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<h3>
Michael R. Crusoe 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>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/6d5e119aaf2d2cee235eb5a17d2cb242af2249b1">6d5e119a</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-18T07:39:05Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">correct the 64bit detection logic
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/c1ce5b305d8010c6c451a4ea9cccaf63048327c4">c1ce5b30</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-18T09:16:29Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disable -fsanitize builds to save resources
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<h4>5 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#8349e79c83e3dffc4d4ae366712ef4e351aebe80">
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debian/patches/correct_64bit_test
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<li class="file-stats">
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debian/patches/no_sanity
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/1cb4b2ab49f3a058f0de9240f448fa42fb33c72e...c1ce5b305d8010c6c451a4ea9cccaf63048327c4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie2 (2.3.5.1-4) unstable; 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Added patch to correct the 64bit detection logic.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Disable -fsanitize builds to save resources</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 16 Dec 2019 10:13:27 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">bowtie2 (2.3.5.1-3) unstable; urgency=medium</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"> * Team upload.</span>
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<li id="8349e79c83e3dffc4d4ae366712ef4e351aebe80">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/1cb4b2ab49f3a058f0de9240f448fa42fb33c72e...c1ce5b305d8010c6c451a4ea9cccaf63048327c4#8349e79c83e3dffc4d4ae366712ef4e351aebe80"><strong>debian/patches/correct_64bit_test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Handle -m64 and -msse2 flags better</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;">--- bowtie2.orig/Makefile</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;">+++ bowtie2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -198,30 +198,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> VERSION := $(shell cat VERSION)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> BITS := 32</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (x86_64,$(shell uname -m))</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;">+ifeq (64,$(shell dpkg-architecture -q DEB_TARGET_ARCH_BITS))</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> BITS := 64</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (amd64,$(shell uname -m))</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- BITS := 64</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (aarch64,$(shell uname -m))</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- BITS := 64</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# msys will always be 32 bit so look at the cpu arch instead.</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ifeq (1,$(MINGW))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- BITS := 64</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- endif</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (32,$(BITS))</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(error bowtie2 compilation requires a 64-bit platform )</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ M64_FLAG := -m64</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ M64_FLAG :=</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> endif</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SSE_FLAG := -msse2</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-M64_FLAG := -m64</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;">-ifeq (aarch64,$(shell uname -m))</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;">+ifeq (amd64,$(dpkg-architecture -q DEB_TARGET_ARCH))</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SSE_FLAG := -msse2</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> SSE_FLAG =</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- M64_FLAG =</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> endif</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> DEBUG_FLAGS := -O0 -g3 $(M64_FLAG) $(SSE_FLAG)</span></pre>
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<li id="41edb87d75827ea69fc4be16c1d2830db9a0eb81">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/1cb4b2ab49f3a058f0de9240f448fa42fb33c72e...c1ce5b305d8010c6c451a4ea9cccaf63048327c4#41edb87d75827ea69fc4be16c1d2830db9a0eb81"><strong>debian/patches/no_sanity</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: save resources by not making/testing the -fsantize variants</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -218,20 +218,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(DEBUG_FLAGS) $(CXXFLAGS))\""</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(RELEASE_FLAGS) $(CXXFLAGS))\""</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (0,$(shell $(CPP) -E -fsanitize=address,undefined btypes.h 2>&1 > /dev/null; echo $$?))</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SANITIZER_FLAGS := -fsanitize=address,undefined</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifndef SANITIZER_FLAGS</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ifeq (0,$(shell $(CPP) -E -fsanitize=address btypes.h 2>&1 > /dev/null; echo $$?))</span></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;">- SANITIZER_FLAGS := -fsanitize=address</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- endif</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifndef SANITIZER_FLAGS</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ifeq (0,$(shell $(CPP) -E -fsanitize=undefined btypes.h 2>&1 > /dev/null; echo $$?))</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SANITIZER_FLAGS := -fsanitize=undefined</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- endif</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> BOWTIE2_BIN_LIST := bowtie2-build-s \</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> bowtie2-build-l \</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> bowtie2-align-s \</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -244,12 +230,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> bowtie2-align-l-debug \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> bowtie2-inspect-s-debug \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> bowtie2-inspect-l-debug</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BOWTIE2_BIN_LIST_SAN := bowtie2-build-s-sanitized \</span></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;">- bowtie2-build-l-sanitized \</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bowtie2-align-s-sanitized \</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bowtie2-align-l-sanitized \</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bowtie2-inspect-s-sanitized \</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bowtie2-inspect-l-sanitized</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> GENERAL_LIST := $(wildcard scripts/*.sh) \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> $(wildcard scripts/*.pl) \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -306,10 +286,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> .PHONY: all allall both both-debug</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> all: $(BOWTIE2_BIN_LIST) ;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-allall: $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) ;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+allall: $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) ;</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> both: bowtie2-align-s bowtie2-build-s bowtie2-align-l bowtie2-build-l ;</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> both-debug: bowtie2-align-s-debug bowtie2-build-s-debug bowtie2-align-l-debug bowtie2-build-l-debug ;</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-both-sanitized: bowtie2-align-s-sanitized bowtie2-build-s-sanitized bowtie2-align-l-sanitized bowtie2-build-l-sanitized ;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> DEFS := -fno-strict-aliasing \</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> -DBOWTIE2_VERSION="\"`cat VERSION`\"" \</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -323,14 +302,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> $(CPPFLAGS) \</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> $(CFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# set compiler flags for all sanitized builds</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$(BOWTIE2_BIN_LIST_SAN): CXXFLAGS += $(SANITIZER_FLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> # bowtie2-build targets</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie2-build-s-sanitized bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> $(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> $(CPPFLAGS) \</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -338,7 +315,7 @@</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> $(LDFLAGS) $(LDLIBS)</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie2-build-l-sanitized bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> $(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> $(CPPFLAGS) \</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -366,7 +343,7 @@</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # bowtie2-align targets</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> #</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie2-align-s-sanitized bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> $(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> $(CPPFLAGS) \</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -374,7 +351,7 @@</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> $(LDFLAGS) $(LDLIBS)</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie2-align-l-sanitized bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> $(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> $(CPPFLAGS) \</span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -404,7 +381,7 @@</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> # bowtie2-inspect targets</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> #</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie2-inspect-s-sanitized bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> $(CXX) $(RELEASE_FLAGS) \</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> $(RELEASE_DEFS) $(CXXFLAGS) \</span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> $(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -413,7 +390,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> $(SHARED_CPPS) \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> $(LDFLAGS) $(LDLIBS)</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie2-inspect-l-sanitized bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> $(CXX) $(RELEASE_FLAGS) \</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> $(RELEASE_DEFS) $(CXXFLAGS) \</span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> $(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -614,7 +591,7 @@</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> .PHONY: clean</span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> clean:</span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) \</span></span>
</pre>
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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;">+ rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) \</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> $(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)) \</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> bowtie2-*.zip</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> rm -f core.* .tmp.head</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/bowtie2</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/bowtie2</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="p">@@ -140,7 +140,6 @@</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> }</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> </span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> my $debug = 0;</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $sanitized = 0;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> my %read_fns = ();</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> my %read_compress = ();</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> my $cap_out = undef; # Filename for passthrough</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="p">@@ -199,10 +198,6 @@</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> $debug = 1;</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> $bt2_args[$i] = undef;</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> }</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if(not $debug and $arg eq "--sanitized") {</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $sanitized = 1;</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $bt2_args[$i] = undef;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> if($arg eq "--no-unal") {</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> $no_unal = 1;</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> $bt2_args[$i] = undef;</span>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="p">@@ -503,9 +498,6 @@</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> if ($debug) {</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> $suffix = "-debug";</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-elsif($sanitized) {</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $suffix = "-sanitized";</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> # Construct command invoking bowtie2-align</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> quote_params(\@bt2_args);</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/bowtie2-build</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/bowtie2-build</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="p">@@ -36,7 +36,6 @@</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> group = parser.add_mutually_exclusive_group()</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> group.add_argument('--debug', action='store_true')</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- group.add_argument('--sanitized', action='store_true')</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> logging.basicConfig(level=logging.ERROR,</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> format='%(levelname)s: %(message)s'</span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="p">@@ -64,10 +63,6 @@</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> build_bin_spec += '-debug'</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> build_bin_l += '-debug'</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> </span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if script_options.sanitized:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- build_bin_spec += '-sanitized'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- build_bin_l += '-sanitized'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> if script_options.large_index:</span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> build_bin_spec = os.path.join(ex_path,build_bin_l)</span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> elif len(argv) >= 2:</span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/bowtie2-inspect</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/bowtie2-inspect</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -34,7 +34,6 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> group = parser.add_mutually_exclusive_group()</span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> group.add_argument('--debug', action='store_true')</span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- group.add_argument('--sanitized', action='store_true')</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> parser.add_argument('--verbose', action='store_true')</span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> parser.add_argument('--large-index', action='store_true')</span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="p">@@ -61,10 +60,6 @@</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> inspect_bin_spec += '-debug'</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> inspect_bin_l += '-debug'</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if script_options.sanitized:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- inpsect_bin_spec += '-sanitized'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- inspect_bin_l += '-sanitized'</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> if script_options.large_index:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> elif len(argv) >= 1:</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/scripts/test/simple_tests.pl</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/scripts/test/simple_tests.pl</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="p">@@ -4602,7 +4602,7 @@</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> close(FA);</span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> if($do_build) {</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> my $build_args = "";</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $cmd = "$bowtie2_build $idx_type --quiet --sanity $build_args $fa .simple_tests.tmp";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $cmd = "$bowtie2_build $idx_type --quiet $build_args $fa .simple_tests.tmp";</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> print "$cmd\n";</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> system($cmd);</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> ($? == 0) || die "Bad exitlevel from bowtie2-build: $?";</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="p">@@ -4804,7 +4804,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> my $tmpfafn = ".simple_tests.pl.fa";</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> my $last_ref = undef;</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> foreach my $large_idx (undef,1) {</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- foreach my $binary_type ("release", "debug", "sanitized") {</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ foreach my $binary_type ("release", "debug") {</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> for (my $ci = 0; $ci < scalar(@cases); $ci++) {</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> my $c = $cases[$ci];</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> last unless defined($c);</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/scripts/test/simple_tests.sh</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/scripts/test/simple_tests.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="216" 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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="p">@@ -21,21 +21,6 @@</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> # simple_tests.sh</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-export ASAN_OPTIONS=halt_on_error=1</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-export UBSAN_OPTIONS=halt_on_error=1</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#make $* bowtie2-align-s \</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-align-l \</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-align-s-debug \</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-align-l-debug \</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-align-s-sanitized \</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-align-l-sanitized \</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-build-s \</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-build-l \</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-build-s-debug \</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-build-l-debug \</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-build-s-sanitized \</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# bowtie2-build-l-sanitized && \</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> perl scripts/test/simple_tests.pl \</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> --bowtie2=./bowtie2 \</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> --bowtie2-build=./bowtie2-build \</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/1cb4b2ab49f3a058f0de9240f448fa42fb33c72e...c1ce5b305d8010c6c451a4ea9cccaf63048327c4#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">@@ -7,3 +7,5 @@ do-not-rebuild-during-test.patch</td>
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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">2to3.patch</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">silence_tbb_deprecation_warning.patch</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">simde</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">correct_64bit_test</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">no_sanity</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/1cb4b2ab49f3a058f0de9240f448fa42fb33c72e...c1ce5b305d8010c6c451a4ea9cccaf63048327c4#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">@@ -12,10 +12,10 @@ export DEB_CFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">EXTRA_OPTIONS =</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">ifneq ($(DEB_<span class="idiff left right">HOS</span>T_ARCH),amd64)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> EXTRA_OPTIONS += NO_TBB=1 POPCNT_CAPABILITY=<span class="idiff left right"> M64_FLAG=</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">ifneq ($(DEB_<span class="idiff left right">TARGE</span>T_ARCH),amd64)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> EXTRA_OPTIONS += NO_TBB=1 POPCNT_CAPABILITY=</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> EXTRA_OPTIONS += POPCNT_CAPABILITY=1<span class="idiff left right"> M64_FLAG=-m64</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> EXTRA_OPTIONS += POPCNT_CAPABILITY=1</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">export EXTRA_OPTIONS</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,12 +34,8 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> bowtie2-align-s-debug \</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> bowtie2-align-l-debug \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> bowtie2-inspect-s-debug \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> bowtie2-inspect-l-debug \</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> bowtie2-align-s-sanitized \</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> bowtie2-align-l-sanitized \</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> bowtie2-build-s-sanitized \</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> bowtie2-build-l-sanitized</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> env --unset=LD_PRELOAD make -j1 test</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> bowtie2-inspect-l-debug</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> make -j1 test</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">endif</span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">override_dh_auto_install:</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">@@ -50,15 +46,15 @@ override_dh_install:</td>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>
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51
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"</span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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="LC56" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> rm -f $(CURDIR)/debian/$(pkg)/usr/bin/bowtie2-buildc</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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