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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/sumaclust">Debian Med / sumaclust</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumaclust/-/commit/b68b92e69e30f83d0a42946a5ad8195515da35ee">b68b92e6</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-08T21:49:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reading ACGT-only sequences safely
Better handling of line changes
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/sumaclust/-/commit/1aa21e7dde4907231c67fe9e91da8d91d54316b2">1aa21e7d</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-04-08T21:57:46+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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<h4>3 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="#72ce93e2d13b8015cb294d3c8b4aac4bfbf1aa6a">
<span class="new-file">
+
debian/patches/reading_only_ACGT_sequences_safely.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/954b3e6a483f5015fc15c858211fd971848b8628...1aa21e7dde4907231c67fe9e91da8d91d54316b2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sumaclust (1.0.35-3) 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"> * Adding a patch to read ACGT-only sequences safely, fixing regression</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> on amd64 (Closes: #956232)</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"> -- Pierre Gruet <pgtdebian@free.fr> Wed, 08 Apr 2020 21:49:49 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">sumaclust (1.0.35-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Updating fix_build patch after new upstream version</span>
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<li id="72ce93e2d13b8015cb294d3c8b4aac4bfbf1aa6a">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/954b3e6a483f5015fc15c858211fd971848b8628...1aa21e7dde4907231c67fe9e91da8d91d54316b2#72ce93e2d13b8015cb294d3c8b4aac4bfbf1aa6a"><strong>debian/patches/reading_only_ACGT_sequences_safely.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Wed, 8 Apr 2020 11:18:01 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Subject: Reading only-ACGT sequences safely</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">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> sumalibs/libfasta/sequence.c | 10 ++++++++--</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 1 file changed, 8 insertions(+), 2 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">diff --git a/sumalibs/libfasta/sequence.c b/sumalibs/libfasta/sequence.c</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index 2cf3d10..db999f8 100755</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sumalibs/libfasta/sequence.c</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;">+++ b/sumalibs/libfasta/sequence.c</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -162,19 +162,25 @@</span> void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> char* seqTemp;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> char c;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int32_t index = 0, seqIndex = 0, len = strlen(seq);</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int32_t index = 1, seqIndex = 0, len = strlen(seq);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> char* seqAlphabets = "acgtACGT";</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> int notAllATGC = 0;</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;">+ int goOnParsing = 1;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);</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="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while (index < len)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while (goOnParsing)</span></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"> c = seq[index++];</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> if (strchr(seqAlphabets, c) != NULL)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> seqTemp[seqIndex++] = tolower(c);</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (c == '\n')</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ goOnParsing = 0; //End of line character terminating the sequence has been reached.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> else if (c != '\n')</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> notAllATGC = 1;</span>
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<pre style="margin: 0;">+<span id="LC35" 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="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (index == len)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ goOnParsing = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if (notAllATGC)</span></pre>
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<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/954b3e6a483f5015fc15c858211fd971848b8628...1aa21e7dde4907231c67fe9e91da8d91d54316b2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_build.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">reading_only_ACGT_sequences_safely.patch</span></pre>
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