmaus2 (2.0.809-1) unstable; urgency=medium</span>
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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"> * Improve cleanup in BwtMergeSortTemplate</span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT(libmaus2,2.0.80<span class="idiff left right">9</span>,[germant@miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">LIBRARY_VERSION=2:80<span class="idiff left right">9</span>:0</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(libmaus2,2.0.8<span class="idiff left right">1</span>0,[germant@miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">LIBRARY_VERSION=2:8<span class="idiff left right">1</span>0:0</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_CANONICAL_SYSTEM</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">AC_CANONICAL_HOST</span>
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<li id="a7f99236fa7771d4b1dc4f0025a0b2881dbb3a8f">
<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#a7f99236fa7771d4b1dc4f0025a0b2881dbb3a8f"><strong>src/libmaus2/suffixsort/BwtMergeBlockSortResult.hpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -99,6 +99,10 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeFilesButBwtAndGt</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">removeFilesButBwtAndGt</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setTempPrefixAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileNameGenerator</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numbwt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numgt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numisa</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="p">{</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">setPrefixAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p">,</span><span class="n" style="color: #333;">numbwt</span><span class="p">,</span><span class="n" style="color: #333;">numgt</span><span class="p">,</span><span class="n" style="color: #333;">numisa</span><span class="p">);</span> <span class="p">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setTempPrefixSingleAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileNameGenerator</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">)</span></span>
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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="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">setPrefixSingleAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p">);</span> <span class="p">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setTempPrefixSingle</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="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dir_name</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="p">{</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">setTempPrefixSingle</span><span class="p">(</span><span class="n" style="color: #333;">dir_name</span><span class="p">);</span> <span class="p">}</span></span>
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102
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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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">autoarray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AutoArray</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeZBlock</span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">getZBlocks</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;">zblocks</span><span class="p">;</span> <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 class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">resizeZBlocks</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">zblocks</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">);</span> <span class="p">}</span></span>
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104
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setZBlock</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeZBlock</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">z</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">zblocks</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;">z</span><span class="p">;</span> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#23edc13602cd8272402debc0ba8dce317b5e3c23"><strong>src/libmaus2/suffixsort/BwtMergeTempFileNameSet.hpp</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">@@ -165,10 +165,58 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setSampledISA</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="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rsampledisa</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">sampledisa</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;">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;">rsampledisa</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setSampledISA</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="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rsampledisa</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">sampledisa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rsampledisa</span><span class="p">;</span> <span class="p">}</span></span>
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167
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setTempPrefixSingle</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="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dir_name</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC169" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">p_dir_name</span><span class="p">(</span><span class="n" style="color: #333;">dir_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC171" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">p_hwt_req</span><span class="p">(</span><span class="n" style="color: #333;">p_dir_name</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"block.hwtreq"</span><span class="p">);</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">p_hwt</span><span class="p">(</span><span class="n" style="color: #333;">p_dir_name</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"block.hwt"</span><span class="p">);</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">p_hist</span><span class="p">(</span><span class="n" style="color: #333;">p_dir_name</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"block.hist"</span><span class="p">);</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">p_hist_freq</span><span class="p">(</span><span class="n" style="color: #333;">p_dir_name</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"block.histfreq"</span><span class="p">);</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">setHWTReq</span> <span class="p">(</span><span class="n" style="color: #333;">p_hwt_req</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">setHWT</span> <span class="p">(</span><span class="n" style="color: #333;">p_hwt</span><span class="p">.</span><span class="n" style="color: #333;">string</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="n" style="color: #333;">setHist</span> <span class="p">(</span><span class="n" style="color: #333;">p_hist</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">setHistFreq</span><span class="p">(</span><span class="n" style="color: #333;">p_hist_freq</span><span class="p">.</span><span class="n" style="color: #333;">string</span><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="p">}</span></span>
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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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setPrefixSingle</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileNameGenerator</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">)</span></span>
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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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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * number of files: 4</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thwtreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".hwtreq"</span><span class="p">;</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">setHWTReq</span><span class="p">(</span><span class="n" style="color: #333;">thwtreq</span><span class="p">);</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thwt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".hwt"</span><span class="p">;</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">setHWT</span><span class="p">(</span><span class="n" style="color: #333;">thwt</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".hist"</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">setHist</span><span class="p">(</span><span class="n" style="color: #333;">thist</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thistfreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".histfreq"</span><span class="p">;</span></span>
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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;">setHistFreq</span><span class="p">(</span><span class="n" style="color: #333;">thistfreq</span><span class="p">);</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="p">}</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">registerAsTempSingle</span><span class="p">()</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="p">{</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getHWT</span><span class="p">());</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getHWTReq</span><span class="p">());</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getHist</span><span class="p">());</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getHistFreq</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <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>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setPrefixSingleAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileNameGenerator</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">)</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="p">{</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">setPrefixSingle</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">registerAsTempSingle</span><span class="p">();</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="p">}</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"></span>
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168
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setPrefix</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileNameGenerator</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numbwt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numgt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numisa</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * number of files: 4 + numgt + numbwt + numisa</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">setPrefixSingle</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</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>
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170
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218
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<pre style="margin: 0;"> <span id="LC218" 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;">gtfilenames</span><span class="p">(</span><span class="n" style="color: #333;">numgt</span><span class="p">);</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;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_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;">num<span class="idiff left right">bw</span>t</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>
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219
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<pre style="margin: 0;">+<span id="LC219" 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;">uint64_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;">num<span class="idiff left right">g</span>t</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>
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172
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="p">{</span></span>
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221
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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;">ostringstream</span> <span class="n" style="color: #333;">ostr</span><span class="p">;</span></span>
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174
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">ostr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'_'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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">@@ -187,16 +235,7 @@ namespace libmaus2</td>
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187
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">".bwt"</span><span class="p">;</span></span>
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188
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">bwtfilenames</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;">ostr</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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189
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="p">}</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"></span>
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191
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">setBWT</span><span class="p">(</span><span class="n" style="color: #333;">bwtfilenames</span><span class="p">);</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thwtreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".hwtreq"</span><span class="p">;</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">setHWTReq</span><span class="p">(</span><span class="n" style="color: #333;">thwtreq</span><span class="p">);</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thwt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".hwt"</span><span class="p">;</span></span>
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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;">setHWT</span><span class="p">(</span><span class="n" style="color: #333;">thwt</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC196" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".hist"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">setHist</span><span class="p">(</span><span class="n" style="color: #333;">thist</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC198" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">thistfreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".histfreq"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">setHist</span><span class="p">(</span><span class="n" style="color: #333;">thistfreq</span><span class="p">);</span></span>
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC240" 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;">isafilenames</span><span class="p">(</span><span class="n" style="color: #333;">numisa</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;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_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;">numisa</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>
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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">@@ -210,15 +249,18 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">setSampledISA</span><span class="p">(</span><span class="n" style="color: #333;">isafilenames</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="p">}</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>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setPrefixAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileNameGenerator</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numbwt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numgt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numisa</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">setPrefix</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p">,</span> <span class="n" style="color: #333;">numbwt</span><span class="p">,</span> <span class="n" style="color: #333;">numgt</span><span class="p">,</span> <span class="n" style="color: #333;">numisa</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">registerAsTempSingle</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC260" 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;">uint64_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;">getGT</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getGT</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="LC262" 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;">uint64_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;">getBWT</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getBWT</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="LC220" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getHWT</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getHist</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC264" 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;">uint64_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;">getSampledISAVector</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">getSampledISAVector</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="LC266" 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="311" 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">@@ -311,7 +353,7 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numgtfiles</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <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="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numgtfiles</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numbwtfiles</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numgtfiles</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numbwtfiles</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left">/* hwtreq */</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* hwt */</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* hist */</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* hist.freq */</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* sample isa */</span></span><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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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"></span>
