Merge pull request #10 from phylo42/develop

v0.2.0 commit

CHANGELOG.txt

@@ -1,23 +1,7 @@
 ============================================================================================================
-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

epik/CMakeLists.txt

@@ -1,6 +1,6 @@
 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)

epik/src/epik/place.cpp

@@ -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);