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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/vg">Debian Med / vg</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vg/commit/f3b6c65275a36ec5b81e1c1c6b7f2ee686980fa4">f3b6c652</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-07T01:43:25Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more hardening tweaks
</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#905bf2aeef99918e81405a9b9d92b52dc1016a00">
debian/patches/hardening_flags
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/vg/commit/f3b6c65275a36ec5b81e1c1c6b7f2ee686980fa4#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,8 @@ Files-Excluded: deps/libdeflate</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> deps/fastahack</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> deps/libVCFH</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> deps/vcflib/libVCFH</span>
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<td class="diff-line-num new old_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">
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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">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> deps/vcflib/tabixpp/htslib</span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> deps/sublinear-Li-Stephens/deps/htslib</span>
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Files: *</span>
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Copyright: © 2014 Erik Garrison</span>
</pre>
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<br>
</li>
<li id="905bf2aeef99918e81405a9b9d92b52dc1016a00">
<a href="https://salsa.debian.org/med-team/vg/commit/f3b6c65275a36ec5b81e1c1c6b7f2ee686980fa4#905bf2aeef99918e81405a9b9d92b52dc1016a00"><strong>debian/patches/hardening_flags</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,7 +62,7 @@</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> $(LIB_DIR)/libsdsl.a: $(SDSL_DIR)/lib/*.cpp $(SDSL_DIR)/include/sdsl/*.hpp</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> ifeq ($(shell uname -s),Darwin)</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="p">@@ -316,1<span class="idiff left right">0 +316,10</span> @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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="LC65" class="line" lang="diff"><span class="p">@@ -316,1<span class="idiff left right">7 +316,17</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> $(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> +rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> +rm -Rf $(CWD)/$(INC_DIR)/vg/io/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,6 +75,14 @@</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> # We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> # If we need either the library or the pkg-config file (which we didn't used to ship), run the whole build.</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> # We use a wildcard match to make sure make understands that both files come from one command run.</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> # See https://stackoverflow.com/a/3077254</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> $(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- +. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR)" LDFLAGS="-L$(CWD)/$(LIB_DIR)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ +. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="-L$(CWD)/$(LIB_DIR) $(LDFLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> # We tell the vcflib build to use our own htslib.</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> # We link it and libdeflate statically (on Linux) because our lib directory won't</span>
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78
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="p">@@ -392,7 +392,7 @@</span></span>
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79
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> +mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -285,6 +293,15 @@</td>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="diff"> multichoose: pre</span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="diff"> cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="p">@@ -174,7 +174,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> $(TABIX): pre</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" HTS_HEADERS="" $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> $(SMITHWATERMAN): pre</span>
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<td class="diff-line-num new new_line" data-linenumber="304" 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="LC304" class="line" lang="diff"> cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="diff"><span class="p">@@ -197,7 +197,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="diff"> $(MAKE) bin/$@</span>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -381,3 +398,12 @@</td>
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381
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="diff"> </span>
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382
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="diff"> install: all</span>
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383
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="diff"> ${MKDIR} -p ${DESTDIR}${PREFIX}/bin</span>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/deps/vcflib/tabixpp/Makefile</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ vg/deps/vcflib/tabixpp/Makefile</span></span>
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<td class="diff-line-num new new_line" data-linenumber="403" 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">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="p">@@ -44,6 +44,5 @@</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> cleanlocal:</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log \</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> tabix.pdf *.class libtabix.*.dylib libtabix.so*</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd htslib && $(MAKE) clean</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> clean:cleanlocal-recur</span></pre>
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<a href="https://salsa.debian.org/med-team/vg/commit/f3b6c65275a36ec5b81e1c1c6b7f2ee686980fa4#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ export LC_ALL=C.UTF-8</td>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">export CFLAGS=$(shell dpkg-buildflags --get CFLAGS)</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">export CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">export L<span class="idiff left right">F</span>FLAGS=$(shell dpkg-buildflags --get LDFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">export L<span class="idiff left right">D</span>FLAGS=$(shell dpkg-buildflags --get LDFLAGS)</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">export CXXFLAGS=$(shell dpkg-buildflags --get CXXFLAGS)</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">%:</span>
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