work in progress; Investigating why it is so slow.

src/DnaSeqStr.h

@@ -8,8 +8,11 @@
 #ifndef DNASEQSTR_H_
 #define DNASEQSTR_H_
 
+#include <iostream>
 #include "FqConstants.h"
 
+using namespace std;
+
 /*
  * Here, for performance matters, do not want to have to do a memmove nor strcpy or strcat to extract only DNA sequence for all
  * the fastq records that we'll have to process (potentially millions). So, use a structure to store start position of DNA sequence in buffer and its length.
@@ -23,13 +26,13 @@
 
 class DnaSeqStr {
 public :
-    char * fq_record_buf; //[MAX_FQ_RECORD_LENGTH];
+    char * const fq_record_buf; //[MAX_FQ_RECORD_LENGTH];
     int start_idx;
     int length;
 
 public:
-    DnaSeqStr() {
-    	fq_record_buf=new char[MAX_FQ_RECORD_LENGTH];
+    DnaSeqStr():fq_record_buf(new char[MAX_FQ_RECORD_LENGTH]) {
+	cout<<"Calling DnaSeqStr constructor"<<endl;
     	length=0;
     	start_idx=0;
     }
@@ -41,7 +44,8 @@ public:
     }
 
     ~DnaSeqStr() {
-    	delete fq_record_buf;
+	cout<<"Calling DnaSeqStr destructor"<<endl;
+    	delete fq_record_buf[];
     }
 };
 

src/fqwriter.cpp

@@ -24,7 +24,7 @@
 #include "srp.h"
 #include "FqBaseBackend.h"
 
-#define DEBUG
+//#define DEBUG
 #ifdef DEBUG
 #include <iostream>
 using namespace std;

src/read_utils.cpp

@@ -29,7 +29,7 @@
 #include "DnaSeqStr.h"
 #include "read_utils.h"
 #include "rock_commons.h"
-#define DEBUG
+//#define DEBUG
 
 #ifdef DEBUG
 #include <cassert>

src/rock.cpp

@@ -47,7 +47,7 @@
 using namespace std;
 
 
-// #define BENCHMARK
+#define BENCHMARK
 #ifdef BENCHMARK
 #include <sys/time.h>
 #include <sys/resource.h>