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<li id="6bce6ba7853cfde7990a59364860c00fbb2922a5">
<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#6bce6ba7853cfde7990a59364860c00fbb2922a5"><strong>src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> libmaus2</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2009-202<span class="idiff left right">1</span> German Tischler-Höhle</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2009-202<span class="idiff left right">2</span> German Tischler-Höhle</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2011-2014 Genome Research Limited</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</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">@@ -108,13 +108,19 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// array of computed LCP values between block and start of next block</span></span>
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<pre style="margin: 0;"> <span id="LC109" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AtomicArray</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_boundedlcpblockvalues</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// base tmp directory name</span></span>
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<pre style="margin: 0;"> <span id="LC112" 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;">string</span> <span class="n" style="color: #333;">tmpdirname</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tmpdirname as path object</span></span>
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<pre style="margin: 0;"> <span id="LC114" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">tmppath</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">ds_tmp_path</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC115" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">base_tmp_path</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC116" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">ds_tmp_path_base_ds_tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">merge_tmp_path</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC118" 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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">ds_tmp_path_merge_ds_tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC120" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DirectoryStructure</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">DSbase</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC121" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DirectoryStructure</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">DSmerge</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC122" 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;">map</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MergeStrategyBlock</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;">string</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">M_merge_dirs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC123" 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;">map</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MergeStrategyBlock</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="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">M_merge_gt_expected</span><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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119
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125
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<pre style="margin: 0;"> <span id="LC125" 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="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeTempFileNameSetVector</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">blocktmpnames</span><span class="p">;</span></span>
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120
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="131" 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">@@ -125,6 +131,8 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">huffman</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HuffmanTree</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">uhnode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC134" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bwtb3m</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MergeTree</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">merge_tree</span><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="LC136" 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="n" style="color: #333;">serialiseNumber</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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ostr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">n</span><span class="p">)</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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseNumber</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">n</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,14 +162,23 @@ namespace libmaus2</td>
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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="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseString</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">tmpdirname</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseString</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">tmppath</span><span class="p">.</span><span class="n" style="color: #333;">string</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="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">StringSerialisation</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">serialiseString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ostr</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">ds_tmp_path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff right">());</span></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="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseString</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">base_tmp_path</span><span class="p">.</span><span class="n" style="color: #333;">string</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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseString</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">ds_tmp_path_base_ds_tmp</span><span class="p">.</span><span class="n" style="color: #333;">string</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>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseString</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">merge_tmp_path</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseString</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">ds_tmp_path_merge_ds_tmp</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberMapSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseMap</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;">ostream</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">chistnoterm</span><span class="p">);</span></span>
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162
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberMapSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseMap</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;">ostream</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">chist</span><span class="p">);</span></span>
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163
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseSignedNumber</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">bwtterm</span><span class="p">);</span></span>
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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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseNumber</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="n" style="color: #333;">maxsym</span><span class="p">);</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">merge_tree</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="p">{</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">serialiseNumber</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><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="n" style="color: #333;">merge_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">serialise</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="p">}</span></span>
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165
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="p">}</span></span>
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166
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"></span>
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167
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">deserialise</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;">istream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">istr</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" 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">@@ -191,10 +208,13 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpdirname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseString</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">tmppath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseString</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">);</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ds_tmp_path</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">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">StringSerialisation</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">deserialiseString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">istr</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">base_tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseString</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path_base_ds_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseString</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><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="n" style="color: #333;">merge_tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseString</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path_merge_ds_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseString</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC218" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DirectoryStructure</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">t_DSbase</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">BwtMergeTempFileNameSetVector</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDirectoryStructure</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;">ds_tmp_path_base_ds_tmp</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">(),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="221" 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="241" 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">@@ -221,6 +241,18 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">chist</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">computeHuffmanTree</span><span class="p">();</span></span>
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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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">have_merge_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialiseNumber</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"></span>
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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;">have_merge_tree</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="p">{</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bwtb3m</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MergeTree</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">t_merge_tree</span><span class="p">(</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bwtb3m</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MergeTree</span><span class="p">(</span><span class="n" style="color: #333;">istr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_merge_tree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">setupMergeDirectoryStructure</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 class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">getFileSize</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">@@ -325,11 +357,14 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">blocksizeprevtwo</span><span class="p">((</span><span class="n" style="color: #333;">blocksize</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">blocksizenexttwo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">blocksize</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">blocksizenexttwo</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="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">preisasamplingrate</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;">min</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">maxpreisasamplingrate</span><span class="p">,</span><span class="n" style="color: #333;">blocksizeprevtwo</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">V_boundedlcpblockvalues</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AtomicArray</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">numblocks</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="LC360" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tmp directory name</span></span>
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328
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpdirname</span><span class="p">(</span><span class="n" style="color: #333;">ensureDirectory</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">tmpfilenamebase</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_tmpdir"</span><span class="p">)),</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// path object for tmp directory name</span></span>
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329
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">tmppath</span><span class="p">(</span><span class="n" style="color: #333;">tmpdirname</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path</span><span class="p">(</span><span class="n" style="color: #333;">ensureDirectory</span><span class="p">(</span><span class="n" style="color: #333;">tmppath</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"ds_tmp"</span><span class="p">)),</span></span>
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">base_tmp_path</span><span class="p">(</span><span class="n" style="color: #333;">ensureDirectory</span><span class="p">(</span><span class="n" style="color: #333;">tmppath</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"base_tmp"</span><span class="p">)),</span></span>
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332
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path_base_ds_tmp</span><span class="p">(</span><span class="n" style="color: #333;">tmppath</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"base_ds.tmp"</span><span class="p">),</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tmp_path</span><span class="p">(</span><span class="n" style="color: #333;">ensureDirectory</span><span class="p">(</span><span class="n" style="color: #333;">tmppath</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"merge_tmp"</span><span class="p">)),</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path_merge_ds_tmp</span><span class="p">(</span><span class="n" style="color: #333;">tmppath</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"merge_ds.tmp"</span><span class="p">),</span></span>
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">DSbase</span><span class="p">(</span></span>
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334
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">BwtMergeTempFileNameSetVector</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDirectoryStructure</span><span class="p">(</span></span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path_base_ds_tmp</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">(),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" 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="375" 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">@@ -340,6 +375,7 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">numthreads</span> <span class="cm" style="color: #998; font-style: italic;">/* gt */</span></span>
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="p">)</span></span>
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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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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">DSmerge</span><span class="p">(),</span></span>
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">blocktmpnames</span><span class="p">(</span></span>
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344
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">new</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeTempFileNameSetVector</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DSbase</span><span class="p">,</span> <span class="n" style="color: #333;">getNumBlocks</span><span class="p">(),</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">numthreads</span> <span class="cm" style="color: #998; font-style: italic;">/* bwt */</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">numthreads</span> <span class="cm" style="color: #998; font-style: italic;">/* gt */</span><span class="p">)</span></span>
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345
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"> <span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="392" 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">@@ -356,12 +392,6 @@ namespace libmaus2</td>
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356
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// there should be at least one block as input size is not zero</span></span>
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357
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">numblocks</span> <span class="p">);</span></span>
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358
