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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/kallisto">Debian Med / kallisto</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/801c272bfe1f90d797cf1ac52611ad4f6a2277d5">801c272b</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-05-16T04:47:02+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to avoid segfault - exit with an error
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<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/547fd1b6a0fade81dea21e8f1093b1ef2c6961c6">547fd1b6</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-05-16T04:47:43+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#7ab5f2eb503b73c3e40637ca4af1bb907a9ebf4e">
debian/patches/Check_busOptions.seq_length_before_accessing.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3...547fd1b6a0fade81dea21e8f1093b1ef2c6961c6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kallisto (0.46.2+dfsg-2) UNRELEASED; 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"> * Patch to avoid segfault (Closes: #960368)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sat, 16 May 2020 04:47:12 +0530</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">kallisto (0.46.2+dfsg-1) unstable; urgency=medium</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"> * Team upload.</span>
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<li id="7ab5f2eb503b73c3e40637ca4af1bb907a9ebf4e">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3...547fd1b6a0fade81dea21e8f1093b1ef2c6961c6#7ab5f2eb503b73c3e40637ca4af1bb907a9ebf4e"><strong>debian/patches/Check_busOptions.seq_length_before_accessing.patch</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">@@ -2,13 +2,13 @@ Description: Check busOptions.seq.empty() before trying to access it,</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> to avoid a segfault. More details can be found at the upstream bug.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Pranav Ballaney <ballaneypranav@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Bug: https://github.com/pachterlab/kallisto/issues/254</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368<span class="idiff left right">#15</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-05-16</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></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;">--- a/src/ProcessReads.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/ProcessReads.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -1408,6 +1408,1<span class="idiff left right">2</span> @@</span> void BUSProcessor::processBuffer() {</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1408,6 +1408,1<span class="idiff left right">3</span> @@</span> void BUSProcessor::processBuffer() {</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> std::vector<int> l(jmax,0);</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> bool singleSeq = busopt.seq.size() ==1 ;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,11 +17,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "No seq technology specified.\n";</span></span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "If you believe this is a bug, please report using reportbug.";</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr.flush();</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit(1);</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> const BUSOptionSubstr seqopt = busopt.seq.front();</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -2145,7 +215<span class="idiff left right">1</span>,7 @@</span> void AlnProcessor::processBufferGenome()</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -2145,7 +215<span class="idiff left right">2</span>,7 @@</span> void AlnProcessor::processBufferGenome()</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> rlen2 = seqs[si2].second;</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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