Added the tiny thread spinlock and started the tiny thread usage impl…

…ementation changes.

Makefile

@@ -5,13 +5,10 @@
 SEQAN_DIR = SeqAn-1.1
 SEQAN_INC = -I $(SEQAN_DIR)
 INC = $(SEQAN_INC)
-GCC_PREFIX = $(shell dirname `which gcc`)
-GCC_SUFFIX =
-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+CPP = g++
 CXX = $(CPP)
+CC = gcc
 HEADERS = $(wildcard *.h)
-BOWTIE_PTHREADS = 1
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 1
 EXTRA_FLAGS =
@@ -25,64 +22,62 @@ WINDOWS = 0
 CYGWIN = 0
 MINGW = 0
 ifneq (,$(findstring CYGWIN,$(shell uname)))
-WINDOWS = 1
-CYGWIN = 1
-# POSIX memory-mapped files not currently supported on Windows
-BOWTIE_MM = 0
-BOWTIE_SHARED_MEM = 0
+    WINDOWS = 1
+    CYGWIN = 1
+    # POSIX memory-mapped files not currently supported on Windows
+    BOWTIE_MM = 0
+    BOWTIE_SHARED_MEM = 0
 else
-ifneq (,$(findstring MINGW,$(shell uname)))
-WINDOWS = 1
-CYGWIN = 1
-# POSIX memory-mapped files not currently supported on Windows
-BOWTIE_MM = 0
-BOWTIE_SHARED_MEM = 0
-endif
+    ifneq (,$(findstring MINGW,$(shell uname)))
+	WINDOWS = 1
+	CYGWIN = 1
+	# POSIX memory-mapped files not currently supported on Windows
+	BOWTIE_MM = 0
+	BOWTIE_SHARED_MEM = 0
+    endif
 endif
 
 MACOS = 0
 ifneq (,$(findstring Darwin,$(shell uname)))
-MACOS = 1
+    MACOS = 1
 endif
 
 LINUX = 0
 ifneq (,$(findstring Linux,$(shell uname)))
-LINUX = 1
-EXTRA_FLAGS += -Wl,--hash-style=both
+    LINUX = 1
+    EXTRA_FLAGS += -Wl,--hash-style=both
 endif
 
 MM_DEF = 
 ifeq (1,$(BOWTIE_MM))
-MM_DEF = -DBOWTIE_MM
+    MM_DEF = -DBOWTIE_MM
 endif
 SHMEM_DEF = 
 ifeq (1,$(BOWTIE_SHARED_MEM))
-SHMEM_DEF = -DBOWTIE_SHARED_MEM
+    SHMEM_DEF = -DBOWTIE_SHARED_MEM
 endif
 PTHREAD_PKG =
 PTHREAD_LIB =
 PTHREAD_DEF =
-ifeq (1,$(BOWTIE_PTHREADS))
-PTHREAD_DEF = -DBOWTIE_PTHREADS
-PTHREAD_LIB = -lpthread
+
 ifeq (1,$(MINGW))
-# pthreads for windows forces us to be specific about the library
-EXTRA_FLAGS = -static-libgcc -static-libstdc++
-PTHREAD_LIB = -lpthread
-endif
+	PTHREAD_LIB = 
+	EXTRA_FLAGS = -static-libgcc -static-libstdc++
+else
+	PTHREAD_LIB = -lpthread
 endif
 
 PREFETCH_LOCALITY = 2
 PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
 
-LIBS = 
-SEARCH_LIBS = $(PTHREAD_LIB)
+LIBS = $(PTHREAD_LIB)
+SEARCH_LIBS = 
 BUILD_LIBS =
 INSPECT_LIBS = 
 
 ifeq (1,$(MINGW))
-BUILD_LIBS = $(PTHREAD_LIB)
-INSPECT_LIBS = $(PTHREAD_LIB)
+    BUILD_LIBS = 
+    INSPECT_LIBS = 
 endif
 
 OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
@@ -100,16 +95,18 @@ VERSION = $(shell cat VERSION)
 
 # msys will always be 32 bit so look at the cpu arch instead.
 ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
-BITS=64
+    ifeq (1,$(MINGW))
+	BITS=64
+    endif
 endif
 
 # Convert BITS=?? to a -m flag
 BITS_FLAG =
 ifeq (32,$(BITS))
-BITS_FLAG = -m32
+    BITS_FLAG = -m32
 endif
 ifeq (64,$(BITS))
-BITS_FLAG = -m64
+    BITS_FLAG = -m64
 endif
 
 DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
@@ -144,16 +141,10 @@ GENERAL_LIST = $(wildcard scripts/*.sh) \
                TUTORIAL \
                VERSION
 
-# This is helpful on Windows under MinGW/MSYS, where Make might go for
-# the Windows FIND tool instead.
-FIND=$(shell which find)
-
 SRC_PKG_LIST = $(wildcard *.h) \
                $(wildcard *.hh) \
                $(wildcard *.c) \
                $(wildcard *.cpp) \
-               $(shell $(FIND) SeqAn-1.1 -name "*.h") \
-               $(shell $(FIND) SeqAn-1.1 -name "*.txt") \
                doc/strip_markdown.pl \
                Makefile \
                $(GENERAL_LIST)

bitset.h

@@ -57,7 +57,6 @@ class SyncBitset {
 	 * error message and quit if allocation fails.
 	 */
 	SyncBitset(uint32_t sz, const char *errmsg = NULL) : _errmsg(errmsg) {
-		MUTEX_INIT(_lock);
 		uint32_t nwords = (sz >> 5)+1; // divide by 32 and add 1
 		try {
 			_words = new uint32_t[nwords];
@@ -94,9 +93,9 @@ class SyncBitset {
 	 */
 	bool test(uint32_t i) {
 		bool ret;
-		MUTEX_LOCK(_lock);
+		mutex_m.lock();
 		ret = testUnsync(i);
-		MUTEX_UNLOCK(_lock);
+		mutex_m.unlock();
 		return ret;
 	}
 
@@ -105,7 +104,7 @@ class SyncBitset {
 	 * it has been set.  Uses synchronization.
 	 */
 	void set(uint32_t i) {
-		MUTEX_LOCK(_lock);
+		mutex_m.lock();
 		while(i >= _sz) {
 			// Slow path: bitset needs to be expanded before the
 			// specified bit can be set
@@ -118,15 +117,15 @@ class SyncBitset {
 		assert(((_words[i >> 5] >> (i & 0x1f)) & 1) == 0);
 		_words[i >> 5] |= (1 << (i & 0x1f));
 		assert(((_words[i >> 5] >> (i & 0x1f)) & 1) == 1);
-		MUTEX_UNLOCK(_lock);
+		mutex_m.unlock();
 	}
 
 	/**
 	 * Set a bit in the vector that might have already been set.  Uses
 	 * synchronization.
 	 */
 	void setOver(uint32_t i) {
-		MUTEX_LOCK(_lock);
+		mutex_m.lock();
 		while(i >= _sz) {
 			// Slow path: bitset needs to be expanded before the
 			// specified bit can be set
@@ -138,7 +137,7 @@ class SyncBitset {
 		assert_lt(i, _sz);
 		_words[i >> 5] |= (1 << (i & 0x1f));
 		assert(((_words[i >> 5] >> (i & 0x1f)) & 1) == 1);
-		MUTEX_UNLOCK(_lock);
+		mutex_m.unlock();
 	}
 
 
@@ -156,7 +155,7 @@ class SyncBitset {
 
 	const char *_errmsg; // error message if an allocation fails
 	uint32_t _sz;        // size as # of bits
-	MUTEX_T _lock;       // mutex
+	MUTEX_T mutex_m;       // mutex
 	uint32_t *_words;    // storage
 };