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"> <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::aio::OutputStreamFactoryContainer::mkdirp(tmpdirname,0700);</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::aio::OutputStreamFactoryContainer::mkdirp(ds_tmp_path.string(),0700);</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::aio::OutputStreamFactoryContainer::mkdirp(base_tmp_path.string(),0700);</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">DSbase</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">doGenerate</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "blocktmpnames=\n" << blocktmpnames->toString();</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">@@ -376,9 +406,17 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">DSmerge</span> <span class="p">)</span> <span class="p">{</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">M_merge_dirs</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamFactoryContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">DSmerge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">doRemove</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamFactoryContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">merge_tmp_path</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">DSbase</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">doRemove</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileRemoval</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeFile</span><span class="p">(</span><span class="n" style="color: #333;">ds_tmp_path_base_ds_tmp</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">OutputStreamFactoryContainer</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">rmdir</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">ds_tmp_path</span></span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">FileRemoval</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">removeFile</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">ds_tmp_path_merge_ds_tmp</span></span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamFactoryContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdirname</span><span class="p">);</span></span>
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC422" 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">@@ -530,6 +568,99 @@ namespace libmaus2</td>
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">huftreeCOS</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">huftreeCOS</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="p">}</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMergeGTExpected</span><span class="p">(</span><span class="n" style="color: #333;">MergeStrategyBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</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="LC573" class="line" lang="cpp"> <span class="p">{</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_merge_gt_expected</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_merge_gt_expected</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="p">)</span> <span class="p">{</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LibMausException</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BwtMergeState::getMergeGTExpected: unable to find node"</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;">endl</span><span class="p">;</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="p">}</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="p">}</span></span>
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585
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<pre style="margin: 0;">+<span id="LC586" 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;">string</span> <span class="n" style="color: #333;">getDirectoryForMerge</span><span class="p">(</span><span class="n" style="color: #333;">MergeStrategyBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</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="LC587" class="line" lang="cpp"> <span class="p">{</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_merge_dirs</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_merge_dirs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="p">)</span> <span class="p">{</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LibMausException</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BwtMergeState::getDirectoryForMerge: unable to find node"</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;">endl</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="p">}</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="p">}</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fillGTExpected</span><span class="p">()</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="p">{</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" 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;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_internal</span><span class="p">;</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" 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;">MergeStrategyMergeInternalSmallBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_internal_small</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" 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;">MergeStrategyMergeExternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_external</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getMergeBlocks</span><span class="p">(</span><span class="n" style="color: #333;">V_internal</span><span class="p">,</span><span class="n" style="color: #333;">V_internal_small</span><span class="p">,</span><span class="n" style="color: #333;">V_external</span><span class="p">);</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">V_internal</span> <span class="p">)</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="n" style="color: #333;">M_merge_gt_expected</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumGtTempFilesRequired</span><span class="p">();</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">V_internal_small</span> <span class="p">)</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">M_merge_gt_expected</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumGtTempFilesRequired</span><span class="p">();</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">V_external</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">M_merge_gt_expected</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumGtTempFilesRequired</span><span class="p">();</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setupMergeDirectoryStructure</span><span class="p">()</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="p">{</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" 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;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_internal</span><span class="p">;</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" 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;">MergeStrategyMergeInternalSmallBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_internal_small</span><span class="p">;</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" 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;">MergeStrategyMergeExternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_external</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getMergeBlocks</span><span class="p">(</span><span class="n" style="color: #333;">V_internal</span><span class="p">,</span><span class="n" style="color: #333;">V_internal_small</span><span class="p">,</span><span class="n" style="color: #333;">V_external</span><span class="p">);</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">num_merge_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">V_internal</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="n" style="color: #333;">V_internal_small</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="n" style="color: #333;">V_external</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"></span>
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626
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<pre style="margin: 0;">+<span id="LC626" 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;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DirectoryStructure</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tDS</span><span class="p">(</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DirectoryStructure</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="n" style="color: #333;">ds_tmp_path_merge_ds_tmp</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="mi" style="color: #099;">64</span> <span class="cm" style="color: #998; font-style: italic;">/* mod */</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="n" style="color: #333;">num_merge_nodes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tmp_path</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">DSmerge</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">tDS</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">DSmerge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setAsciiFlag</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">V_internal</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">M_merge_dirs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</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;">DSmerge</span><span class="p">)[</span><span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">V_internal_small</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="n" style="color: #333;">M_merge_dirs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</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;">DSmerge</span><span class="p">)[</span><span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">V_external</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">M_merge_dirs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</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;">DSmerge</span><span class="p">)[</span><span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setMergeTree</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;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bwtb3m</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MergeTree</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r_merge_tree</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r_merge_tree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC651" 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;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_internal</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC652" 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;">MergeStrategyMergeInternalSmallBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_internal_small</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC653" 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;">MergeStrategyMergeExternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V_external</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getMergeBlocks</span><span class="p">(</span><span class="n" style="color: #333;">V_internal</span><span class="p">,</span><span class="n" style="color: #333;">V_internal_small</span><span class="p">,</span><span class="n" style="color: #333;">V_external</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">setupMergeDirectoryStructure</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">DSmerge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">doGenerate</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">M_merge_dirs</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamFactoryContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">,</span><span class="mo" style="color: #099;">0700</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sortresult</span><span class="p">.</span><span class="n" style="color: #333;">setTempPrefixSingle</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC666" 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">@@ -824,6 +955,13 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">verbose</span></span>
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC958" 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;">gtpartnames</span><span class="p">(</span><span class="n" style="color: #333;">zblocks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">z</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;">z</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gtpartnames</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="n" style="color: #333;">z</span> <span class="p">)</span> <span class="p">{</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gtpartname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatNumber</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".gt"</span><span class="p">;</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">gtpartname</span><span class="p">);</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="n" style="color: #333;">gtpartnames</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtpartname</span><span class="p">;</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"> <span class="p">}</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"></span>
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827
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// gap array</span></span>
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828
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Gsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cblocksize</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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829
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="903" 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="1041" 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">@@ -903,7 +1041,6 @@ namespace libmaus2</td>
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903
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1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">zabsblockpos</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zblocks</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">].</span><span class="n" style="color: #333;">getZAbsPos</span><span class="p">();</span></span>
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904
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">zabsblockpos</span> <span class="p">[</span> <span class="n" style="color: #333;">zactive</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blockstart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cblocksize</span><span class="p">;</span></span>
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905
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="cpp"></span>
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906
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<pre style="margin: 0;">-<span id="LC906" 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;">gtpartnames</span><span class="p">(</span><span class="n" style="color: #333;">zactive</span><span class="p">);</span></span>
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907
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="cpp"></span>
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908
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1045
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">logstr</span> <span class="p">)</span></span>
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909
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1058" 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">@@ -921,9 +1058,8 @@ namespace libmaus2</td>
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921
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="cpp"></span>
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922
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1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeZBlock</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">zblock</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zblocks</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">];</span></span>
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="cpp"></span>
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924
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<pre style="margin: 0;">-<span id="LC924" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gtpartname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtmpgen</span><span class="p">.</span><span class="n" style="color: #333;">getFileName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatNumber</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".gt"</span><span class="p">;</span></span>
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925
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TempFileRemovalContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addTempFile</span><span class="p">(</span><span class="n" style="color: #333;">gtpartname</span><span class="p">);</span></span>
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926
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">gtpartnames</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtpartname</span><span class="p">;</span></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gtpartname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtpartnames</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"></span>
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="cpp"> <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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928
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> ::libmaus2::huffman::HuffmanEncoderFileStd GTHEF(gtpartname);</span></span>
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929
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1098" 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">@@ -962,7 +1098,7 @@ namespace libmaus2</td>
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parallel</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StdSpinLock</span> <span class="n" style="color: #333;">gslock</span><span class="p">;</span></span>
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1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp"></span>
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964
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1100
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(_OPENMP)</span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma omp parallel for</span></span>
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma omp parallel for<span class="idiff left right"> num_threads(numthreads)</span></span></span>
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966
