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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kraken2">Debian Med / kraken2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken2/-/commit/48fd98765e2e0f5d6af41ed6baa9608bc4fbe917">48fd9876</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-12T23:23:46+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.1</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
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docs/MANUAL.html
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docs/top.html
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<li class="file-stats">
<a href="#82902ec2642f154b058c3bb5e4075825a0309054">
install_kraken2.sh
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<li class="file-stats">
<a href="#60d24a9b10d0c9b92816752f0cb482ca74a70e81">
scripts/standard_installation.sh
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<li class="file-stats">
<a href="#f30b8b3c4747cea09ac3e97bb6227cd001693d6c">
src/hyperloglogplus.h
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/kraken2/-/commit/48fd98765e2e0f5d6af41ed6baa9608bc4fbe917#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.1.1] - 2020-11-08</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">-</span> Compilation error with GCC 10, omission of cstdint header</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">-</span> Removed --skip-maps from standard install due to addition of plasmids,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"> which require acc/taxid maps</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.1.0] - 2020-10-13</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Added</span></span>
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<a href="https://salsa.debian.org/med-team/kraken2/-/commit/48fd98765e2e0f5d6af41ed6baa9608bc4fbe917#4ed8d2333b1b6ed5fa2f86af766e794d0c45ec8a"><strong>docs/MANUAL.html</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pretoc"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: #000080;">></span>Kraken taxonomic sequence classification system<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"version"</span><span class="nt" style="color: #000080;">></span>Version 2.1.<span class="idiff left right">0</span><span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"version"</span><span class="nt" style="color: #000080;">></span>Version 2.1.<span class="idiff left right">1</span><span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="html"> <span class="nt" style="color: #000080;"><p></span>Operating Manual<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pretoc"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: #000080;">></span>Kraken taxonomic sequence classification system<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"version"</span><span class="nt" style="color: #000080;">></span>Version 2.1.<span class="idiff left right">0</span><span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"version"</span><span class="nt" style="color: #000080;">></span>Version 2.1.<span class="idiff left right">1</span><span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="html"> <span class="nt" style="color: #000080;"><p></span>Operating Manual<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<a href="https://salsa.debian.org/med-team/kraken2/-/commit/48fd98765e2e0f5d6af41ed6baa9608bc4fbe917#82902ec2642f154b058c3bb5e4075825a0309054"><strong>install_kraken2.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"2.1.<span class="idiff left right">0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"2.1.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</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="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$2</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<a href="https://salsa.debian.org/med-team/kraken2/-/commit/48fd98765e2e0f5d6af41ed6baa9608bc4fbe917#60d24a9b10d0c9b92816752f0cb482ca74a70e81"><strong>scripts/standard_installation.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +26,7 @@ if [ -n "$KRAKEN2_USE_FTP" ]; then</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">ftp_flag</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--use-ftp"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell">kraken2-build <span class="nt" style="color: #000080;">--db</span> <span class="nv" style="color: #008080;">$KRAKEN2_DB_NAME</span> <span class="nt" style="color: #000080;">--download-taxonomy</span> <span class="nt" style="color: #000080;"><span class="idiff left">--skip-maps</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$masking_flag</span> <span class="nv" style="color: #008080;">$protein_flag</span> <span class="nv" style="color: #008080;">$ftp_flag</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">kraken2-build <span class="nt" style="color: #000080;">--db</span> <span class="nv" style="color: #008080;">$KRAKEN2_DB_NAME</span> <span class="nt" style="color: #000080;">--download-taxonomy</span> <span class="nv" style="color: #008080;">$masking_flag</span> <span class="nv" style="color: #008080;">$protein_flag</span> <span class="nv" style="color: #008080;">$ftp_flag</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell">kraken2-build <span class="nt" style="color: #000080;">--db</span> <span class="nv" style="color: #008080;">$KRAKEN2_DB_NAME</span> <span class="nt" style="color: #000080;">--download-library</span> archaea <span class="nv" style="color: #008080;">$masking_flag</span> <span class="nv" style="color: #008080;">$protein_flag</span> <span class="nv" style="color: #008080;">$ftp_flag</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell">kraken2-build <span class="nt" style="color: #000080;">--db</span> <span class="nv" style="color: #008080;">$KRAKEN2_DB_NAME</span> <span class="nt" style="color: #000080;">--download-library</span> bacteria <span class="nv" style="color: #008080;">$masking_flag</span> <span class="nv" style="color: #008080;">$protein_flag</span> <span class="nv" style="color: #008080;">$ftp_flag</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell">kraken2-build <span class="nt" style="color: #000080;">--db</span> <span class="nv" style="color: #008080;">$KRAKEN2_DB_NAME</span> <span class="nt" style="color: #000080;">--download-library</span> viral <span class="nv" style="color: #008080;">$masking_flag</span> <span class="nv" style="color: #008080;">$protein_flag</span> <span class="nv" style="color: #008080;">$ftp_flag</span></span>
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<li id="f30b8b3c4747cea09ac3e97bb6227cd001693d6c">
