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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/hisat2">Debian Med / hisat2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/4ef97c9b487a9ab25dba854109eb78fea5ec1308">4ef97c9b</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-27T16:55:24+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/riscv5: fix compilation on riscv5
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<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/b3a001b6a035e318f0ab954e91f21a17e9579320">b3a001b6</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-27T17:34:03+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
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<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/5c4b14b9b0cbab8d6667ac3848219e7942101290">5c4b14b9</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-27T17:34:32+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
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<h4>4 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="#b0b5d0b5434debb7bde2b700fc3de6e2397593c6">
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+
debian/patches/riscv5
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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/hisat2/-/compare/ef149b86ac639fd8bafcd909f62ad912a8124e1a...5c4b14b9b0cbab8d6667ac3848219e7942101290#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hisat2 (2.2.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debian/patches/riscv5: fix compilation on riscv5</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</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"> -- Michael R. Crusoe <crusoe@debian.org> Wed, 27 Jan 2021 17:34:32 +0100</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">hisat2 (2.2.1-1) 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"> [ Steffen Moeller ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/hisat2/-/compare/ef149b86ac639fd8bafcd909f62ad912a8124e1a...5c4b14b9b0cbab8d6667ac3848219e7942101290#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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="8" 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">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> help2man <!nodoc>,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> pandoc <!nodoc>,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3:any <!nodoc></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/hisat2</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/hisat2.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://daehwankimlab.github.io/hisat2/</span>
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<li id="b0b5d0b5434debb7bde2b700fc3de6e2397593c6">
<a href="https://salsa.debian.org/med-team/hisat2/-/compare/ef149b86ac639fd8bafcd909f62ad912a8124e1a...5c4b14b9b0cbab8d6667ac3848219e7942101290#b0b5d0b5434debb7bde2b700fc3de6e2397593c6"><strong>debian/patches/riscv5</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Fix compilation on riscv5</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;">--- hisat2.orig/alphabet.cpp</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;">+++ hisat2/alphabet.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -400,7 +400,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </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;">-char mask2iupac[16] = {</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;">+int mask2iupac[16] = {</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> -1,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 'A', // 0001</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 'C', // 0010</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hisat2.orig/alphabet.h</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hisat2/alphabet.h</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -65,7 +65,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> /// corresponding 2-bit nucleotide</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> extern uint8_t nuccol2nuc[5][5];</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> /// Convert a 4-bit mask into an IUPAC code</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extern char mask2iupac[16];</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;">+extern int mask2iupac[16];</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"> /// Convert an ascii color to an ascii dna char</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> extern char col2dna[];</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;">--- hisat2.orig/sstring.h</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;">+++ hisat2/sstring.h</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -3326,7 +3326,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> char toChar(size_t idx) const {</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> assert_range((int)this->cs_[idx], 0, 15);</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return mask2iupac[(int)this->cs_[idx]];</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;">+ return (char)mask2iupac[(int)this->cs_[idx]];</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> /**</span></pre>
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<a href="https://salsa.debian.org/med-team/hisat2/-/compare/ef149b86ac639fd8bafcd909f62ad912a8124e1a...5c4b14b9b0cbab8d6667ac3848219e7942101290#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">@@ -5,3 +5,4 @@ compilerflags</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">simde</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">python3</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">fix-manual</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">riscv5</span></pre>
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