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1103
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<pre style="margin: 0;"> <span id="LC1103" 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;">uint64_t</span> <span class="n" style="color: #333;">t</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;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cblocks</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span> <span class="p">)</span></span>
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968
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1136" 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">@@ -1000,7 +1136,6 @@ namespace libmaus2</td>
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1000
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// length of text file in symbols</span></span>
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1001
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1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bwtb3m</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MergeStrategyMergeGapRequest</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">msmgr</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// merge request</span></span>
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1002
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1138
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<pre style="margin: 0;"> <span id="LC1138" 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="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mergedgtname</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// previous gt file name</span></span>
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::string const & newmergedgtname, // new gt file name</span></span>
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1004
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DArray</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">accD</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// accumulated symbol freqs for block</span></span>
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">numthreads</span><span class="p">,</span></span>
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1141
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<pre style="margin: 0;"> <span id="LC1141" 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;">ostream</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">logstr</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1749" 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="1884" 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">@@ -1749,7 +1884,6 @@ namespace libmaus2</td>
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1884
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<pre style="margin: 0;"> <span id="LC1884" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">verbose</span></span>
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1885
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<pre style="margin: 0;"> <span id="LC1885" class="line" lang="cpp"> <span class="p">)</span></span>
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1886
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<pre style="margin: 0;"> <span id="LC1886" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1752" class="line" lang="cpp"></span>
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1887
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<pre style="margin: 0;"> <span id="LC1887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">logstr</span> <span class="p">)</span></span>
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1888
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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">logstr</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] Merging BWT blocks MergeStrategyMergeInternalBlock."</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;">endl</span><span class="p">;</span></span>
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1889
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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1919" 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">@@ -1785,7 +1919,7 @@ namespace libmaus2</td>
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1785
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1919
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// gt bit array,</span></span>
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1786
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1920
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// huffman shaped wavelet tree and</span></span>
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1787
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1921
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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// histogram</span></span>
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1788
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<pre style="margin: 0;">-<span id="LC1788" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setTempPrefixAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p"><span class="idiff left">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* no preset bwt file names */</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* no preset gt file names */</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* no preset isa */</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1922" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">// </span>result.setTempPrefix<span class="idiff right">Single</span>AndRegisterAsTemp(gtmpgen);</span></span>
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1923
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<pre style="margin: 0;"> <span id="LC1923" class="line" lang="cpp"></span>
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1790
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1924
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">logstr</span> <span class="p">)</span></span>
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1791
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1925
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<pre style="margin: 0;"> <span id="LC1925" 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="1855" 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="1989" 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">@@ -1855,6 +1989,7 @@ namespace libmaus2</td>
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1855
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1989
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<pre style="margin: 0;"> <span id="LC1989" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">logstr</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] renaming gt files"</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;">endl</span><span class="p">;</span></span>
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1856
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1990
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<pre style="margin: 0;"> <span id="LC1990" class="line" lang="cpp"> <span class="p">}</span></span>
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1857
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<td class="new_line diff-line-num" data-linenumber="1991" 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">
1991
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<pre style="margin: 0;"> <span id="LC1991" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="1992" 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">
1992
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<pre style="margin: 0;">+<span id="LC1992" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// move gt files for left block to output by renaming them</span></span>
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1858
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1993
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<pre style="margin: 0;"> <span id="LC1993" 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;">oldgtnames</span><span class="p">;</span></span>
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1859
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<td class="new_line diff-line-num" data-linenumber="1994" 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">
1994
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<pre style="margin: 0;"> <span id="LC1994" 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;">uint64_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;">blockresults</span><span class="p">.</span><span class="n" style="color: #333;">getFiles</span><span class="p">().</span><span class="n" style="color: #333;">getGT</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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1860
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1995
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<pre style="margin: 0;"> <span id="LC1995" 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="1866" 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="2001" 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">@@ -1866,6 +2001,7 @@ namespace libmaus2</td>
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1866
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2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamFactoryContainer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">blockresults</span><span class="p">.</span><span class="n" style="color: #333;">getFiles</span><span class="p">().</span><span class="n" style="color: #333;">getGT</span><span class="p">()[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">renamed</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1867
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2002
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<pre style="margin: 0;"> <span id="LC2002" class="line" lang="cpp"> <span class="p">}</span></span>
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1868
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2003
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<pre style="margin: 0;"> <span id="LC2003" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1869" 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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2004
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<pre style="margin: 0;">+<span id="LC2004" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// concatenate new gt files and old ones to obtain output gt files</span></span>
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1869
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2005
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<pre style="margin: 0;"> <span id="LC2005" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setGT</span><span class="p">(</span><span class="n" style="color: #333;">stringVectorAppend</span><span class="p">(</span><span class="n" style="color: #333;">GACR</span><span class="p">.</span><span class="n" style="color: #333;">gtpartnames</span><span class="p">,</span><span class="n" style="color: #333;">oldgtnames</span><span class="p">));</span></span>
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1870
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2006
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<pre style="margin: 0;"> <span id="LC2006" class="line" lang="cpp"></span>
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1871
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2007
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<pre style="margin: 0;"> <span id="LC2007" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">timing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RealTimeClock</span> <span class="n" style="color: #333;">rtc</span><span class="p">;</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1931" 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="2067" 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">@@ -1931,184 +2067,6 @@ namespace libmaus2</td>
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1931
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2067
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1932" 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">
1932
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2068
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<pre style="margin: 0;"> <span id="LC2068" class="line" lang="cpp"> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1933" 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">
1933
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<td class="new_line diff-line-num" data-linenumber="2069" 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">
2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1934" 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">
1934
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1934" class="line" lang="cpp"> <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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1935
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<pre style="margin: 0;">-<span id="LC1935" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( verbose >= 5 && logstr )</span></span>
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1936
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<pre style="margin: 0;">-<span id="LC1936" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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1937
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<pre style="margin: 0;">-<span id="LC1937" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> (*logstr) << "[V] computing work packets" << std::endl;</span></span>
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1938
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<pre style="margin: 0;">-<span id="LC1938" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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1939
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<pre style="margin: 0;">-<span id="LC1939" class="line" lang="cpp"></span>
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1940
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<pre style="margin: 0;">-<span id="LC1940" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const logG = std::max(libmaus2::math::ilog(Gsize),static_cast<unsigned int>(1));</span></span>
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1941
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<pre style="margin: 0;">-<span id="LC1941" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const logG2 = logG*logG;</span></span>
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1942
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<pre style="margin: 0;">-<span id="LC1942" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // target number of G samples</span></span>
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1943
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<pre style="margin: 0;">-<span id="LC1943" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const tnumGsamp = std::max(Gsize / logG2,static_cast<uint64_t>(256*numthreads));</span></span>
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1944
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<pre style="margin: 0;">-<span id="LC1944" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const Gsampleblocksize = (Gsize + tnumGsamp - 1) / tnumGsamp;</span></span>
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1945
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<pre style="margin: 0;">-<span id="LC1945" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // number of G samples</span></span>
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1946
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<pre style="margin: 0;">-<span id="LC1946" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const numGsamp = (Gsize + Gsampleblocksize - 1) / Gsampleblocksize;</span></span>
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1947
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<pre style="margin: 0;">-<span id="LC1947" class="line" lang="cpp"></span>
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1948
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<pre style="margin: 0;">-<span id="LC1948" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::autoarray::AutoArray < uint64_t > Gsamples(numGsamp,false);</span></span>
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1949
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<pre style="margin: 0;">-<span id="LC1949" class="line" lang="cpp"></span>
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1950
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<pre style="margin: 0;">-<span id="LC1950" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #if defined(_OPENMP)</span></span>
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1951
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<pre style="margin: 0;">-<span id="LC1951" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #pragma omp parallel for num_threads(numthreads)</span></span>
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1952
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<pre style="margin: 0;">-<span id="LC1952" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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1953
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<pre style="margin: 0;">-<span id="LC1953" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> for ( uint64_t t = 0; t < numGsamp; ++t )</span></span>
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1954
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<pre style="margin: 0;">-<span id="LC1954" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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1955
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<pre style="margin: 0;">-<span id="LC1955" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const low = t * Gsampleblocksize;</span></span>
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1956
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<pre style="margin: 0;">-<span id="LC1956" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const high = std::min(low + Gsampleblocksize, Gsize);</span></span>
