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require 'formula'
class Abyss < Formula
homepage 'http://www.bcgsc.ca/platform/bioinfo/software/abyss'
url 'http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz'
sha1 '763dc423054421829011844ceaa5e18dc43f1ca9'
head 'https://github.com/sjackman/abyss.git'
# Only header files are used from these packages, so :build is appropriate
depends_on 'boost' => :build
depends_on 'google-sparsehash' => :build
# Snow Leopard comes with mpi but Lion does not
depends_on 'open-mpi' if MacOS.version >= :lion
# strip breaks the ability to read compressed files.
skip_clean 'bin'
# Fix a compiler error on OS X 10.8 Mountain Lion.
# This issue is fixed upstream:
# https://github.com/sjackman/abyss/issues/13
def patches
DATA
end
def install
system "./configure", "--disable-dependency-tracking",
"--prefix=#{prefix}"
system "make install"
end
def test
system "#{bin}/ABYSS", "--version"
end
end
__END__
diff --git a/Graph/ContigGraphAlgorithms.h b/Graph/ContigGraphAlgorithms.h
index 023a898..0eac936 100644
--- a/Graph/ContigGraphAlgorithms.h
+++ b/Graph/ContigGraphAlgorithms.h
@@ -329,7 +329,7 @@ size_t addComplementaryEdges(ContigGraph<DG>& g)
if (!found) {
add_edge(vc, uc, g[e], static_cast<DG&>(g));
numAdded++;
- } else if (g[e] != g[f]) {
+ } else if (!(g[e] == g[f])) {
// The edge properties do not agree. Select the better.
g[e] = g[f] = BetterDistanceEst()(g[e], g[f]);
}
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