Merge branch 'master' of https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library

Author: Mengyao Zhao

src/.gitignore

@@ -0,0 +1,12 @@
+*.*~
+example_c
+example_cpp
+libssw.so
+libsswjni.so
+ssw.jar
+ssw.o
+ssw/Aligner.class
+ssw/Alignment.class
+ssw/Example.class
+ssw_cpp.o
+ssw_test 

src/Makefile

@@ -41,7 +41,7 @@ $(JAVA_JAR): $(JAVA_OBJ)
 	jar cvfe $@ ssw.Example $^
 
 %.class: %.java
-	javac $<
+	javac -cp ./ $<
 
 ssw.o: ssw.c ssw.h
 	$(CC) -c -o $@ $< $(CFLAGS)

src/ssw_cpp.cpp

@@ -26,24 +26,24 @@ void BuildSwScoreMatrix(const uint8_t& match_score,
 
   // The score matrix looks like
   //                 // A,  C,  G,  T,  N
-  //  score_matrix_ = { 2, -2, -2, -2,  0, // A
-  //                   -2,  2, -2, -2,  0, // C
-  //                   -2, -2,  2, -2,  0, // G
-  //                   -2, -2, -2,  2,  0, // T
-  //                    0,  0,  0,  0,  0};// N
+  //  score_matrix_ = { 2, -2, -2, -2, -2, // A
+  //                   -2,  2, -2, -2, -2, // C
+  //                   -2, -2,  2, -2, -2, // G
+  //                   -2, -2, -2,  2, -2, // T
+  //                   -2, -2, -2, -2, -2};// N
 
   int id = 0;
   for (int i = 0; i < 4; ++i) {
     for (int j = 0; j < 4; ++j) {
       matrix[id] = ((i == j) ? match_score : static_cast<int8_t>(-mismatch_penalty));
       ++id;
     }
-    matrix[id] = 0;
+    matrix[id] = static_cast<int8_t>(-mismatch_penalty); // For N
     ++id;
   }
 
   for (int i = 0; i < 5; ++i)
-    matrix[id++] = 0;
+    matrix[id++] = static_cast<int8_t>(-mismatch_penalty); // For N
 
 }