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1957
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<pre style="margin: 0;">-<span id="LC1957" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> assert ( high >= low );</span></span>
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1958
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<pre style="margin: 0;">-<span id="LC1958" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t s = 0;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1959" 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">
1959
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<pre style="margin: 0;">-<span id="LC1959" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> G_array_iterator gp = GACR.G.begin() + low;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1960" 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">
1960
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1960" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> for ( uint64_t i = low; i < high; ++i )</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1961" 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">
1961
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1961" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s += *(gp++);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1962" 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">
1962
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1962" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s += (high-low);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1963" 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">
1963
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1963" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( high == Gsize && high != low )</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1964" 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">
1964
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1964" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s -= 1;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1965" 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">
1965
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1965" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> Gsamples[t] = s;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1966" 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">
1966
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1966" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1967" 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">
1967
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1967" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1968" 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">
1968
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1968" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #if 0</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1969" 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">
1969
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1969" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> std::vector<uint64_t> G_A(Gsamples.begin(),Gsamples.end());</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1970" 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">
1970
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1970" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> std::vector<uint64_t> G_B(Gsamples.begin(),Gsamples.end());</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1971" 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">
1971
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1971" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1972" 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">
1972
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1972" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::util::PrefixSums::prefixSums(G_A.begin(),G_A.end());</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1973" 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">
1973
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1973" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::util::PrefixSums::parallelPrefixSums(G_A.begin(),G_A.end(),numthreads);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1974" 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">
1974
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1974" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1975" 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">
1975
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1975" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1976" 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">
1976
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1976" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const Gsum = libmaus2::util::PrefixSums::parallelPrefixSums(Gsamples.begin(),Gsamples.end(),numthreads);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1977" 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">
1977
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1977" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1978" 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">
1978
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1978" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( verbose >= 5 && logstr )</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1979" 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">
1979
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1979" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1980" 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">
1980
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1980" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> (*logstr) << "[V] G size " << Gsize << " number of G samples " << numGsamp << std::endl;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1981" 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">
1981
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1981" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1982" 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">
1982
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1982" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1983" 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">
1983
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1983" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const Gsumperthread = (Gsum + numthreads-1)/numthreads;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1984" 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">
1984
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1984" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> std::vector < std::pair<uint64_t,uint64_t> > wpacks;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1985" 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">
1985
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1985" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks = std::vector < std::pair<uint64_t,uint64_t> >(numthreads);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1986" 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">
1986
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1986" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #if defined(_OPENMP)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1987" 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">
1987
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1987" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #pragma omp parallel for num_threads(numthreads)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1988" 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">
1988
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1988" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1989" 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">
1989
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1989" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> for ( uint64_t i = 0; i < numthreads; ++i )</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1990" 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">
1990
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1990" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1991" 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">
1991
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1991" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const target = i * Gsumperthread;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1992" 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">
1992
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1992" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const * p = ::std::lower_bound(Gsamples.begin(),Gsamples.end(),target);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1993" 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">
1993
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC1993" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1994" 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">
1994
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1994" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( p == Gsamples.end() )</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1995" 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">
1995
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1995" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> --p;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1996" 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">
1996
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1996" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> while ( *p > target )</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1997" 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">
1997
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1997" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> --p;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1998" 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">
1998
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1998" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1999" 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">
1999
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC1999" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> assert ( *p <= target );</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2000" 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">
2000
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2000" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2001" 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">
2001
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2001" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t iv = (p - Gsamples.begin()) * Gsampleblocksize;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2002" 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">
2002
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2002" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t s = *p;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2003" 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">
2003
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2003" class="line" lang="cpp"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2004" 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">
2004
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2004" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> G_array_iterator gp = GACR.G.begin() + iv;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2005" 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">
2005
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2005" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> while ( s < target && iv < Gsize )</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2006" 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">
2006
</td>
<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2006" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2007" 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">
2007
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2007" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s += (*(gp++))+1;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2008" 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">
2008
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<td class="new_line diff-line-num old" data-linenumber="2070" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2008" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> iv++;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2009" 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">
2009
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<pre style="margin: 0;">-<span id="LC2009" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2010
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<pre style="margin: 0;">-<span id="LC2010" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( iv == Gsize )</span></span>
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2011
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<pre style="margin: 0;">-<span id="LC2011" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s -= 1;</span></span>
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2012
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<pre style="margin: 0;">-<span id="LC2012" class="line" lang="cpp"></span>
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2013
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<pre style="margin: 0;">-<span id="LC2013" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks[i].first = iv;</span></span>
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2014
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<pre style="margin: 0;">-<span id="LC2014" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( i )</span></span>
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2015
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<pre style="margin: 0;">-<span id="LC2015" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks[i-1].second = iv;</span></span>
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2016
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<pre style="margin: 0;">-<span id="LC2016" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // std::cerr << "i=" << i << " iv=" << iv << " Gsize=" << Gsize << std::endl;</span></span>
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2017
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<pre style="margin: 0;">-<span id="LC2017" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2018
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<pre style="margin: 0;">-<span id="LC2018" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks.back().second = Gsize;</span></span>
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2019
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<pre style="margin: 0;">-<span id="LC2019" class="line" lang="cpp"></span>
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2020
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<pre style="margin: 0;">-<span id="LC2020" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // remove empty packages</span></span>
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2021
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<pre style="margin: 0;">-<span id="LC2021" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2022
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<pre style="margin: 0;">-<span id="LC2022" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t o = 0;</span></span>
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2023
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2023" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> for ( uint64_t i = 0; i < wpacks.size(); ++i )</span></span>
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2024
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2024" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( wpacks[i].first != wpacks[i].second )</span></span>
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2025
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2025" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks[o++] = wpacks[i];</span></span>
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2026
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2026" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks.resize(o);</span></span>
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2027
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2027" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2028
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2028" class="line" lang="cpp"></span>
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2029
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2029" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> std::vector < uint64_t > P;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2030" 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">
2030
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2030" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> P.resize(wpacks.size()+1);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2031" 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">
2031
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2031" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #if defined(_OPENMP)</span></span>
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2032
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<td class="new_line diff-line-num old" data-linenumber="2070" 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="LC2032" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #pragma omp parallel for num_threads(numthreads)</span></span>
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2033
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<pre style="margin: 0;">-<span id="LC2033" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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<pre style="margin: 0;">-<span id="LC2034" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> for ( uint64_t i = 0; i < wpacks.size(); ++i )</span></span>
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2035
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<pre style="margin: 0;">-<span id="LC2035" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2036
