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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/97052bc2de1b271f368dd8415cfafde5356e2fe8">97052bc2</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-25T14:14:12+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reproducible builds: filter out -ffile-prefix-map
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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="#76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
debian/patches/reproducible.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/97052bc2de1b271f368dd8415cfafde5356e2fe8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie2 (2.4.1-5) 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"> * Reproducible builds: filter out -ffile-prefix-map</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #961494</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"> -- Andreas Tille <tille@debian.org> Mon, 25 May 2020 14:13:25 +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">bowtie2 (2.4.1-4) 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"> * Team upload.</span>
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<li id="76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/97052bc2de1b271f368dd8415cfafde5356e2fe8#76258ff6f1526200cf3fda90e9f37fd9ee4b4364"><strong>debian/patches/reproducible.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">@@ -3,9 +3,9 @@ Description: make build reproducible</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> hostname, time, etc. from the binary. It also ensures a stable</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> sorting order for all wildcard expansions in the Makefile.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <sascha@steinbiss.name></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">bowtie2.orig</span>/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b<span class="idiff left right">owtie2</span>/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -31,7 +31,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" 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="LC8" class="line" lang="diff"><span class="p">@@ -31,7 +31,7 @@</span><span class="idiff left right"> CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> CXX ?= $(CPP)</span>
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<pre style="margin: 0;"> <span id="LC11" 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">@@ -14,20 +14,20 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> BOWTIE_MM := 1</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> BOWTIE_SHARED_MEM :=</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"><span class="p">@@ -236,8 +236,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -236,8 +236,8 @@</span><span class="idiff left right"> DEBUG_FLAGS := -O0 -g3 $(SSE_FLAG)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> RELEASE_FLAGS := -O3 $(SSE_FLAG) -funroll-loops -g3</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> NOASSERT_FLAGS := -DNDEBUG</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> FILE_FLAGS := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(CXXFLAGS)\""</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(DEBUG_FLAGS) $(CXXFLAGS))\""</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(RELEASE_FLAGS) $(CXXFLAGS))\""</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%<span class="idiff left right"> -ffile-prefix-map=%</span>,$(DEBUG_FLAGS) $(CXXFLAGS))\""</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%<span class="idiff left right"> -ffile-prefix-map=%</span>,$(RELEASE_FLAGS) $(CXXFLAGS))\""</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> BOWTIE2_BIN_LIST := bowtie2-build-s \</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> bowtie2-build-l \</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;">--- <span class="idiff left right">bowtie2.orig</span>/bt2_build.cpp</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;">+++ b<span class="idiff left right">owtie2</span>/bt2_build.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="p">@@ -561,15 +561,15 @@</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;">--- <span class="idiff left right">a</span>/bt2_build.cpp</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;">+++ b/bt2_build.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -561,15 +561,15 @@</span><span class="idiff left right"> int bowtie_build(int argc, const char **</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> } else {</span>
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32
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;</span>
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33
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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="52" 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">@@ -52,9 +52,9 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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52
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> return 0;</span>
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53
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> }</span>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">bowtie2.orig</span>/bt2_inspect.cpp</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b<span class="idiff left right">owtie2</span>/bt2_inspect.cpp</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="p">@@ -445,15 +445,15 @@</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/bt2_inspect.cpp</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bt2_inspect.cpp</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -445,15 +445,15 @@</span><span class="idiff left right"> int main(int argc, char **argv) {</span></span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> } else {</span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;</span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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="79" 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">@@ -79,9 +79,9 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> return 0;</span>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> }</span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> </span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">bowtie2.orig</span>/bt2_search.cpp</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b<span class="idiff left right">owtie2</span>/bt2_search.cpp</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="p">@@ -5145,15 +5145,15 @@</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/bt2_search.cpp</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bt2_search.cpp</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="p">@@ -5145,15 +5145,15 @@</span><span class="idiff left right"> int bowtie(int argc, const char **argv)</span></span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> } else {</span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;</span>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" 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="106" 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">@@ -106,14 +106,15 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> return 0;</span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> }</span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> {</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">bowtie2.orig</span>/CMakeLists.txt</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b<span class="idiff left right">owtie2</span>/CMakeLists.txt</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="p">@@ -275,7 +275,<span class="idiff left right">8 @@</span></span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="p">@@ -275,7 +275,<span class="idiff left">9 @@</span></span><span class="idiff right"> endif()</span></span>
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112
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"> include_directories(${PROJECT_SOURCE_DIR})</span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> get_directory_property(COMPILER_DEFS COMPILE_DEFINITIONS)</span>
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<td class="diff-line-num old_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_definitions(-DCOMPILER_OPTIONS="${CMAKE_CXX_FLAGS}")</span></span>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+string(REGEX REPLACE "-fdebug-prefix-map=[^ ]* " "" COMP_OPTS ${CMAKE_CXX_FLAGS})</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+string(REGEX REPLACE "-ffile-prefix-map=[^ ]* " "" COMP_OPTS ${COMP_OPTS})</span></span>
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117
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+add_definitions(-DCOMPILER_OPTIONS="${COMP_OPTS}")</span></span>
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118
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> </span>
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119
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> add_executable(bowtie2-align-s ${SEARCH_CPPS} ${SHARED_CPPS})</span>
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