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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>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/vg/commit/5c1e0b81867baf83961fd19ad33cde3528981996">5c1e0b81</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T15:40:42+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">libVCFH is unneeded
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<h4>2 changed files:</h4>
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+
debian/patches/libVCFH_unneeded
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debian/patches/series
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<h4>Changes:</h4>
<li id="cfaa6fb2c1b74a35dd749f0c897acefbfe259b80">
<a href="https://salsa.debian.org/med-team/vg/commit/5c1e0b81867baf83961fd19ad33cde3528981996#cfaa6fb2c1b74a35dd749f0c897acefbfe259b80"><strong>debian/patches/libVCFH_unneeded</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: libVCFH is unneeded</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;">--- vg.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;">+++ vg/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -36,7 +36,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> # Define libraries to link against. Make sure to always link statically against</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> # htslib and libdeflate and Protobuf so that we can use position-dependent code</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # there for speed.</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;">-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lz -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lz -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # Use pkg-config to find Cairo and all the libs it uses</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> LD_LIB_FLAGS += $(shell pkg-config --libs cairo jansson)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/vg/commit/5c1e0b81867baf83961fd19ad33cde3528981996#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">@@ -25,3 +25,4 @@ static</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">use_packaged_lz4</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">parallize_better</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">use_packaged_libtsl-hopscotch-map-dev</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">libVCFH_unneeded</span></pre>
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