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<pre style="margin: 0;">-<span id="LC2036" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const low = wpacks[i].first;</span></span>
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2037
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<pre style="margin: 0;">-<span id="LC2037" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const high = wpacks[i].second;</span></span>
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2038
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<pre style="margin: 0;">-<span id="LC2038" class="line" lang="cpp"></span>
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2039
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<pre style="margin: 0;">-<span id="LC2039" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> G_array_iterator gp = GACR.G.begin() + low;</span></span>
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2040
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<pre style="margin: 0;">-<span id="LC2040" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t s = 0;</span></span>
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2041
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<pre style="margin: 0;">-<span id="LC2041" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> for ( uint64_t i = low; i < high; ++i )</span></span>
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2042
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<pre style="margin: 0;">-<span id="LC2042" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s += *(gp++);</span></span>
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2043
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<pre style="margin: 0;">-<span id="LC2043" class="line" lang="cpp"></span>
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2044
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<pre style="margin: 0;">-<span id="LC2044" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> P[i] = s;</span></span>
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2045
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<pre style="margin: 0;">-<span id="LC2045" class="line" lang="cpp"></span>
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2046
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<pre style="margin: 0;">-<span id="LC2046" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2047
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<pre style="margin: 0;">-<span id="LC2047" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::util::PrefixSums::prefixSums(P.begin(),P.end());</span></span>
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2048
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<pre style="margin: 0;">-<span id="LC2048" class="line" lang="cpp"></span>
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2049
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<pre style="margin: 0;">-<span id="LC2049" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #if 0</span></span>
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2050
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<pre style="margin: 0;">-<span id="LC2050" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // std::cerr << "(computing work packets...";</span></span>
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2051
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<pre style="margin: 0;">-<span id="LC2051" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> P.push_back(0);</span></span>
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2052
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<pre style="margin: 0;">-<span id="LC2052" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t ilow = 0;</span></span>
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2053
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<pre style="margin: 0;">-<span id="LC2053" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> //</span></span>
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2054
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<pre style="margin: 0;">-<span id="LC2054" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const totalsuf = result.getCBlockSize();</span></span>
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2055
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<pre style="margin: 0;">-<span id="LC2055" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // number of packets</span></span>
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2056
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<pre style="margin: 0;">-<span id="LC2056" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const numpack = numthreads;</span></span>
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2057
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<pre style="margin: 0;">-<span id="LC2057" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // suffixes per thread</span></span>
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2058
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<pre style="margin: 0;">-<span id="LC2058" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const tpacksize = (totalsuf + numpack-1)/numpack;</span></span>
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2059
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<pre style="margin: 0;">-<span id="LC2059" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> while ( ilow != Gsize )</span></span>
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2060
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<pre style="margin: 0;">-<span id="LC2060" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2061
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<pre style="margin: 0;">-<span id="LC2061" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t s = 0;</span></span>
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2062
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<pre style="margin: 0;">-<span id="LC2062" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t ihigh = ilow;</span></span>
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2063
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<pre style="margin: 0;">-<span id="LC2063" class="line" lang="cpp"></span>
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2064
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<pre style="margin: 0;">-<span id="LC2064" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( verbose >= 5 && logstr )</span></span>
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2065
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<pre style="margin: 0;">-<span id="LC2065" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2066
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<pre style="margin: 0;">-<span id="LC2066" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> (*logstr) << "[V] ilow=" << ilow << std::endl;</span></span>
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2067
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<pre style="margin: 0;">-<span id="LC2067" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2068
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<pre style="margin: 0;">-<span id="LC2068" class="line" lang="cpp"></span>
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2069
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<pre style="margin: 0;">-<span id="LC2069" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> while ( ihigh != Gsize && s < tpacksize )</span></span>
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2070
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<pre style="margin: 0;">-<span id="LC2070" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> s += (GACR.G[ihigh++]+1);</span></span>
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2071
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<pre style="margin: 0;">-<span id="LC2071" class="line" lang="cpp"></span>
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2072
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<pre style="margin: 0;">-<span id="LC2072" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> uint64_t const p = s-(ihigh-ilow);</span></span>
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2073
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<pre style="margin: 0;">-<span id="LC2073" class="line" lang="cpp"></span>
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2074
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<pre style="margin: 0;">-<span id="LC2074" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( ihigh+1 == Gsize && GACR.G[ihigh] == 0 )</span></span>
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2075
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<pre style="margin: 0;">-<span id="LC2075" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> ihigh++;</span></span>
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2076
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<pre style="margin: 0;">-<span id="LC2076" class="line" lang="cpp"></span>
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2077
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<pre style="margin: 0;">-<span id="LC2077" class="line" lang="cpp"></span>
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2078
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<pre style="margin: 0;">-<span id="LC2078" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( verbose >= 5 && logstr )</span></span>
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2079
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<pre style="margin: 0;">-<span id="LC2079" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2080
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<pre style="margin: 0;">-<span id="LC2080" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> (*logstr) << "[V] ihigh=" << ilow << std::endl;</span></span>
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2081
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<pre style="margin: 0;">-<span id="LC2081" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2082
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<pre style="margin: 0;">-<span id="LC2082" class="line" lang="cpp"></span>
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2083
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<pre style="margin: 0;">-<span id="LC2083" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // std::cerr << "[" << ilow << "," << ihigh << ")" << std::endl;</span></span>
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2084
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<pre style="margin: 0;">-<span id="LC2084" class="line" lang="cpp"></span>
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2085
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<pre style="margin: 0;">-<span id="LC2085" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> assert ( p == std::accumulate(GACR.G.begin()+ilow,GACR.G.begin()+ihigh,0ull) );</span></span>
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2086
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<pre style="margin: 0;">-<span id="LC2086" class="line" lang="cpp"></span>
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2087
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<pre style="margin: 0;">-<span id="LC2087" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( verbose >= 5 && logstr )</span></span>
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2088
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<pre style="margin: 0;">-<span id="LC2088" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2089
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<pre style="margin: 0;">-<span id="LC2089" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> (*logstr) << "[V] accumulate check done" << std::endl;</span></span>
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2090
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<pre style="margin: 0;">-<span id="LC2090" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2091
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<pre style="margin: 0;">-<span id="LC2091" class="line" lang="cpp"></span>
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2092
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<pre style="margin: 0;">-<span id="LC2092" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> P.push_back(P.back() + p);</span></span>
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2093
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<pre style="margin: 0;">-<span id="LC2093" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> wpacks.push_back(std::pair<uint64_t,uint64_t>(ilow,ihigh));</span></span>
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2094
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> encfilenames.push_back(</span></span>
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2095
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<pre style="margin: 0;">-<span id="LC2095" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> gtmpgen.getFileName()</span></span>
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2096
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<pre style="margin: 0;">-<span id="LC2096" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> // result.getFiles().getBWT()</span></span>
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2097
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<pre style="margin: 0;">-<span id="LC2097" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> + "_"</span></span>
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2098
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<pre style="margin: 0;">-<span id="LC2098" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> + ::libmaus2::util::NumberSerialisation::formatNumber(encfilenames.size(),6)</span></span>
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2099
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<pre style="margin: 0;">-<span id="LC2099" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> + ".bwt"</span></span>
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2100
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<pre style="margin: 0;">-<span id="LC2100" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> );</span></span>
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2101
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<pre style="margin: 0;">-<span id="LC2101" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> ::libmaus2::util::TempFileRemovalContainer::addTempFile(encfilenames.back());</span></span>
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2102
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<pre style="margin: 0;">-<span id="LC2102" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> ilow = ihigh;</span></span>
</pre>
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2103
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<pre style="margin: 0;">-<span id="LC2103" class="line" lang="cpp"></span>
</pre>
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2104
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<pre style="margin: 0;">-<span id="LC2104" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if ( verbose >= 5 && logstr )</span></span>
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2105
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<pre style="margin: 0;">-<span id="LC2105" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2106
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<pre style="margin: 0;">-<span id="LC2106" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> (*logstr) << "[V] end of single loop" << std::endl;</span></span>
</pre>
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2107
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<pre style="margin: 0;">-<span id="LC2107" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2108
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<pre style="margin: 0;">-<span id="LC2108" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2109
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<pre style="margin: 0;">-<span id="LC2109" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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2110
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<pre style="margin: 0;">-<span id="LC2110" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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2111
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<pre style="margin: 0;">-<span id="LC2111" class="line" lang="cpp"></span>
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2112
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2070
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<pre style="margin: 0;"> <span id="LC2070" 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;">encfilenames</span><span class="p">(</span><span class="n" style="color: #333;">wpacks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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2113
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2071
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<pre style="margin: 0;"> <span id="LC2071" 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;">uint64_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;">wpacks</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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2114
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2072
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<pre style="margin: 0;"> <span id="LC2072" 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="2317" 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="2275" 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">@@ -2317,7 +2275,7 @@ namespace libmaus2</td>
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2317
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2275
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<pre style="margin: 0;"> <span id="LC2275" class="line" lang="cpp"> <span class="n" style="color: #333;">gapfilenames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">newgapname</span><span class="p">);</span></span>
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2318
