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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/kmc">Debian Med / kmc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmc/-/commit/2c774faee6366277c0635087864a0b0387eb7dd0">2c774fae</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-08T21:05:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add cap-default-thread-count.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmc/-/commit/21a8986abf04ae4a18ff6a6fda4dc4715246c95e">21a8986a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-08T21:07:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix d/watch to find newer upstream versions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmc/-/commit/887d06e89860999a01c065917abcd32b71b02705">887d06e8</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-08T21:17:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update autopkgtest
The idea is to test both single-threaded and multi-threaded runs of
kmc. This should allow one to rule out threading specific issues.
There is also a test explicitly specifying a higher thread count,
which is known to break, using kmc 2.3, but which is fixed in kmc
3.1.1. This test is commented out with a fixme marker for the moment.
The problem for now with kmc 3.1.1 is that it dropped support for
almost all architectures, except x86_64, hence not having updated
right away.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmc/-/commit/34231fb9309ff6967bc1e93a34a0fe6f0d5334b4">34231fb9</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-08T21:22:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#6e1b0e482bf583cc58e9f938c81af654e7181ae9">
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+
debian/patches/cap-default-thread-count.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#181f11327f8d244d67aab845056d5536f09b2ccb">
debian/tests/build-lib
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kmc (2.3+dfsg-10) 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"> * Add cap-default-thread-count.patch. (Closes: #954270)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix d/watch to find newer upstream versions.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Update autopkgtest: test single-threaded and default option independently.</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"> -- Étienne Mollier <etienne.mollier@mailoo.org> Tue, 08 Dec 2020 21:21:51 +0100</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">kmc (2.3+dfsg-9) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="6e1b0e482bf583cc58e9f938c81af654e7181ae9">
<a href="https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4#6e1b0e482bf583cc58e9f938c81af654e7181ae9"><strong>debian/patches/cap-default-thread-count.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: cap default thread count to 24 threads</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> New upstream versions fix this issue more appropriately, and past kmc 3 this</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> patch should be dropped. Update to kmc 3 is not obvious due to the new version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> being heavily optimized against x86_64, and failing to build from source on any</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> other architecture sadly.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Bug: https://github.com/refresh-bio/KMC/issues/82#issuecomment-451616129</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954270</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Applied-Upstream: 3.1.1</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 2020-12-08</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kmc.orig/kmc_tools/parameters_parser.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kmc/kmc_tools/parameters_parser.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -60,6 +60,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> //defaults</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> config.avaiable_threads = thread::hardware_concurrency();</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //cap defaults to 24 threads due to Debian Bug#954270</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( config.avaiable_threads > 24 )</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config.avaiable_threads = 24;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> //override defaults if specified</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> for( ; pos < argc && argv[pos][0] == '-' ; ++pos)</span></pre>
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<a href="https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,3 +5,4 @@ hardening</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">0007-Use-standard-compiler-environment-variables.patch</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">spelling</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">newish_gcc_build_fix.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">cap-default-thread-count.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4#181f11327f8d244d67aab845056d5536f09b2ccb"><strong>debian/tests/build-lib</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">@@ -13,12 +13,32 @@ g++ kmc_dump/*cpp -std=c++11 -lkmc -o $WORKDIR/my_kmcdump</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"build: OK"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$WORKDIR</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">kmc <span class="nt" style="color: #000080;">-ci1</span> <span class="nt" style="color: #000080;">-m1</span> <span class="nt" style="color: #000080;">-k28</span> <span class="nv" style="color: #008080;">$ORIGDIR</span>/debian/tests/sample_6.fastq.gz 1 <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Running kmc (single threaded)'</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">kmc <span class="nt" style="color: #000080;">-ci1</span> <span class="nt" style="color: #000080;">-m1</span> <span class="nt" style="color: #000080;">-k28</span> <span class="nt" style="color: #000080;">-t1</span> <span class="nv" style="color: #008080;">$ORIGDIR</span>/debian/tests/sample_6.fastq.gz 1 <span class="nb" style="color: #0086b3;">.</span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-Al</span></span>
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18
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1.kmc_suf <span class="o" style="font-weight: 600;">]</span></span>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1.kmc_pre <span class="o" style="font-weight: 600;">]</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"kmc: OK"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"kmc<span class="idiff left right"> (single threaded)</span>: OK"</span></span>
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21
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell">./my_kmcdump 1 out</span>
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23
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> out <span class="o" style="font-weight: 600;">]</span></span>
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24
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run: OK"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FIXME: uncomment the below test once kmc is updated to version 3.1.1 or more.</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Multi-threaded runs have been known to be faulty (#954270).</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo 'Running kmc (32 threads)'</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#rm -f 1.kmc_suf 1.kmc_pre</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#kmc -ci1 -m1 -k28 -t32 $ORIGDIR/debian/tests/sample_6.fastq.gz 1 .</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#ls -Al</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#[ -s 1.kmc_suf ]</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#[ -s 1.kmc_pre ]</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo "kmc (32 threads): OK"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># In the end, default options should, ideally, work on any configuration.</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Running kmc (default thread count)'</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> 1.kmc_suf 1.kmc_pre</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">kmc <span class="nt" style="color: #000080;">-ci1</span> <span class="nt" style="color: #000080;">-m1</span> <span class="nt" style="color: #000080;">-k28</span> <span class="nv" style="color: #008080;">$ORIGDIR</span>/debian/tests/sample_6.fastq.gz 1 <span class="nb" style="color: #0086b3;">.</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-Al</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1.kmc_suf <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1.kmc_pre <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"kmc (default thread count): OK"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kmc/-/compare/090409638404d0682d00f03cb8478d0caac64a4c...34231fb9309ff6967bc1e93a34a0fe6f0d5334b4#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@ version=4</td>
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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">opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/kmc_$1.tar.gz/" \</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> https://github.com/marekkokot/KMC/releases \</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> .*/archive/<span class="idiff left right">v?</span>(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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