From a0014ac62aeadefe8257ce8bc1e43e47f6ceab0e Mon Sep 17 00:00:00 2001
From: Veronique Legrand <veronique.legrand@pasteur.fr>
Date: Thu, 10 Apr 2025 14:34:36 +0200
Subject: [PATCH] work in progress; Investigating why it is so slow.
---
src/DnaSeqStr.h | 12 ++++++++----
src/fqwriter.cpp | 2 +-
src/read_utils.cpp | 2 +-
src/rock.cpp | 2 +-
4 files changed, 11 insertions(+), 7 deletions(-)
diff --git a/src/DnaSeqStr.h b/src/DnaSeqStr.h
index 5d412e1..b9cb795 100644
--- a/src/DnaSeqStr.h
+++ b/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[];
}
};
diff --git a/src/fqwriter.cpp b/src/fqwriter.cpp
index a0e2e09..37045e3 100644
--- a/src/fqwriter.cpp
+++ b/src/fqwriter.cpp
@@ -24,7 +24,7 @@
#include "srp.h"
#include "FqBaseBackend.h"
-#define DEBUG
+//#define DEBUG
#ifdef DEBUG
#include <iostream>
using namespace std;
diff --git a/src/read_utils.cpp b/src/read_utils.cpp
index 71f9367..32b9bb1 100644
--- a/src/read_utils.cpp
+++ b/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>
diff --git a/src/rock.cpp b/src/rock.cpp
index 05cf096..652d721 100755
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -47,7 +47,7 @@
using namespace std;
-// #define BENCHMARK
+#define BENCHMARK
#ifdef BENCHMARK
#include <sys/time.h>
#include <sys/resource.h>
--
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