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2276
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<pre style="margin: 0;"> <span id="LC2276" class="line" lang="cpp"> <span class="p">}</span></span>
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2319
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2277
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<pre style="margin: 0;"> <span id="LC2277" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2320" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bwt name</span></span>
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2278
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<pre style="margin: 0;">+<span id="LC2278" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left">create new names for the input </span>bwt name<span class="idiff right">s</span></span></span>
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2321
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2279
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<pre style="margin: 0;"> <span id="LC2279" 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;">newbwtnames</span><span class="p">;</span></span>
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2322
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2280
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<pre style="margin: 0;"> <span id="LC2280" 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;">uint64_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;">mergereq</span><span class="p">.</span><span class="n" style="color: #333;">children</span><span class="p">[</span><span class="n" style="color: #333;">bb</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sortresult</span><span class="p">.</span><span class="n" style="color: #333;">getFiles</span><span class="p">().</span><span class="n" style="color: #333;">getBWT</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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2323
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2281
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<pre style="margin: 0;"> <span id="LC2281" 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="2377" 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="2335" 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">@@ -2377,7 +2335,6 @@ namespace libmaus2</td>
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2377
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2335
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<pre style="margin: 0;"> <span id="LC2335" class="line" lang="cpp"> <span class="n" style="color: #333;">GapArrayComputationResult</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GACR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">computeGapArray</span><span class="p">(</span></span>
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2378
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2336
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<pre style="margin: 0;"> <span id="LC2336" class="line" lang="cpp"> <span class="n" style="color: #333;">gtmpgen</span><span class="p">,</span><span class="n" style="color: #333;">fn</span><span class="p">,</span><span class="n" style="color: #333;">fs</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">mergereq</span><span class="p">.</span><span class="n" style="color: #333;">gaprequests</span><span class="p">[</span><span class="n" style="color: #333;">bx</span><span class="p">]),</span></span>
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2379
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2337
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<pre style="margin: 0;"> <span id="LC2337" class="line" lang="cpp"> <span class="n" style="color: #333;">mergedgtname</span><span class="p">,</span></span>
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2380
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<pre style="margin: 0;">-<span id="LC2380" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//newmergedgtname,</span></span>
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2381
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2338
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<pre style="margin: 0;"> <span id="LC2338" class="line" lang="cpp"> <span class="n" style="color: #333;">accD</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span></span>
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2382
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2339
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<pre style="margin: 0;"> <span id="LC2339" class="line" lang="cpp"> <span class="n" style="color: #333;">numthreads</span><span class="p">,</span></span>
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2383
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2340
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<pre style="margin: 0;"> <span id="LC2340" class="line" lang="cpp"> <span class="n" style="color: #333;">logstr</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2531" 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">@@ -2574,7 +2531,7 @@ namespace libmaus2</td>
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2574
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2531
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<pre style="margin: 0;"> <span id="LC2531" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// gt bit array,</span></span>
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2575
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2532
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<pre style="margin: 0;"> <span id="LC2532" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// huffman shaped wavelet tree and</span></span>
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2576
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2533
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<pre style="margin: 0;"> <span id="LC2533" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// histogram</span></span>
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2577
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<pre style="margin: 0;">-<span id="LC2577" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setTempPrefixAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p"><span class="idiff left">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* no preset bwt file names */</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* no preset gt file names */</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* no preset isa */</span></span><span class="p">);</span></span>
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2534
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<pre style="margin: 0;">+<span id="LC2534" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">// </span>result.setTempPrefix<span class="idiff right">Single</span>AndRegisterAsTemp(gtmpgen);</span></span>
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2578
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2535
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<pre style="margin: 0;"> <span id="LC2535" class="line" lang="cpp"></span>
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2579
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2536
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<pre style="margin: 0;"> <span id="LC2536" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if we merge only two blocks together, then we do not need to write the gap array to disk</span></span>
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2580
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2537
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<pre style="margin: 0;"> <span id="LC2537" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">mergereq</span><span class="p">.</span><span class="n" style="color: #333;">children</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3161" 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="3118" 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">@@ -3161,13 +3118,10 @@ namespace libmaus2</td>
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3161
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3118
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<pre style="margin: 0;"> <span id="LC3118" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setCBlockSize</span> <span class="p">(</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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3162
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3119
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<pre style="margin: 0;"> <span id="LC3119" 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;">uint64_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;">mergereq</span><span class="p">.</span><span class="n" style="color: #333;">children</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="n" style="color: #333;">i</span> <span class="p">)</span></span>
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3163
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3120
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<pre style="margin: 0;"> <span id="LC3120" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setCBlockSize</span><span class="p">(</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">getCBlockSize</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mergereq</span><span class="p">.</span><span class="n" style="color: #333;">children</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;">sortresult</span><span class="p">.</span><span class="n" style="color: #333;">getCBlockSize</span><span class="p">()</span> <span class="p">);</span></span>
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3164
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<pre style="margin: 0;">-<span id="LC3164" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set up</span></span>
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3165
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<pre style="margin: 0;">-<span id="LC3165" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// filenames of output bwt,</span></span>
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3166
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<pre style="margin: 0;">-<span id="LC3166" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sampled inverse suffix array filename,</span></span>
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3167
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<pre style="margin: 0;">-<span id="LC3167" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// gt bit array,</span></span>
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3121
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<pre style="margin: 0;">+<span id="LC3121" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set up file names for</span></span>
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3168
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3122
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<pre style="margin: 0;"> <span id="LC3122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// huffman shaped wavelet tree and</span></span>
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3169
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3123
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<pre style="margin: 0;"> <span id="LC3123" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// histogram</span></span>
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3170
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<pre style="margin: 0;">-<span id="LC3170" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setTempPrefixAndRegisterAsTemp</span><span class="p">(</span><span class="n" style="color: #333;">gtmpgen</span><span class="p"><span class="idiff left">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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3124
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<pre style="margin: 0;">+<span id="LC3124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">// </span>result.setTempPrefix<span class="idiff right">Single</span>AndRegisterAsTemp(gtmpgen);</span></span>
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3171
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3125
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<pre style="margin: 0;"> <span id="LC3125" class="line" lang="cpp"></span>
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3172
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3126
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<pre style="margin: 0;"> <span id="LC3126" class="line" lang="cpp"> <span class="p">{</span></span>
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3173
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3127
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<pre style="margin: 0;"> <span id="LC3127" 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;">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="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gapfilenames</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3986" 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="3940" 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">@@ -3986,6 +3940,8 @@ namespace libmaus2</td>
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3986
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3940
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<pre style="margin: 0;"> <span id="LC3940" class="line" lang="cpp"> <span class="n" style="color: #333;">constructMergeTree</span><span class="p">(</span><span class="n" style="color: #333;">logstr</span><span class="p">,</span><span class="n" style="color: #333;">options</span><span class="p">,</span><span class="n" style="color: #333;">state</span><span class="p">,</span><span class="n" style="color: #333;">fn</span><span class="p">,</span><span class="n" style="color: #333;">rlencoderblocksize</span><span class="p">)</span></span>
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3987
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3941
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<pre style="margin: 0;"> <span id="LC3941" class="line" lang="cpp"> <span class="p">);</span></span>
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3988
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3942
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<pre style="margin: 0;"> <span id="LC3942" class="line" lang="cpp"></span>
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3943
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<pre style="margin: 0;">+<span id="LC3943" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span><span class="p">.</span><span class="n" style="color: #333;">setMergeTree</span><span class="p">(</span><span class="n" style="color: #333;">mergetree</span><span class="p">);</span></span>
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3944
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<pre style="margin: 0;">+<span id="LC3944" class="line" lang="cpp"></span>
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3989
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3945
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<pre style="margin: 0;"> <span id="LC3945" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// inner node queue</span></span>
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3990
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3946
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<pre style="margin: 0;"> <span id="LC3946" 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;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itodo</span><span class="p">;</span></span>
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3991
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3947
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<pre style="margin: 0;"> <span id="LC3947" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4033" 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="3989" 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">@@ -4033,6 +3989,8 @@ namespace libmaus2</td>
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4033
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3989
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<pre style="margin: 0;"> <span id="LC3989" class="line" lang="cpp"></span>
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4034
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3990
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<pre style="margin: 0;"> <span id="LC3990" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">mergetree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">checkSerialisation</span><span class="p">()</span> <span class="p">);</span></span>
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4035
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3991
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<pre style="margin: 0;"> <span id="LC3991" class="line" lang="cpp"></span>
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3992
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<pre style="margin: 0;">+<span id="LC3992" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span><span class="p">.</span><span class="n" style="color: #333;">fillGTExpected</span><span class="p">();</span></span>
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3993
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<pre style="margin: 0;">+<span id="LC3993" class="line" lang="cpp"></span>
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4036
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3994
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<pre style="margin: 0;"> <span id="LC3994" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">logstr</span> <span class="p">)</span></span>
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4037
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3995
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<pre style="margin: 0;"> <span id="LC3995" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">logstr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] checked serialisation after filling gap request objects"</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;">endl</span><span class="p">;</span></span>
