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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/amos">Debian Med / amos</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b">169d23fe</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-05-02T21:18:35+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Outdated c++, needs considerable work
</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#8c36d68ffcfd2f47eee7a3d364126fbadd14bee7">
<span class="new-file">
+
debian/patches/narrowing.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">amos (3.1.0-1) UNRELEASED; urgency=low</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"> * Initial release (Closes: #897191).</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [Andreas Tille]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Draft packaging</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [Afif Elghraoui]</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Finalized packaging</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> [Steffen Moeller]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Added license text to d/copyright</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * (mostly) fixed narrowing build problem in src/AMOS</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Does not build because of hash_multimap issue</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> -- Afif Elghraoui <afif@ghraoui.name> Wed, 12 Aug 2015 00:52:14 -0700</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,10 +11,10 @@ Build-Depends: debhelper (>= 9),</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python,</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> perl</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.6</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.1.3</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: http://amos.sourceforge.net/</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Vcs-Browser: http<span class="idiff left right">://anonscm.debian.org/cgit/debian-med/amos.git</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Vcs-<span class="idiff left right">Svn: git://anonscm.debian.org/debian-med</span>/amos.git</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Vcs-Browser: http<span class="idiff left right">s://salsa.debian.org/med-team/amos</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Vcs-<span class="idiff left right">Git: https://salsa.debian.org/med-team</span>/amos.git</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: amos-assembler</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -9,3 +9,14 @@ License: Artistic</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Copyright: © 2012 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">License: Artistic</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: Artistic</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> This program is free software; you can redistribute it and/or modify it</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> under the terms of the "Artistic License" which comes with Debian.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> On Debian systems, the complete text of the Artistic License</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> can be found in "/usr/share/common-licenses/Artistic".</span></pre>
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<li id="8c36d68ffcfd2f47eee7a3d364126fbadd14bee7">
<a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b#8c36d68ffcfd2f47eee7a3d364126fbadd14bee7"><strong>debian/patches/narrowing.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: amos/src/AMOS/utility_AMOS.cc</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;">--- amos.orig/src/AMOS/utility_AMOS.cc</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;">+++ amos/src/AMOS/utility_AMOS.cc</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24,6 +24,8 @@ const char COMPLEMENT_DNA[256] =</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> 80, 81,'Y','S','A', 85,'B','W','X','R', 90, 91, 92, 93, 94, 95,</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 96,'t','v','g','h',101,102,'c','d',105,106,'m',108,'k','n',111,</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 112,113,'y','s','a',117,'b','w','x','r',122,123,124,125,126,127,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/*</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ these are not char values</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> 128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -32,6 +34,17 @@ const char COMPLEMENT_DNA[256] =</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> 208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> 224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> 240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255</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;">+*/</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -128, -127, -126, -125, -124, -123, -122, -121, -120, -119, -118,</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;">+ -117, -116, -115, -114, -113, -112, -111, -110, -109, -108, -107,</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -106, -105, -104, -103, -102, -101, -100, -99, -98, -97, -96, -95,</span></span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -94, -93, -92, -91, -90, -89, -88, -87, -86, -85, -84, -83, -82,</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -81, -80, -79, -78, -77, -76, -75, -74, -73, -72, -71, -70, -69,</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -68, -67, -66, -65, -64, -63, -62, -61, -60, -59, -58, -57, -56,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -55, -54, -53, -52, -51, -50, -49, -48, -47, -46, -45, -44, -43,</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;">+ -42, -41, -40, -39, -38, -37, -36, -35, -34, -33, -32, -31, -30,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -29, -28, -27, -26, -25, -24, -23, -22, -21, -20, -19, -18, -17,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -16, -15, -14, -13, -12, -11, -10, -9, -8, -7, -6, -5, -4, -3, -2, -1</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #999;">Index: amos/src/AMOS/inttypes_AMOS.hh</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- amos.orig/src/AMOS/inttypes_AMOS.hh</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ amos/src/AMOS/inttypes_AMOS.hh</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -75,8 +75,12 @@ inline uint8_t Char2Qual (char qual)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> //!</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> inline std::string Decode (NCode_t ncode)</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> {</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX,</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'};</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // this is buggy</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char buff[4];</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buff[0] = ncode%128;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buff[1] = (ncode/256)%128;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buff[2] = (ncode/256/256)%128;</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buff[3] = '\0';</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> return buff;</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">narrowing.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">#DH_VERBOSE = 1</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">DPKG_EXPORT_BUILDFLAGS = 1</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">#</span>DPKG_EXPORT_BUILDFLAGS = 1</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">#</span>include /usr/share/dpkg/default.mk</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">%:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">#override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># ./configure --prefix=$(CURDIR)/debian/tmp --enable-AMOScmp=yes --enable-all=no</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span></pre>
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