*** empty log message ***

Makefile

@@ -56,7 +56,7 @@ LIBS =
 SEARCH_LIBS = $(PTHREAD_LIB)
 BUILD_LIBS =
 
-SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp
+SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp
 OTHER_CPPS = ccnt_lut.cpp hit.cpp ref_read.cpp alphabet.c
 SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
 MAQ_H   = $(wildcard maq_convert/*.h)

log.cpp

@@ -0,0 +1,7 @@
+/*
+ * log.cpp
+ */
+
+#include "log.h"
+
+SyncLogger glog;

log.h

@@ -0,0 +1,31 @@
+#ifndef LOG_H_
+#define LOG_H_
+
+#include <iostream>
+#include "threading.h"
+
+class SyncLogger {
+public:
+	SyncLogger() {
+		MUTEX_INIT(lock_);
+	}
+
+	void msg(const char *s) {
+		MUTEX_LOCK(lock_);
+		std::cout << s << std::endl;
+		MUTEX_UNLOCK(lock_);
+	}
+
+	void msg(const std::string& s) {
+		MUTEX_LOCK(lock_);
+		std::cout << s << std::endl;
+		MUTEX_UNLOCK(lock_);
+	}
+
+private:
+	MUTEX_T lock_;
+};
+
+extern SyncLogger glog;
+
+#endif /*LOG_H_*/

pool.h

@@ -11,6 +11,7 @@
 #include <string.h>
 #include <stdlib.h>
 #include "bitset.h"
+#include "log.h"
 
 /**
  * Very simple allocator for fixed-size chunks of memory.  Chunk size
@@ -89,7 +90,11 @@ class ChunkPool {
 		}
 		void * ptr = (void *)(&pool_[cur * chunkSz_]);
 		bits_.set(cur);
-		if(verbose) cout << "Freeing chunk with offset: " << cur << endl;
+		if(verbose) {
+			stringstream ss;
+			ss << "Allocating chunk with offset: " << cur;
+			glog.msg(ss.str());
+		}
 		cur_ = cur;
 		return ptr;
 	}
@@ -101,7 +106,11 @@ class ChunkPool {
 		uint32_t off = (uint32_t)((int8_t*)ptr - pool_);
 		assert_eq(0, off % chunkSz_);
 		off /= chunkSz_;
-		if(verbose) cout << "Freeing chunk with offset: " << off << endl;
+		if(verbose) {
+			stringstream ss;
+			ss << "Freeing chunk with offset: " << cur_;
+			glog.msg(ss.str());
+		}
 		bits_.clear(off);
 	}
 
@@ -229,15 +238,19 @@ class AllocOnlyPool {
 	void free(T* t) {
 		assert(t != NULL);
 		if(pool_->verbose) {
-			cout << "Freeing a " << name_ << endl;
+			stringstream ss;
+			ss << "Freeing a " << name_;
+			glog.msg(ss.str());
 		}
 		if(cur_ > 0 && t == &pools_[curPool_][cur_-1]) {
 			cur_--;
 			ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T)));
 			if(cur_ == 0 && curPool_ > 0) {
 				assert_eq(curPool_+1, pools_.size());
 				if(pool_->verbose) {
-					cout << "Freeing a pool" << endl;
+					stringstream ss;
+					ss << "Freeing a " << name_ << " pool";
+					glog.msg(ss.str());
 				}
 				pool_->free(pools_.back());
 				pools_.pop_back();
@@ -255,15 +268,19 @@ class AllocOnlyPool {
 	void free(T* t, uint32_t num) {
 		assert(t != NULL);
 		if(pool_->verbose) {
-			cout << "Freeing a " << name_ << "; num " << num << endl;
+			stringstream ss;
+			ss << "Freeing " << num << " " << name_ << "s";
+			glog.msg(ss.str());
 		}
 		if(num <= cur_ && t == &pools_[curPool_][cur_ - num]) {
 			cur_ -= num;
 			ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T)));
 			if(cur_ == 0 && curPool_ > 0) {
 				assert_eq(curPool_+1, pools_.size());
 				if(pool_->verbose) {
-					cout << "Freeing a pool" << endl;
+					stringstream ss;
+					ss << "Freeing a " << name_ << " pool";
+					glog.msg(ss.str());
 				}
 				pool_->free(pools_.back());
 				pools_.pop_back();