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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedtools">Debian Med / bedtools</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a">7e36fe2e</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-01-23T11:47:03+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed build failure.
</pre>
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<h4>4 changed files:</h4>
<ul>
<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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<a href="#49ca19704f11c8ca01105bc2a3f3cf7983aa49f0">
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+
debian/patches/fix_intersect_test.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bedtools (2.29.2+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bedtools (2.29.2+dfsg-1) <span class="idiff left right">unstable</span>; 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"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right">* BLOCKER: Tests for 'intersect' fail</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> https://github.com/arq5x/bedtools2/issues/814</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fixed failing intersect.new #78 test as instructed on</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> https://github.com/arq5x/bedtools2/issues/814</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right">* Standard-Version: 4.5.0</span></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"> -- Steffen Moeller <moeller@debian.org> Sat, 18 Jan 2020 01:44:47 +0100</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<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">@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> liblzma-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> samtools</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bedtools</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bedtools.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/arq5x/bedtools2</span>
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<a href="https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a#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="gh" style="color: #999;">Index: bedtools/test/intersect/new_test-intersect.sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/intersect/new_test-intersect.sh</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -975,8 +975,8 @@</span> rm exp obs</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> # Test intersect preserve the text header in bam</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> ############################################################</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> echo -e " intersect.new.t78...\c"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo -e "@HD VN:1.5 SO:coordinate" > exp</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo "@HD VN:1.5 SO:coordinate" | samtools view -b | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo -e "@HD VN:1.5 SO:coordinate" > exp</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "@HD VN:1.5 SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> check exp obs</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> rm exp obs</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> [[ $FAILURES -eq 0 ]] || exit 1;</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,3 +6,4 @@ remove_barski_binding_site.png.patch</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># not Debian-specific, upstream has worked on that, too</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">#flag_no_overwrite</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">fix_intersect_test.patch</span></pre>
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