related to https://github.com/Homebrew/homebrew-science/pull/4954

refresh-bio · Feb 8, 2017 · 9726a71 · 9726a71
1 parent f5fbff6
commit 9726a71
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Showing 4 changed files with 10 additions and 9 deletions.
diff --git a/kmer_counter/first_dispatch.h b/kmer_counter/first_dispatch.h
@@ -21,6 +21,7 @@ Date   : 2017-01-28
 #include "defs.h"
 #include "timer.h"
 #include <thread>
+#include <array>
 #include "asmlib_wrapper.h"
 #include "intr_copy.h"
 
@@ -101,7 +102,7 @@ class CRangeQueue
 template <typename KMER_T, typename COUNTER_TYPE>
 void pierwsze_kolko_etap1(uint32_t th_id, KMER_T *kmers, uint64 n_recs, uint32_t n_threads,
 	//	uint64_t per_thread, std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> &histos,
-	uint64_t per_thread, std::vector<COUNTER_TYPE[256]> &histos,
+	uint64_t per_thread, std::vector<std::array<COUNTER_TYPE, 256>> &histos,
 	uint32 byte, CRangeQueue& rq)
 	//(std::thread([th_id, kmers, n_recs, n_threads, per_thread, &histos, byte]
 {
@@ -197,10 +198,10 @@ template <typename KMER_T, typename COUNTER_TYPE>
 void pierwsze_kolko_etap2(uint32_t th_id, KMER_T *kmers, KMER_T* tmp,
 	uint64 n_recs, uint32_t n_threads, uint64_t per_thread, uint32 byte,
 	//	std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> &histos,
-	std::vector<COUNTER_TYPE[256]> &histos,
+	std::vector<std::array<COUNTER_TYPE, 256>> &histos,
 	std::vector<uchar*> &_raw_buffers,
 	//	std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> &threads_histos,
-	std::vector<COUNTER_TYPE[256]> &threads_histos,
+	std::vector<std::array<COUNTER_TYPE, 256>> &threads_histos,
 	CMemoryPool* pmm_radix_buf,
 	CRangeQueue& rq)
 	//std::thread([th_id, kmers, tmp, n_recs, n_threads, per_thread, byte, 
@@ -379,10 +380,10 @@ template <typename KMER_T, typename COUNTER_TYPE>
 void pierwsze_kolko_etap3(uint32_t th_id, KMER_T *kmers, KMER_T* tmp,
 	uint64 n_recs, uint32_t n_threads, uint64_t per_thread, uint32 byte,
 	//	std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> &histos,
-	std::vector<COUNTER_TYPE[256]> &histos,
+	std::vector<std::array<COUNTER_TYPE, 256>> &histos,
 	std::vector<uchar*> &_raw_buffers,
 	//	std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> &threads_histos,
-	std::vector<COUNTER_TYPE[256]> &threads_histos,
+	std::vector<std::array<COUNTER_TYPE, 256>> &threads_histos,
 	CMemoryPool* pmm_radix_buf,
 	CRangeQueue& rq)
 

diff --git a/kmer_counter/radix.h b/kmer_counter/radix.h
@@ -489,7 +489,7 @@ namespace RadixSort
 		uint64 per_thread = n_recs / n_threads;
 
 		std::vector<std::thread> threads;
-		std::vector<COUNTER_TYPE[256]> histos(n_threads);
+		std::vector<std::array<COUNTER_TYPE,256>> histos(n_threads);
 		ALIGN_ARRAY COUNTER_TYPE globalHisto[256] = {};
 		for (uint32_t th_id = 0; th_id < n_threads; ++th_id)
 		{
@@ -577,7 +577,7 @@ namespace RadixSort
 		}
 
 		std::vector<uchar*> _raw_buffers(n_threads);
-		std::vector<COUNTER_TYPE[256]> threads_histos(n_threads);
+		std::vector<std::array<COUNTER_TYPE,256>> threads_histos(n_threads);
 
 		for (uint32_t th_id = 0; th_id < n_threads; ++th_id)
 		{

diff --git a/kmer_counter/raduls_impl.h b/kmer_counter/raduls_impl.h
@@ -545,7 +545,7 @@ namespace RadulsSort
 
 		std::vector<std::thread> threads;
 		//	std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> histos(MAGIC_NUMBER * n_threads);
-		std::vector<COUNTER_TYPE[256]> histos(MAGIC_NUMBER * n_threads);
+		std::vector<std::array<COUNTER_TYPE, 256>> histos(MAGIC_NUMBER * n_threads);
 		ALIGN_ARRAY COUNTER_TYPE globalHisto[256] = {};
 		for (uint32_t th_id = 0; th_id < n_threads; ++th_id)
 		{
@@ -596,7 +596,7 @@ namespace RadulsSort
 
 		std::vector<uchar*> _raw_buffers(MAGIC_NUMBER * n_threads);
 		//	std::vector<ALIGN_ARRAY COUNTER_TYPE[256]> threads_histos(MAGIC_NUMBER * n_threads);
-		std::vector<COUNTER_TYPE[256]> threads_histos(MAGIC_NUMBER * n_threads);
+		std::vector<std::array<COUNTER_TYPE, 256>> threads_histos(MAGIC_NUMBER * n_threads);
 
 		for (uint32_t th_id = 0; th_id < n_threads; ++th_id)
 		{

diff --git a/kmer_counter/x64/Release/kmer.obj b/kmer_counter/x64/Release/kmer.obj