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commit: f22bb3be4e8f283831edc5f4c38a839442355644 |
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Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com> |
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AuthorDate: Wed Apr 14 13:07:12 2021 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Wed Apr 14 13:07:12 2021 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f22bb3be |
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|
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sci-biology/abyss: fix PathConsensus crashes |
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|
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Fixes: https://github.com/bcgsc/abyss/issues/267 |
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Fix crashes of PathConsensus during long-scaffolding |
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step per @sjackman suggestions. |
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|
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Add back 2.2.5 version which does not have yet the |
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RResolver which addition broke the paired de Bruijn |
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graph assembly approach and since that only the |
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Bloom filter-based approach works in 2.3.0. |
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|
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Package-Manager: Portage-3.0.18, Repoman-3.0.3 |
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Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com> |
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|
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.../abyss/{abyss-2.3.0.ebuild => abyss-2.2.5-r1.ebuild} | 4 ++++ |
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.../abyss/{abyss-2.3.0.ebuild => abyss-2.3.0-r1.ebuild} | 4 ++++ |
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sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch | 11 +++++++++++ |
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.../abyss/files/abyss-2.2.5-PathConsensus-assert.patch | 11 +++++++++++ |
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4 files changed, 30 insertions(+) |
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|
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diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild b/sci-biology/abyss/abyss-2.2.5-r1.ebuild |
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similarity index 91% |
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copy from sci-biology/abyss/abyss-2.3.0.ebuild |
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copy to sci-biology/abyss/abyss-2.2.5-r1.ebuild |
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index 95438d3b4..d9134813b 100644 |
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--- a/sci-biology/abyss/abyss-2.3.0.ebuild |
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+++ b/sci-biology/abyss/abyss-2.2.5-r1.ebuild |
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@@ -27,6 +27,10 @@ DEPEND="${RDEPEND} |
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dev-lang/ghc |
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)" |
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|
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+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch |
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+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch |
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+ ) |
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+ |
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# todo: --enable-maxk=N configure option |
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# todo: fix automagic mpi toggling |
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|
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|
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diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild b/sci-biology/abyss/abyss-2.3.0-r1.ebuild |
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similarity index 91% |
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rename from sci-biology/abyss/abyss-2.3.0.ebuild |
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rename to sci-biology/abyss/abyss-2.3.0-r1.ebuild |
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index 95438d3b4..d9134813b 100644 |
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--- a/sci-biology/abyss/abyss-2.3.0.ebuild |
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+++ b/sci-biology/abyss/abyss-2.3.0-r1.ebuild |
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@@ -27,6 +27,10 @@ DEPEND="${RDEPEND} |
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dev-lang/ghc |
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)" |
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|
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+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch |
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+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch |
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+ ) |
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+ |
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# todo: --enable-maxk=N configure option |
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# todo: fix automagic mpi toggling |
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|
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|
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diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch |
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new file mode 100644 |
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index 000000000..95181f082 |
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--- /dev/null |
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+++ b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch |
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@@ -0,0 +1,11 @@ |
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+--- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.000000000 +0200 |
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++++ abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000 +0200 |
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+@@ -171,7 +171,7 @@ |
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+ template <typename T> |
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+ ContigProperties& operator+=(ContigProperties& a, const T& b) |
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+ { |
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+- assert((int)a.length + (int)b.distance > 0); |
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++ assert((int)a.length + (int)b.distance >= 0); |
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+ a.length += b.distance; |
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+ return a; |
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+ } |
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|
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diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch |
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new file mode 100644 |
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index 000000000..754e25acc |
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--- /dev/null |
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+++ b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch |
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@@ -0,0 +1,11 @@ |
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+--- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.000000000 +0200 |
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++++ abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000 +0200 |
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+@@ -379,7 +379,7 @@ |
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+ unsigned overlap, Sequence& seq, |
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+ const Sequence& s, const ContigNode& node, const Path& path) |
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+ { |
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+- assert(s.length() > overlap); |
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++ assert(s.length() >= overlap); |
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+ Sequence ao; |
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+ Sequence bo(s, 0, overlap); |
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+ Sequence o; |
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