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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/milib">Debian Med / milib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/49df3ad1300032a9cabc7b9de7d6946294ff42d8">49df3ad1</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:31:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/03ca7e47bdefe055d227cde5e123bc3d5293bc66">03ca7e47</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:31:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.13</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/079163b20f6f22a5a7249fc42e492b20c74a0f6b">079163b2</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:31:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.13'
Update to upstream version '1.13'
with Debian dir 56d928ae73523651fb1efb8272b0dc30dac79b9f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/f9ab1e167c2d119eb8103e6967531821d661c793">f9ab1e16</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:31:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/249c65e23a79dd54252537d8cbae00b0bbab7f25">249c65e2</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:31:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/b96278bc104343fb64f864c7b4df0b443d4164cf">b96278bc</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:32:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/fd519d64c2d3bbf65d79d5eed02312cabc9a8d4d">fd519d64</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:32:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/milib/-/commit/afc51608b61ee2c15cabcf4eedbf2f9bd9ec6e9f">afc51608</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-13T21:40:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Addressed FTBFS
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#d6354b0fe764a3a8308bbe501b7c172d4ca0171e">
debian/patches/jaxb.patch
</a>
</li>
<li class="file-stats">
<a href="#e7bd6732713676cce9d73c2c0fa62970153d0c9d">
<span class="new-file">
+
debian/patches/removeHostnameFromPomXml.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#bf3de485311a96f3adb884ed6a20110983f6ccc9">
init.sh
</a>
</li>
<li class="file-stats">
<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">
pom.xml
</a>
</li>
<li class="file-stats">
<a href="#9d54a1ab46c2ed9cac7e8bd7b7a17e22c50e4a68">
src/main/java/com/milaboratory/cli/ACommandWithSmartOverwriteWithSingleInput.java
</a>
</li>
<li class="file-stats">
<a href="#f94ece8dfd56cc1ce69f456f09f03bd061329d90">
src/main/java/com/milaboratory/core/Range.java
</a>
</li>
<li class="file-stats">
<a href="#d30548631ae99562207840c92d23c2cda6e82368">
src/main/java/com/milaboratory/core/alignment/Alignment.java
</a>
</li>
<li class="file-stats">
<a href="#9941b4e602de710ce53af87a1e20b60f2108e6b6">
<span class="new-file">
+
src/main/java/com/milaboratory/core/alignment/AlignmentElement.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#fc56abea593d723499169f3756c5fed25950efe4">
<span class="new-file">
+
src/main/java/com/milaboratory/core/alignment/AlignmentElementType.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#545881f00a0d0747e68f31f7f99f39f61504beb8">
src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java
</a>
</li>
<li class="file-stats">
<a href="#1874bfd036f7e14047ca4e458ba23b5a9e088374">
src/main/java/com/milaboratory/core/sequence/AminoAcidSequence.java
</a>
</li>
<li class="file-stats">
<a href="#5561e666532b3b453213c61963110cd1774d062d">
src/main/java/com/milaboratory/core/sequence/GeneticCode.java
</a>
</li>
<li class="file-stats">
<a href="#a53c88c7b896b60f4bb8da5302bb1314ed8abdea">
src/main/java/com/milaboratory/core/sequence/NucleotideSequence.java
</a>
</li>
<li class="file-stats">
<a href="#e120a4fe12d77829e958bf6a2e8e14b143dfc5ba">
src/main/java/com/milaboratory/core/sequence/SequencesUtils.java
</a>
</li>
<li class="file-stats">
<a href="#c5a9e0d8e5b6ed2d241dd1417ef21fa0c1889b69">
src/main/java/com/milaboratory/core/sequence/Wildcard.java
</a>
</li>
<li class="file-stats">
<a href="#8024ecd5b10c0b93d3991fa11b58692e9a97b0a4">
src/main/java/com/milaboratory/core/sequence/quality/QualityTrimmer.java
</a>
</li>
<li class="file-stats">
<a href="#513eac4b9486839d9fff59bdabc4ada6b307c1e1">
src/main/java/com/milaboratory/core/sequence/quality/ReadTrimmerReport.java
</a>
</li>
<li class="file-stats">
<a href="#17299f92228991eb94a2a05627982c35b7ec64c3">
src/main/java/com/milaboratory/util/VersionInfo.java
</a>
</li>
<li class="file-stats">
<a href="#2a6bcceeb5a423b4d775c94e3152cd9926ce5211">
src/main/resources/parameters/kaligner_parameters.json
→
src/main/resources/parameters_resource/kaligner_parameters.json
</a>
</li>
<li class="file-stats">
<a href="#e7c3e0452e271a2b2e5b17ba06eb5f201a72161e">
src/test/java/com/milaboratory/core/alignment/AlignmentTest.java
</a>
</li>
<li class="file-stats">
<a href="#afbb798c5ec71ce698a213ea62d7bb00c00dbd3a">
src/test/java/com/milaboratory/core/motif/MotifUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#9f6dbdcb50c013e3c6c05d41cefc28f379e30997">
<span class="new-file">
+
src/test/java/com/milaboratory/core/sequence/GeneticCodeTest.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#68a3596717095221f2b2fa630afb69d0e338b829">
src/test/java/com/milaboratory/core/sequence/NucleotideSequencesTest.java
</a>
</li>
<li class="file-stats">
<a href="#b3ee3da7c33a6e1e5272695a812186e8dad5a1c5">
src/test/java/com/milaboratory/core/sequence/SequencesUtilsTest.java
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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<p style="font-size: small; color: #777;">
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<a href="https://salsa.debian.org/med-team/milib/-/compare/65157c35b8cbe14928d7ff056b14cbb2ae96c779...afc51608b61ee2c15cabcf4eedbf2f9bd9ec6e9f">View it on GitLab</a>.
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