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Use RowDiff with DBGHashFast in test_aligner_labeled #505

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9ed4bfd
Use RowDiff with DBGHashFast
adamant-pwn Oct 15, 2024
275149e
Fix unit test and compilation errors
adamant-pwn Oct 16, 2024
40cb43e
vla-cxx-extension -> vla-extension (older versions don't support it)
adamant-pwn Oct 16, 2024
0767479
Add GDB debugging to integration test + fix
adamant-pwn Oct 16, 2024
6c89455
Update
adamant-pwn Oct 16, 2024
fac4222
Update
adamant-pwn Oct 16, 2024
29ded0f
Throw on invalid final state
adamant-pwn Oct 16, 2024
aa8b9fb
Distinguish dummy nodes and nodes with zero outdegree
adamant-pwn Oct 16, 2024
2d1379e
Fixes
adamant-pwn Oct 16, 2024
2bfaa47
Apply review suggestions
adamant-pwn Nov 4, 2024
b9f4da0
Merge remote-tracking branch 'origin/master' into rowdiff-2
hmusta Dec 3, 2024
c808190
Multithreaded get_last
hmusta Dec 4, 2024
c13196f
Update row_diff_builder.cpp
hmusta Dec 4, 2024
e706240
Update row_diff_builder.cpp
hmusta Dec 4, 2024
7a2f680
parallel row_diff_traverse
hmusta Feb 7, 2025
a0828ef
fix
hmusta Feb 7, 2025
d43903f
fix
hmusta Feb 7, 2025
9751cbb
minor
hmusta Feb 7, 2025
2c887e7
Merge remote-tracking branch 'origin/master' into rowdiff-2
hmusta Feb 7, 2025
4f94d96
Merge branch 'rowdiff' into rowdiff-2
hmusta Feb 7, 2025
86a8667
test
hmusta Feb 10, 2025
66cf80c
multi-threaded call_nodes
hmusta Feb 10, 2025
9283562
use parallel call_nodes
hmusta Feb 10, 2025
23bbb34
cleanup
hmusta Feb 10, 2025
8b8d26b
disable automatic valid_edges_ generation
hmusta Feb 10, 2025
de88200
avoid node dropout and unnecessary atomic checks
hmusta Feb 10, 2025
89f725d
progress bar
hmusta Feb 10, 2025
9b5c019
multithreaded dbg succinct call_nodes
hmusta Feb 10, 2025
85750c3
fix integration test
hmusta Feb 10, 2025
32849af
fix
hmusta Feb 10, 2025
798d0d2
multithreaded call_nodes on masked graphs
hmusta Feb 10, 2025
9008f56
compile on mac
hmusta Feb 10, 2025
58e28d5
disable old DBGSuccinct check when loading rowdiff
hmusta Feb 11, 2025
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Update row_diff_builder.cpp
hmusta authored Dec 4, 2024
commit c13196fcdf9b37aedb3518041eb13f61fd03ac2f
4 changes: 3 additions & 1 deletion metagraph/src/annotation/row_diff_builder.cpp
Original file line number Diff line number Diff line change
@@ -273,6 +273,7 @@ std::shared_ptr<const bit_vector> get_last(const graph::DeBruijnGraph &graph) {
} else {
sdsl::bit_vector last_bv(graph.max_index() + 1);

__atomic_thread_fence(__ATOMIC_RELEASE);
#pragma omp parallel for num_threads(get_num_threads()) schedule(static)
for (node_index v = 1; v <= graph.max_index(); ++v) {
if (!graph.in_graph(v))
@@ -282,8 +283,9 @@ std::shared_ptr<const bit_vector> get_last(const graph::DeBruijnGraph &graph) {
graph.call_outgoing_kmers(v, [&](node_index u, char c) {
last = std::max(last, std::pair{c, u});
});
last_bv[last.second] = true;
set_bit(last_bv.data(), last.second, true, __ATOMIC_RELAXED);
});
__atomic_thread_fence(__ATOMIC_ACQUIRE);
return std::make_shared<bit_vector_stat>(std::move(last_bv));
}
}