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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedtools">Debian Med / bedtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/24473a22bc2de1443a2d1e5138317e644a06ada0">24473a22</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-10-28T16:40:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permisions of .sam files
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/7d70784388073ae200f359e43a6da8f074c94729">7d707843</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-10-28T16:41:15+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Delete test binary to make sure it will not be installed
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/438dfd51ae9fcd6429bff4bdef1328ae54b98aab">438dfd51</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-10-28T16:41:40+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#49ca19704f11c8ca01105bc2a3f3cf7983aa49f0">
debian/patches/fix_intersect_test.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/9889a387f292fabdb790f306a905cf805a56e55b...438dfd51ae9fcd6429bff4bdef1328ae54b98aab#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">bedtools (2.29.2+dfsg-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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3
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Remove the need for samtools via patch from upstream.</span>
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<td class="diff-line-num new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Include patch from Bernhard Übelacker to fix 32-bit builds. TODO: the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">@@ -9,6 +10,11 @@ bedtools (2.29.2+dfsg-4) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num new_line" data-linenumber="10" 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new_line" data-linenumber="11" 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new_line" data-linenumber="12" 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">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Fix permisions of .sam files</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * Delete test binary to make sure it will not be installed</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> * DEP3</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 14 Feb 2020 16:50:58 +0100</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">bedtools (2.29.2+dfsg-3) unstable; urgency=medium</span>
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<li id="49ca19704f11c8ca01105bc2a3f3cf7983aa49f0">
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/9889a387f292fabdb790f306a905cf805a56e55b...438dfd51ae9fcd6429bff4bdef1328ae54b98aab#49ca19704f11c8ca01105bc2a3f3cf7983aa49f0"><strong>debian/patches/fix_intersect_test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-01-23 11:47:03 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix the intersect test</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Index: bedtools/test/intersect/new_test-intersect.sh</span>
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2
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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3
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/intersect/new_test-intersect.sh</span></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/9889a387f292fabdb790f306a905cf805a56e55b...438dfd51ae9fcd6429bff4bdef1328ae54b98aab#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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="diff-line-num unfold js-unfold new_line" data-linenumber="43" 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">@@ -43,6 +43,7 @@ override_dh_fixperms-arch:</td>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> chmod -x $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/bedtools/genomes/*.genome</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> find $(CURDIR)/debian -name "*.bed" -executable -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> find $(CURDIR)/debian -name "*.sam" -executable -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> find $(CURDIR)/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;</span>
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47
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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48
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">override_dh_auto_test:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,6 +52,7 @@ ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386 armel armhf mipse</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> mv test/shuffle debian/</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> find . -name htsutil -delete</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386 armel armhf mipsel))</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> mv debian/shuffle test/</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">endif</span>
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