From e2d2d9b6f83fe75a591de9c35235815c5e64cfb0 Mon Sep 17 00:00:00 2001 From: jamshed Date: Mon, 24 Oct 2022 14:15:38 -0400 Subject: [PATCH 1/7] Fix version --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 2352cd80..c14824a6 100644 --- 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 2.1.0 LANGUAGES CXX C ) From 9d84c7252f12e1c9d3735c4019f1a94b8aae09d9 Mon Sep 17 00:00:00 2001 From: jamshed Date: Fri, 28 Oct 2022 12:38:52 -0400 Subject: [PATCH 2/7] Possibly speedup MPHF query with large `k` https://github.com/rizkg/BBHash/issues/20 --- include/BBHash/BooPHF.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/BBHash/BooPHF.h b/include/BBHash/BooPHF.h index 1c7fb449..f9ba3867 100644 --- 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; From f8bbcc17c7b4a23524ff6e69b592f164f5ea9561 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Wed, 23 Nov 2022 10:58:44 -0500 Subject: [PATCH 3/7] update with conda variables --- src/CMakeLists.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 1854aa48..5426da0e 100644 --- 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++fs) +endif() # Link the executable to the required libraries. target_link_libraries(${PROJECT_NAME} PRIVATE cfcore_static) From da41bb49361133474c5118a3b87473e07a872268 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Wed, 23 Nov 2022 12:52:56 -0500 Subject: [PATCH 4/7] update with conda variables --- src/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 5426da0e..01f42991 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -100,7 +100,7 @@ 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++fs) + target_link_libraries(cfcore_static PRIVATE c++experimental) endif() # Link the executable to the required libraries. From b71e9436c2adf7256df22ae022e021a3716ca298 Mon Sep 17 00:00:00 2001 From: jamshed Date: Sun, 4 Dec 2022 21:55:40 -0500 Subject: [PATCH 5/7] Fix deadlock at GFA-reduced o/p completion with #seqs-with-valid-bases < k --- src/CdBG_GFA_Reduced_Writer.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/CdBG_GFA_Reduced_Writer.cpp b/src/CdBG_GFA_Reduced_Writer.cpp index 83889f0a..cfd11b5d 100644 --- a/src/CdBG_GFA_Reduced_Writer.cpp +++ b/src/CdBG_GFA_Reduced_Writer.cpp @@ -67,7 +67,10 @@ void CdBG::write_sequence_tiling(Job_Queue& job // The sequence does not contain any unitig (possible if there's no valid k-mer in the sequence). if(!left_unitig.is_valid()) + { + job_queue.finish_job(); continue; + } // Write the path ID. From 9a47e0692e624fdd2163775f3e7f43e194a9dea3 Mon Sep 17 00:00:00 2001 From: jamshed Date: Mon, 5 Dec 2022 11:29:16 -0500 Subject: [PATCH 6/7] Clear temp files for b71e9436c2adf7256df22ae022e021a3716ca298 --- src/CdBG_GFA_Reduced_Writer.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/CdBG_GFA_Reduced_Writer.cpp b/src/CdBG_GFA_Reduced_Writer.cpp index cfd11b5d..1e9e0cfa 100644 --- a/src/CdBG_GFA_Reduced_Writer.cpp +++ b/src/CdBG_GFA_Reduced_Writer.cpp @@ -68,6 +68,7 @@ void CdBG::write_sequence_tiling(Job_Queue& 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; } From 2db0961ac7644813db5c2d263b41f8faa21cbfc9 Mon Sep 17 00:00:00 2001 From: jamshed Date: Mon, 5 Dec 2022 13:34:58 -0500 Subject: [PATCH 7/7] Bump patch version --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index c14824a6..2911143a 100644 --- 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 2.1.0 + VERSION 2.1.1 LANGUAGES CXX C )