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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/alien-hunter">Debian Med / alien-hunter</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/alien-hunter/-/commit/66f6f201b1c67b8395defcf432fcbe8373f6d0d1">66f6f201</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T22:16:25+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/alien-hunter/-/commit/c1d00253fef7e462f4bf1192c7a8c5d99e1bcbd0">c1d00253</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T22:17:12+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Raising Standards version to 4.6.0 (no change)
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/alien-hunter/-/commit/e81dc56adc13d5c5ff6775d789e451b03b9afb35">e81dc56a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T22:17:57+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/alien-hunter/-/commit/48e220e1d1bb06832a01475b5a5b384e8cfebc44">48e220e1</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T22:29:54+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding an explicit cast to comply with new biojava 1.9 implementation
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/alien-hunter/-/commit/ca1711855a8eb0486c77426d00afd418bddf9623">ca171185</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T23:12:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to experimental
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ce413548740c417114d8499e502a89a17462349b">
<span class="new-file">
+
debian/patches/20_type_StatePath_States.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">alien-hunter (1.7-9) experimental; urgency=medium</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Adding an explicit cast to comply with new biojava 1.9 implementation</span>
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<td class="new_line diff-line-num new" data-linenumber="6" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Raising Standards version to 4.6.0 (no change)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="8" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> Sun, 10 Apr 2022 22:30:11 +0200</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">alien-hunter (1.7-8) unstable; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,9 +4,9 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> libbiojava-java,</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> libbiojava-java<span class="idiff left right addition"> (>= 1:1.9.5+dfsg)</span>,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> default-jdk</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right deletion">5.1</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right addition">6.0</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/alien-hunter</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/alien-hunter.git</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://www.sanger.ac.uk/science/tools/alien-hunter</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">@@ -17,7 +17,7 @@ Architecture: all</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libbytecode-java,</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> libbiojava-java,</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> libbiojava-java<span class="idiff left right addition"> (>= 1:1.9.5+dfsg)</span>,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libcommons-cli-java,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> libcommons-collections3-java,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libcommons-dbcp-java,</span>
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<li id="ce413548740c417114d8499e502a89a17462349b">
<a href="https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623#ce413548740c417114d8499e502a89a17462349b"><strong>debian/patches/20_type_StatePath_States.patch</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: casting an Object to String to comply to biojava 1.9 implementation</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/ChangepointLeft.java</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> for(int j = i*60; j < Math.min((i+1)*60, statePath.length()); j++) {</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> //System.out.print(statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0));</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char state=statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> //it prints the states in binary mode for art user_graph</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> if(state == 'a'){</span>
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17
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ChangepointRight.java</span></span>
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19
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> for(int j = i*60; j < Math.min((i+1)*60, statePath.length()); j++) {</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> //System.out.print(statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0));</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char state=statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0);</span></span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char state=statePath.symbolAt((String)(StatePath.STATES), j+1).getName().charAt(0);</span></span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> count++;</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> //it prints the states in binary mode for art user_graph</span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if(state == 'a'){</span></pre></td>
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<a href="https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">10_fix_classpath.patch</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">10_location_of_perl.patch</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">20_type_StatePath_States.patch</span></pre></td>
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<a href="https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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 @@ executable=alien_hunter</td>
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> dh $@</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_auto_build:</span>
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9
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation -Xlint:unchecked *.java</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> CLASSPATH=/usr/share/java/biojava<span class="idiff left right addition">-core</span>.jar javac -Xlint:deprecation -Xlint:unchecked *.java</span>
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10
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">override_dh_auto_clean:</span>
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12
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12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> rm -f *.class $(executable).1</span>
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