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Merge pull request #10 from phylo42/develop
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v0.2.0 commit
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nromashchenko authored Sep 29, 2023
2 parents f24aab8 + a4d0b7d commit 31cbdf7
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28 changes: 6 additions & 22 deletions CHANGELOG.txt
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============================================================================================================
v0.1.3
- Changed the database name convention (omega parameter)
- PhyML parser rolled back to slow and naive solution due to breaking updates in last PhyML versions

============================================================================================================
v0.1.2
- The database name convention has changed to be consistent to the latest versions of RAPPASv1 (java)
- The default omega value now is 1.5
- Updated core to v0.1.7, which supports ambiguous bases

============================================================================================================
v0.1.1

- New construction algorithm: now the construction is done by completing two steps.
In the first one, hashmaps of group nodes are built independently and stored on disk in ${workdir}/hashmaps.
After, they are merged into a database hashmap.
- AR Probability matrix is destroyed after the first stage of the algorithm.
It makes the peak RAM consumption approximately to be max(proba matrix size, final database size).

============================================================================================================
v0.1.0
First released version.
v0.2.0
- Supported partial loading of databases with phylo-k-mer filtering (--mu, --max-ram)
- Reintroduced parallelism (--threads)
- Reworked LWR formula so that it is normalized over all branches of the tree
- Various improvements and fixes
- Removed the old changelog since it was related to the functionality that had migrated to IPK
2 changes: 1 addition & 1 deletion epik/CMakeLists.txt
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cmake_minimum_required(VERSION 3.10 FATAL_ERROR)

set(ENABLE_OMP ON)
set(ENABLE_OMP OFF)
set(ENABLE_SSE OFF)
set(ENABLE_AVX2 OFF)
set(ENABLE_AVX512 OFF)
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2 changes: 2 additions & 0 deletions epik/src/epik/place.cpp
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Expand Up @@ -200,6 +200,8 @@ std::vector<placement> filter_by_ratio(const std::vector<placement>& placements,

placed_collection placer::place(const std::vector<seq_record>& seq_records, size_t num_threads)
{
(void)num_threads;

/// There may be identical sequences with different headers. We group them
/// by the sequence content to not to place the same sequences more than once
const auto sequence_map = group_by_sequence_content(seq_records);
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2 changes: 1 addition & 1 deletion i2l

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