update patch and version pulled

COMBINE-lab · Nov 29, 2022 · b995054 · b995054
1 parent da41bb4
commit b995054
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Showing 2 changed files with 46 additions and 67 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -172,11 +172,11 @@ endif()
 message("Build system will fetch and install KMC3")
 ExternalProject_Add(prj_kmc
     DOWNLOAD_DIR        ${CMAKE_SOURCE_DIR}/external
-    DOWNLOAD_COMMAND    curl -k -L https://github.com/refresh-bio/KMC/archive/refs/tags/v3.2.1.tar.gz -o KMC-3.2.1.tar.gz &&
-                        tar -xzf KMC-3.2.1.tar.gz &&
-                        rm KMC-3.2.1.tar.gz
+    DOWNLOAD_COMMAND    curl -k -L https://github.com/refresh-bio/KMC/archive/50eb19013e4eafa8034037ac43b7119c544377ed.tar.gz -o KMC-latest.tar.gz &&
+                        tar -xzf KMC-latest.tar.gz &&
+                        rm KMC-latest.tar.gz
     PATCH_COMMAND       patch --strip 1 < ${CMAKE_SOURCE_DIR}/patches/kmc_patch.diff
-    SOURCE_DIR          ${CMAKE_SOURCE_DIR}/external/KMC-3.2.1
+    SOURCE_DIR          ${CMAKE_SOURCE_DIR}/external/KMC-50eb19013e4eafa8034037ac43b7119c544377ed
     BUILD_IN_SOURCE     TRUE
     INSTALL_DIR         ${CMAKE_SOURCE_DIR}/external/
     CONFIGURE_COMMAND   ""

diff --git a/patches/kmc_patch.diff b/patches/kmc_patch.diff
@@ -1,17 +1,17 @@
-diff --git a/Makefile b/Makefile
-index bc07d35..4bfd785 100644
---- a/Makefile
-+++ b/Makefile
-@@ -13,15 +13,11 @@
+diff --git KMC-50eb19013e4eafa8034037ac43b7119c544377ed/Makefile KMC-latest/Makefile
+index d286f4f..3c62fe3 100644
+--- KMC-50eb19013e4eafa8034037ac43b7119c544377ed/Makefile
++++ KMC-latest/Makefile
+@@ -13,15 +13,11 @@ OUT_BIN_DIR = bin
  OUT_INCLUDE_DIR = include
 
  ifeq ($(UNAME_S),Darwin)
--	CC = /usr/local/bin/g++-10
+-	CC = g++-11
 -
 -	CFLAGS	= -Wall -O3 -m64 -static-libgcc -static-libstdc++ -pthread -std=c++14
 -	CLINK	= -lm -static-libgcc -static-libstdc++ -O3 -pthread -std=c++14
-+	CFLAGS	= -Wall -O3 -m64 -pthread -std=c++14
-+	CLINK	= -lm -O3 -pthread -std=c++14
++	CFLAGS  = -Wall -O3 -m64 -pthread -std=c++14
++	CLINK   = -lm -O3 -pthread -std=c++14
 
  	PY_KMC_API_CFLAGS = -Wl,-undefined,dynamic_lookup -fPIC -Wall -shared -std=c++14 -O3
  else
@@ -20,7 +20,7 @@ index bc07d35..4bfd785 100644
  	CFLAGS	= -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14
  	CLINK	= -lm -static -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14
 
-@@ -61,7 +57,7 @@
+@@ -61,7 +57,7 @@ ifeq ($(UNAME_S),Darwin)
  	$(KMC_TOOLS_DIR)/libs/libz.1.2.5.dylib \
  	$(KMC_TOOLS_DIR)/libs/libbz2.1.0.5.dylib
 
@@ -29,19 +29,19 @@ index bc07d35..4bfd785 100644
  else
  	RADULS_OBJS = \
  	$(KMC_MAIN_DIR)/raduls_sse2.o \
-diff --git a/kmc_CLI/kmc.cpp b/kmc_CLI/kmc.cpp
-index 15e579e..1d62040 100644
---- a/kmc_CLI/kmc.cpp
-+++ b/kmc_CLI/kmc.cpp
-@@ -1,5 +1,7 @@
- #define _CRT_SECURE_NO_WARNINGS
- #include "../kmc_core/kmc_runner.h"
-+#include <random>
-+#include <algorithm>
+diff --git KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_CLI/kmc.cpp KMC-latest/kmc_CLI/kmc.cpp
+index 15e579e..97b4af4 100644
+--- KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_CLI/kmc.cpp
++++ KMC-latest/kmc_CLI/kmc.cpp
+@@ -3,6 +3,7 @@
  #include <cstring>
  #include <iostream>
  #include <fstream>
-@@ -246,6 +248,9 @@ bool parse_parameters(int argc, char* argv[], Params& params)
++#include <random>
+ #include <algorithm>
+ #include <iomanip>
+ using namespace std;
+@@ -246,6 +247,9 @@ bool parse_parameters(int argc, char* argv[], Params& params)
  		stage2Params.SetOutputFileName(argv[i++]);
  	stage1Params.SetTmpPath(argv[i++]);
 
