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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/kmc">Debian Med / kmc</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/138139b6c593e31ea5a9ab6ea61cc9fe4094b1c4">138139b6</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:22:14+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/b2aeea28a47c7e2027f92a287296eccf8992a579">b2aeea28</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:22:15+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 3.2.2+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/6358df74d06ded2a5da4dcc02e6ca377f33700d3">6358df74</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:22:16+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/3.2.2+dfsg'
Update to upstream version '3.2.2+dfsg'
with Debian dir 8fff6d5c6d6eb16c8bdd5ae7b8c12c5e8d050398</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/76c28005433dee9f861ec02cc275fbd7d5d76296">76c28005</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:22:16+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Standards-Version: 4.6.2
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/73a8656fdfa38f08d1b2d489c02c1c0b45cda094">73a8656f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:22:31+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/17626d22cd6aa023568cd7b5f4e04df0ae21e2e8">17626d22</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:32:50+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>use-shared-libs patch: refresh; forward not-needed.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/e84c68c1a2ba4c6e7c16623f4e5ca5dcc2729343">e84c68c1</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:44:12+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>makefile.patch: refresh; forwarding not-needed.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/68444b4673a1e6408b6ad6d249626e5edb895a15">68444b46</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:46:31+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>0005-Add-static-library-target-to-makefile.patch: refresh.
Also, forwarding is deemed not-needed for this yet-another Makefile
change.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/b85413ca119bbbc6bb243863a6bc26c1b454ffa9">b85413ca</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T10:47:29+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>disable-python-bindings.patch: refresh.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/a73564a9c171f81c8eeac61e2775049e3066eb21">a73564a9</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T11:04:26+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>makefile.patch: fixup.
We want CXXFLAGS to include -fsigned-char to spare ourselves some
char related patches.
Gbp-Dch: ignore
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/633c229a0cb1fc2f2c2a66f95be98b8e209c8604">633c229a</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T11:05:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>simde patch: refresh.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/a505a826079a8a315ccf1a88b6aaff557f097768">a505a826</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T11:05:40+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>support-mixed-march.patch: refresh.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/0429b35f672edbf645dc03cf93deab8ed75b4cd3">0429b35f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T11:14:00+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>simde patch: fix missing endif.
Gbp-Dch: ignore
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/b258550a72bf280920ec8d0f6a63253b0cf8daea">b258550a</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T11:18:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>remove last occurrence to 3rd_party in Makefile.
This change is yet another fixup to makefile.patch, which also
restores 0005-Add-static-library-target-to-makefile.patch in its
original state.
Gbp-Dch: ignore
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kmc/-/commit/b80a4bb1aad615cdd24477a1e50df34c65c816ad">b80a4bb1</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-17T11:21:05+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>update changelog
Note that the new kmc version is still affected by #1037708.
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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.github/workflows/main.yml
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.gitignore
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<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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debian/changelog
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debian/control
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debian/patches/0005-Add-static-library-target-to-makefile.patch
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debian/patches/disable-python-bindings.patch
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debian/patches/makefile.patch
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debian/patches/simde
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debian/patches/support-mixed-march.patch
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debian/patches/use-shared-libs
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kmc.sln
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kmc_api/kmc_file.cpp
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kmc_api/kmc_file.h
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kmc_api/kmer_api.cpp
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kmc_api/kmer_api.h
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kmc_api/kmer_defs.h
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kmc_api/mmer.cpp
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kmc_api/mmer.h
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kmc_core/bam_utils.h
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kmc_core/binary_reader.h
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kmc_core/bkb_merger.h
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<a href="#3412f84f4765893d3af65f0ee99b77302fb3d531">
kmc_core/bkb_reader.cpp
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<a href="#33000c2ff574159ec4d9660113d815f4200a6a69">
kmc_core/bkb_reader.h
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kmc_core/bkb_sorter.h
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The diff was not included because it is too large.
</h5>
</div>
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