Merge branch 'develop'

COMBINE-lab · Dec 5, 2022 · 013196d · 013196d
2 parents abe687a + 2db0961
commit 013196d
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Showing 4 changed files with 11 additions and 2 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,7 +8,7 @@ cmake_minimum_required(VERSION 3.14)
 # Name the project, its version, and languages used in it.
 set(PROJECT_NAME cuttlefish)
 project(${PROJECT_NAME}
-        VERSION 2.0.0
+        VERSION 2.1.1
         LANGUAGES CXX C
         )
 

diff --git a/include/BBHash/BooPHF.h b/include/BBHash/BooPHF.h
@@ -1021,7 +1021,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
 		}
 
 
-		uint64_t lookup(elem_t elem)
+		uint64_t lookup(const elem_t& elem)
 		{
 			if(! _built) return ULLONG_MAX;
 

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -97,6 +97,11 @@ target_link_libraries(cfcore_static PRIVATE BZip2::BZip2)
 # Link the cfcore_static library to the threads package in the platform.
 target_link_libraries(cfcore_static PRIVATE ${CMAKE_THREAD_LIBS_INIT})
 
+# when building on conda on OSX with clang, we apparently need to explicitly
+# link the filesystem library, see (https://github.com/bioconda/bioconda-recipes/pull/37269/files)
+if("$ENV{CF_INSTALL}" STREQUAL "conda" AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    target_link_libraries(cfcore_static PRIVATE c++experimental)
+endif()
 
 # Link the executable to the required libraries.
 target_link_libraries(${PROJECT_NAME} PRIVATE cfcore_static)

diff --git a/src/CdBG_GFA_Reduced_Writer.cpp b/src/CdBG_GFA_Reduced_Writer.cpp
@@ -67,7 +67,11 @@ void CdBG<k>::write_sequence_tiling(Job_Queue<std::string, Oriented_Unitig>& job
 
         // The sequence does not contain any unitig (possible if there's no valid k-mer in the sequence).
         if(!left_unitig.is_valid())
+        {
+            remove_temp_files(job_queue.next_job_to_finish());
+            job_queue.finish_job();
             continue;
+        }
 
 
         // Write the path ID.