<a href="https://salsa.debian.org/med-team/kraken2/-/commit/48fd98765e2e0f5d6af41ed6baa9608bc4fbe917#f30b8b3c4747cea09ac3e97bb6227cd001693d6c"><strong>src/hyperloglogplus.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,24 +5,23 @@</td>
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<pre style="margin: 0;"> <span id="LC5" 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="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7" 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="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Implementation of 64-bit HyperLogLog algorithm by Flajolet et al.,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * with sparse mode for increased precision with low cardinalities (Stefan Heule et al.), and<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Implementation of 64-bit HyperLogLog algorithm by Flajolet et al.,</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * with sparse mode for increased precision with low cardinalities (Stefan Heule et al.), and</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * an improved estimator that does not rely on empirical bias correction data (Otmar Ertl)</span></span>
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<pre style="margin: 0;"> <span id="LC11" 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="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef HYPERLOGLOGPLUS_H_</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define HYPERLOGLOGPLUS_H_</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include<vector></span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include<unordered_set></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "kraken2_headers.h"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define HLL_DEBUG</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define HLL_DEBUG2</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HLL_DEBUG<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HLL_DEBUG</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define D(x) x</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define D(x)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,7 +35,7 @@ typedef unordered_set<uint32_t> SparseListType;</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Other possible SparseList types:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// // typedef vector<uint32_t> SparseListType;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The sorted vector implementation is pretty inefficient currently, as the vector</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// is always kept sorted.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// is always kept sorted.</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// //typedef unordered_set<uint32_t, NoHash<uint32_t> > SparseListType;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// No real performance gain from using the hash value directly - and probably problems</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// with the bucket assignment, since unordered_set expects size_t hashes</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -59,10 +58,10 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">HASH</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bit_mixer</span><span class="p">)</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sparse versions of p and m</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">pPrime</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">25</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// precision when using a sparse representation<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">pPrime</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">25</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// precision when using a sparse representation</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// which encodes the rank + index in 32 bits:</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 25 bits for index +<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 6 bits for rank +<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 25 bits for index +</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 6 bits for rank +</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1 flag bit indicating if bits p..pPrime are 0</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mPrime</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> <span class="n" style="color: #333;">pPrime</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 2^pPrime</span></span>
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<pre style="margin: 0;"> <span id="LC67" 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">@@ -93,10 +92,10 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cardinality</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// returns ertlCardinality()</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// returns ertlCardinality()</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// HLL++ estimator of Heule et al., 2015. Uses empirical bias correction factors</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">heuleCardinality</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">correct_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">heuleCardinality</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">correct_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC96" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Improved estimator of Ertl, 2017. Does not rely on empirical data</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">ertlCardinality</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="LC99" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fla<span class="idiff left right">y</span>olet's cardinality estimator without bias correction</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fla<span class="idiff left right">j</span>olet's cardinality estimator without bias correction</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">flajoletCardinality</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">use_sparse_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC100" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nObserved</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,4 +107,3 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/* HYPERLOGLOGPLUS_H_ */</span></span></pre>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"></span></pre>
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