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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/soapaligner">Debian Med / soapaligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/commit/0a7d74828ab909ff1ab0f6c9cfeb7d2dd37ee9b2">0a7d7482</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-05T13:04:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Architecture: any-amd64 x32
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/commit/191005b3a22a8facd889c8756e0c5c5754c17611">191005b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-05T13:44:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Force propagation of hardening options (no idea why this is necessary)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/commit/296ab910cdf7a92792bd8de070de171342166ee0">296ab910</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-05T13:50:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/commit/7e8bd159fa492b883bdea5adefabda1eb67aaf16">7e8bd159</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-05T13:51:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#f110b569f01a58cd8e5c4c5b37fecc1c94f619b5">
debian/patches/linkerror.patch
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
<span class="new-file">
+
debian/patches/spelling.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">soapaligner (2.20-3) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</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"> * Architecture: any-amd64 x32</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #903003</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * More sensible date for reproducible builds (SOURCE_DATE_EPOCH)</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Force propagation of hardening options</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Fix spelling</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 05 Jul 2018 13:51:03 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">soapaligner (2.20-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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="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 @@ Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: http://soap.genomics.org.cn/soapaligner.html</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Package: soapaligner</span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Architecture: any<span class="idiff left right">-amd64 x32</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Description: aligner of short reads of next generation sequencers</span>
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<li id="f110b569f01a58cd8e5c4c5b37fecc1c94f619b5">
<a href="https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16#f110b569f01a58cd8e5c4c5b37fecc1c94f619b5"><strong>debian/patches/linkerror.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">@@ -2,11 +2,9 @@ Author: Steffen Moeller</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Last-Update: 2018-05-04 18:33:03 +0200</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Description: Fix build</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 class="gh" style="color: #999;">Index: soapaligner/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- soapaligner.orig/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ soapaligner/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -32,8 +32,8 @@ ifeq (YES, $(PROFILE))</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -37,8 +37,8 @@ ifeq (YES, $(PROFILE))</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> CFLAGS += $(PROFILE_FLAGS)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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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">@@ -17,16 +15,14 @@ Index: soapaligner/Makefile</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> .SUFFIX: .c .o</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> .c.o:</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">65,3 +65</span>,5 @@ kstring.o:kstring.h</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">70,3 +70</span>,5 @@ kstring.o:kstring.h</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> clean:</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> rm -f *.o $(PROG)</span>
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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;">+</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;">+.PHONY: clean</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gh" style="color: #999;">Index: soapaligner/Match.c</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- soapaligner.orig/Match.c</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ soapaligner/Match.c</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Match.c</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Match.c</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -74,7 +74,8 @@</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"> }</span>
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<a href="https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16#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">compiler_options.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">linkerror.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">UsageDoublette.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">spelling.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix spelling</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Thu, 05 Jul 2018 13:04:29 +0200</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/soap.1</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/soap.1</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -69,7 +69,7 @@ Totally allowed mismatches in one read,</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> Allow gap size in one read, [0]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> .TP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> .B -M INT</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;">-Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]</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;">+Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> .RS</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> .TP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> 0: exact match only</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -88,7 +88,7 @@ SOAP2 output format contains following c</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> .PP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> 1. reads name / reads ID (if -t is available)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> .P</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;">-2. reads sequence (if read align to reverse strand, here is the reverse sequence of orignal read)</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;">+2. reads sequence (if read align to reverse strand, here is the reverse sequence of original read)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> .P</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> 3. quality sequence (if input is fasta reads, the column will be all 'h', and the sequence is backward if reads mapping reverse )</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> .P</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;">--- a/soap.c</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;">+++ b/soap.c</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -119,7 +119,7 @@ static void Usage(void) {</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> fprintf(stdout, "\t-b <str> query b file\n");</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> fprintf(stdout, "\t-D <str> reference sequences indexing table, *.index format\n");</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> fprintf(stdout, "\t-o <str> output alignment file(txt)\n");</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;">- fprintf(stdout, "\t-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]\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;">+ fprintf(stdout, "\t-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> "\t 0: exact match only\n"</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> "\t 1: 1 mismatch match only\n"</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> "\t 2: 2 mismatch match only\n"</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/soap.man</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;">+++ b/soap.man</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -71,7 +71,7 @@ CCOOMMMMAANNDD AANNDD OOPPT</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> --gg IINNTT Allow gap size in one read, [0]</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> --MM IINNTT Match mode for each read or the seed part of read, which</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- shouldn't contain more than 2 mismaches, [4]</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;">+ shouldn't contain more than 2 mismatches, [4]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> 0: exact match only</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -2,14 +2,13 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -*- makefile -*-</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Uncomment this to turn on verbose mode.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">DEB_BUILD_MAINT_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">DH_VERBOSE</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">DFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-DMAKE_TIME</span><span class="o" style="font-weight: 600;">=</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"be reproducible"</span><span class="se" style="color: #d14;">\"</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-flto</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-flto</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-Wl</span>,-flto</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">DFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-DMAKE_TIME</span><span class="o" style="font-weight: 600;">=</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"SOURCE_DATE_EPOCH"</span><span class="se" style="color: #d14;">\"</span></span>
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11
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">DEB_BUILD_MAINT_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">CFLAGS</span><span class="o" style="font-weight: 600;">:=</span><span class="nt" style="color: navy;">-flto</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-buildflags <span class="nt" style="color: navy;">--get</span> CFLAGS<span class="nv" style="color: teal;">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">CXXFLAGS</span><span class="o" style="font-weight: 600;">:=</span><span class="nt" style="color: navy;">-flto</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-buildflags <span class="nt" style="color: navy;">--get</span> CXXFLAGS<span class="nv" style="color: teal;">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">LDFLAGS</span><span class="o" style="font-weight: 600;">:=</span><span class="nt" style="color: navy;">-Wl</span>,-flto <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-buildflags <span class="nt" style="color: navy;">--get</span> LDFLAGS<span class="nv" style="color: teal;">)</span></span>
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13
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></span>
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14
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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15
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"> dh <span class="nv" style="color: teal;">$@</span> </span></pre>
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