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4038
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3996
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<pre style="margin: 0;"> <span id="LC3996" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4030" 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">@@ -4072,6 +4030,10 @@ namespace libmaus2</td>
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4072
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4030
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<pre style="margin: 0;"> <span id="LC4030" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">logstr</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;">endl</span><span class="p">;</span></span>
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4073
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4031
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<pre style="margin: 0;"> <span id="LC4031" class="line" lang="cpp"> <span class="p">}</span></span>
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4074
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4032
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<pre style="margin: 0;"> <span id="LC4032" class="line" lang="cpp"></span>
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4033
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<pre style="margin: 0;">+<span id="LC4033" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">l_merge_tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">state</span><span class="p">.</span><span class="n" style="color: #333;">getDirectoryForMerge</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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4034
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<pre style="margin: 0;">+<span id="LC4034" class="line" lang="cpp"></span>
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4035
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<pre style="margin: 0;">+<span id="LC4035" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// p->sortresult.setTempPrefixSingle(l_merge_tmp_dir);</span></span>
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4036
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<pre style="margin: 0;">+<span id="LC4036" class="line" lang="cpp"></span>
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4075
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4037
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<pre style="margin: 0;"> <span id="LC4037" class="line" lang="cpp"> <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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4076
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4038
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<pre style="margin: 0;"> <span id="LC4038" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> std::ostringstream tmpstr;</span></span>
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4077
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4039
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<pre style="margin: 0;"> <span id="LC4039" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> tmpstr << options.tmpfilenamebase << "_" << std::setfill('0') << std::setw(6) << (mtmpid++);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4080" 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="4042" 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">@@ -4080,6 +4042,8 @@ namespace libmaus2</td>
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4080
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4042
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<pre style="margin: 0;"> <span id="LC4042" 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;">ostringstream</span> <span class="n" style="color: #333;">sparsetmpstr</span><span class="p">;</span></span>
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4081
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4043
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<pre style="margin: 0;"> <span id="LC4043" class="line" lang="cpp"> <span class="n" style="color: #333;">sparsetmpstr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">sparsetmpfilenamebase</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_"</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;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">'0'</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;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">mtmpid</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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4082
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4044
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<pre style="margin: 0;"> <span id="LC4044" class="line" lang="cpp"></span>
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4045
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<pre style="margin: 0;">+<span id="LC4045" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::size_t const gt_expected = state.getMergeGTExpected(p);</span></span>
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4046
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<pre style="margin: 0;">+<span id="LC4046" class="line" lang="cpp"></span>
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4083
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4047
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<pre style="margin: 0;"> <span id="LC4047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bwtb3m</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">)</span></span>
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4084
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4048
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<pre style="margin: 0;"> <span id="LC4048" class="line" lang="cpp"> <span class="p">{</span></span>
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4085
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4049
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<pre style="margin: 0;"> <span id="LC4049" class="line" lang="cpp"> <span class="n" style="color: #333;">mergeBlocks</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4140" 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="4104" 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">@@ -4140,6 +4104,10 @@ namespace libmaus2</td>
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4140
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4104
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<pre style="margin: 0;"> <span id="LC4104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">logstr</span> <span class="p">)</span></span>
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4141
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4105
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<pre style="margin: 0;"> <span id="LC4105" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">logstr</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[M"</span><span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">mcnt</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MemUsage</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">autoarray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AutoArrayMemUsage</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;">endl</span><span class="p">;</span></span>
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4142
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4106
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<pre style="margin: 0;"> <span id="LC4106" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4107
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<pre style="margin: 0;">+<span id="LC4107" class="line" lang="cpp"></span>
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4108
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<pre style="margin: 0;">+<span id="LC4108" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::size_t const gt_produced = p->sortresult.getFiles().getGT().size();</span></span>
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4109
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<pre style="margin: 0;">+<span id="LC4109" class="line" lang="cpp"></span>
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4110
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<pre style="margin: 0;">+<span id="LC4110" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "gt_expected=" << gt_expected << " gt_produced=" << gt_produced << std::endl;</span></span>
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4143
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4111
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<pre style="margin: 0;"> <span id="LC4111" class="line" lang="cpp"> <span class="p">}</span></span>
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4144
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4112
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<pre style="margin: 0;"> <span id="LC4112" class="line" lang="cpp"></span>
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4145
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4113
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<pre style="margin: 0;"> <span id="LC4113" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">memperthread</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">mem</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">numthreads</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">numthreads</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#544bbc78e83add663505786a84e9c3021c826425"><strong>src/libmaus2/suffixsort/bwtb3m/MergeStrategyBaseBlock.hpp</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">@@ -33,6 +33,11 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeBlockSortRequest</span> <span class="n" style="color: #333;">sortreq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" 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;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">querypos</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getNumGtTempFilesRequired</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="LC37" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sortresult</span><span class="p">.</span><span class="n" style="color: #333;">getFiles</span><span class="p">().</span><span class="n" style="color: #333;">getGT</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">equal</span><span class="p">(</span><span class="n" style="color: #333;">MergeStrategyBlock</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">O</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="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="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyBaseBlock</span> <span class="k" style="font-weight: 600;">const</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;">O</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#abc051354cc3c15fdf03d1a3a92187108d6dc32c"><strong>src/libmaus2/suffixsort/bwtb3m/MergeStrategyBlock.hpp</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">@@ -238,6 +238,7 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fillNodeMap</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;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span> <span class="n" style="color: #333;">MergeStrategyBlock</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">M</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setParentId</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">parentid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">collectBaseBlockIds</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;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">V</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getNumGtTempFilesRequired</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<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>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">MergeStrategyBlock</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">MSB</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#d74d3fb91360d8a835161a332cb5e683eef62bbb"><strong>src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeBlock.hpp</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">@@ -41,6 +41,15 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* number of children unfinished */</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">unfinishedChildren</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getNumGtTempFilesRequired</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="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">children</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">children</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumGtTempFilesRequired</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;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gaprequests</span> <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;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumGtTempFilesRequired</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;">n</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fillNodeMap</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;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span> <span class="n" style="color: #333;">MergeStrategyBlock</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">M</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>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">M</span><span class="p">[</span><span class="n" style="color: #333;">nodeid</span><span class="p">]</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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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#f5317e989ea71106d5c87c33e735f9a00a3f4d6c"><strong>src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequest.hpp</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">@@ -38,6 +38,11 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">into</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" 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="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">suffixsort</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BwtMergeZBlock</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">zblocks</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getNumGtTempFilesRequired</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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">zblocks</span><span class="p">.</span><span class="n" style="color: #333;">size</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>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">==</span><span class="p">(</span><span class="n" style="color: #333;">MergeStrategyMergeGapRequest</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">O</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="LC47" class="line" lang="cpp"> <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;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">into</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">O</span><span class="p">.</span><span class="n" style="color: #333;">into</span> <span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/f487c23719ada369798f125fb6b89e15a8dfb4d0#1b92add32e64064816c27ce5d24c732587fa9d20"><strong>src/libmaus2/suffixsort/bwtb3m/MergeTree.hpp</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">@@ -147,6 +147,24 @@ namespace libmaus2</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">getMergeBlocks</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="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;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">V_internal</span><span class="p">,</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" 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;">MergeStrategyMergeInternalSmallBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">V_internal_small</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" 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;">MergeStrategyMergeExternalBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">V_external</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <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="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">node_map</span> <span class="p">)</span> <span class="p">{</span></span>
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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;">auto</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"></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="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</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="n" style="color: #333;">V_internal</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyMergeInternalBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">));</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" 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="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyMergeInternalSmallBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">V_internal_small</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyMergeInternalSmallBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</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="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="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyMergeExternalBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">V_external</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MergeStrategyMergeExternalBlock</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">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="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="p">}</span></span>
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150
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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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151
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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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152
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">MergeTree</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">MT</span><span class="p">)</span></span>
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