Updated DNACLUST Source Code

Author: Harihara Subrahmaniam Muralidharan

Experiments/Run_Benchmarks/Benchmark_CDHIT.sh

@@ -7,7 +7,7 @@
 #SBATCH --time=5-00:00:00
 #SBATCH --qos=large
 #SBATCH --mem=36gb
-#SBATCH --cpus-per-task=8
+#SBATCH --cpus-per-task=16
 #SBATCH --nodelist=tern00
 
 module load cdhit

dnaclust/Makefile

@@ -27,6 +27,7 @@ fasta.o: src/fasta.cpp src/fasta.hpp
 	$(CXX) -c $(CXXFLAGS) src/fasta.cpp
 
 clean:
+	rm -rf bin
 	mkdir bin
 	mv dnaclust bin/
 	mv fastaselect bin/

dnaclust/src/Global_Variables.hpp

@@ -8,6 +8,9 @@ typedef intptr_t Index;
 typedef int32_t CostType;
 typedef std::vector<Index> IndexVector;
 typedef std::vector<char> BoolVector;
+enum BackPointer {LEFT, DOWN, DOWN_LEFT, ROOT};
+typedef multi_dim::Matrix<CostType> DpTable;
+typedef multi_dim::Matrix<BackPointer> BackPointerTable;
 
 const CharType endOfStringChar = '\0';
 const CharType invalidChar = '^';