@@ -51,7 +51,7 @@ index 15e579e..1d62040 100644
  	std::vector<std::string> input_file_names;	
  	if (input_file_name[0] != '@')
  		input_file_names.push_back(input_file_name);
-@@ -264,7 +269,7 @@ bool parse_parameters(int argc, char* argv[], Params& params)
+@@ -264,7 +268,7 @@ bool parse_parameters(int argc, char* argv[], Params& params)
  				input_file_names.push_back(s);
 
  		in.close();
@@ -60,10 +60,10 @@ index 15e579e..1d62040 100644
  	}
  	stage1Params.SetInputFiles(input_file_names);
 
-diff --git a/kmc_api/kmer_defs.h b/kmc_api/kmer_defs.h
+diff --git KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_api/kmer_defs.h KMC-latest/kmc_api/kmer_defs.h
 index 90b0db4..4fe8aaf 100644
---- a/kmc_api/kmer_defs.h
-+++ b/kmc_api/kmer_defs.h
+--- KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_api/kmer_defs.h
++++ KMC-latest/kmc_api/kmer_defs.h
 @@ -34,7 +34,7 @@
 
 
@@ -73,35 +73,11 @@ index 90b0db4..4fe8aaf 100644
  	#include <iostream>
 
  #else
-diff --git a/kmc_core/defs.h b/kmc_core/defs.h
-index 75afc97..e0ec1df 100644
---- a/kmc_core/defs.h
-+++ b/kmc_core/defs.h
-@@ -8,6 +8,7 @@
-   Date   : 2022-01-04
- */
-
-+
- #ifndef _DEFS_H
- #define _DEFS_H
-
-@@ -32,6 +33,7 @@
-
- #define COMPACT_CUMSUM_PART_SIZE (1<<10)
-
-+
- #define KMER_X		3
-
- #define STATS_FASTQ_SIZE (1 << 28)
-@@ -66,6 +68,7 @@
- #define MAX_SR		128
-
- //Range of number of sorter threads pre sorter in strict memory mode
-+
- #define MIN_SMSO	1
- #define MAX_SMSO	16
-
-@@ -109,8 +112,8 @@ using uint64 = uint64_t;
+diff --git KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_core/defs.h KMC-latest/kmc_core/defs.h
+index 75afc97..65322d3 100644
+--- KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_core/defs.h
++++ KMC-latest/kmc_core/defs.h
+@@ -109,8 +109,8 @@ using uint64 = uint64_t;
  #include <string.h>
 
  #include <stdio.h>
@@ -112,30 +88,33 @@ index 75afc97..e0ec1df 100644
 
  #endif
 
-diff --git a/kmc_core/queues.h b/kmc_core/queues.h
-index 17a0465..2c0e587 100644
---- a/kmc_core/queues.h
-+++ b/kmc_core/queues.h
-@@ -11,6 +11,8 @@
+diff --git KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_core/queues.h KMC-latest/kmc_core/queues.h
+index 17a0465..4711f26 100644
+--- KMC-50eb19013e4eafa8034037ac43b7119c544377ed/kmc_core/queues.h
++++ KMC-latest/kmc_core/queues.h
+@@ -11,6 +11,9 @@
  #ifndef _QUEUES_H
  #define _QUEUES_H
 
++
 +#include <algorithm>
 +#include <random>
  #include "defs.h"
  #include <stdio.h>
  #include <tuple>
-@@ -571,6 +573,9 @@ public:
+@@ -570,7 +573,10 @@ public:
+ 	}
  	void init_random()
  	{
- 		lock_guard<mutex> lck(mtx);
-+	        std::random_device rd;
-+		std::mt19937 g(rd());
-+ 
+-		lock_guard<mutex> lck(mtx);
++	  lock_guard<mutex> lck(mtx);
++	  std::random_device rd;
++ 	  std::mt19937 g(rd());
++
  		vector<pair<int32, int64>> bin_sizes;
 
  		for (auto& p : m)
-@@ -589,7 +594,7 @@ public:
+@@ -589,7 +595,7 @@ public:
  		for (uint32 i = no_sort_end; i < bin_sizes.size(); ++i)
  			random_bins.push_back(bin_sizes[i].first);