path: root/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch

Description: Renamed ChunkPool class to bowtieChunkPool.
 SeqAn has a class with the same name and fatal name collision happens.
Forwarded: no
Author: Ognyan Kulev <ogi@debian.org>
Last-Update: 2013-04-18

--- a/aligner.h
+++ b/aligner.h
@@ -337,7 +337,7 @@ public:
 		bool verbose,
 		bool quiet,
 		int maxBts,
-		ChunkPool *pool,
+		bowtieChunkPool *pool,
 		int *btCnt = NULL,
 		AlignerMetrics *metrics = NULL) :
 		Aligner(true, rangeMode),
@@ -544,7 +544,7 @@ protected:
 	bool quiet_; // don't print informational/warning info
 
 	const int maxBts_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	int *btCnt_;
 	AlignerMetrics *metrics_;
 };
@@ -585,7 +585,7 @@ public:
 		bool verbose,
 		bool quiet,
 		int maxBts,
-		ChunkPool *pool,
+		bowtieChunkPool *pool,
 		int *btCnt) :
 		Aligner(true, rangeMode),
 		refs_(refs),
@@ -1358,7 +1358,7 @@ protected:
 	bool quiet_;
 
 	int maxBts_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	int *btCnt_;
 
 	// Range-finding state for first mate
@@ -1482,7 +1482,7 @@ public:
 		bool verbose,
 		bool quiet,
 		int maxBts,
-		ChunkPool *pool,
+		bowtieChunkPool *pool,
 		int *btCnt) :
 		Aligner(true, rangeMode),
 		refs_(refs),
@@ -2035,7 +2035,7 @@ protected:
 	TDriver* driver_;
 
 	// Pool for distributing chunks of best-first path descriptor memory
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 
 	bool verbose_;
 	bool quiet_;
--- a/aligner_0mm.h
+++ b/aligner_0mm.h
@@ -32,7 +32,7 @@ public:
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -124,7 +124,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	bool maqPenalty_;
@@ -164,7 +164,7 @@ public:
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -366,7 +366,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- a/aligner_1mm.h
+++ b/aligner_1mm.h
@@ -32,7 +32,7 @@ public:
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -161,7 +161,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool maqPenalty_;
@@ -201,7 +201,7 @@ public:
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -478,7 +478,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- a/aligner_23mm.h
+++ b/aligner_23mm.h
@@ -33,7 +33,7 @@ public:
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -231,7 +231,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool maqPenalty_;
@@ -273,7 +273,7 @@ public:
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -675,7 +675,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- a/aligner_seed_mm.h
+++ b/aligner_seed_mm.h
@@ -37,7 +37,7 @@ public:
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -554,7 +554,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	bool strandFix_;
@@ -598,7 +598,7 @@ public:
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -1375,7 +1375,7 @@ private:
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- a/ebwt_search.cpp
+++ b/ebwt_search.cpp
@@ -111,7 +111,7 @@ static bool strandFix;  // attempt to fi
 static bool randomizeQuals; // randomize quality values
 static bool stats; // print performance stats
 static int chunkPoolMegabytes;    // max MB to dedicate to best-first search frames per thread
-static int chunkSz;    // size of single chunk disbursed by ChunkPool
+static int chunkSz;    // size of single chunk disbursed by bowtieChunkPool
 static bool chunkVerbose; // have chunk allocator output status messages?
 static bool recal;
 static int recalMaxCycle;
@@ -223,7 +223,7 @@ static void resetOptions() {
 	randomizeQuals			= false; // randomize quality values
 	stats					= false; // print performance stats
 	chunkPoolMegabytes		= 64;    // max MB to dedicate to best-first search frames per thread
-	chunkSz					= 256;   // size of single chunk disbursed by ChunkPool (in KB)
+	chunkSz					= 256;   // size of single chunk disbursed by bowtieChunkPool (in KB)
 	chunkVerbose			= false; // have chunk allocator output status messages?
 	recal					= false;
 	recalMaxCycle			= 64;
@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
 
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 	UnpairedExactAlignerV1Factory alSEfact(
 			ebwt,
 			NULL,
@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat
 	// Global initialization
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 
 	Unpaired1mmAlignerV1Factory alSEfact(
 			ebwtFw,
@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
 
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 	Unpaired23mmAlignerV1Factory alSEfact(
 			ebwtFw,
 			&ebwtBw,
@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt
 	// Global initialization
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 
 	AlignerMetrics *metrics = NULL;
 	if(stats) {
--- a/ebwt_search_backtrack.h
+++ b/ebwt_search_backtrack.h
@@ -2724,7 +2724,7 @@ public:
 			bool verbose,
 			bool quiet,
 			bool mate1,
-			ChunkPool* pool,
+			bowtieChunkPool* pool,
 			int *btCnt) :
 			SingleRangeSourceDriver<EbwtRangeSource>(
 					params, rs, fw, sink, sinkPt, os, verbose,
@@ -2927,7 +2927,7 @@ public:
 			bool verbose,
 			bool quiet,
 			bool mate1,
-			ChunkPool* pool,
+			bowtieChunkPool* pool,
 			int *btCnt = NULL) :
 			params_(params),
 			rs_(rs),
@@ -2986,7 +2986,7 @@ protected:
 	bool verbose_;
 	bool quiet_;
 	bool mate1_;
-	ChunkPool* pool_;
+	bowtieChunkPool* pool_;
 	int *btCnt_;
 };
 
--- a/pool.h
+++ b/pool.h
@@ -19,13 +19,13 @@
  * is set at construction time.  Heap memory is only allocated at
  * construction and deallocated at destruction.
  */
-class ChunkPool {
+class bowtieChunkPool {
 public:
 	/**
 	 * Initialize a new pool with an initial size of about 'bytes'
 	 * bytes.  Exit with an error message if we can't allocate it.
 	 */
-	ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
+	bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
 		verbose(verbose_), patid(0), pool_(NULL), cur_(0),
 		chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz),
 		bits_(lim_), exhaustCrash_(false),
@@ -38,7 +38,7 @@ public:
 			}
 		} catch(std::bad_alloc& e) {
 			ThreadSafe _ts(&gLock);
-			std::cerr << "Error: Could not allocate ChunkPool of "
+			std::cerr << "Error: Could not allocate bowtieChunkPool of "
 			          << totSz << " bytes" << std::endl;
 			exhausted();
 			throw 1; // Exit if we haven't already
@@ -48,7 +48,7 @@ public:
 	/**
 	 * Delete all the pools.
 	 */
-	~ChunkPool() {
+	~bowtieChunkPool() {
 		if(pool_ != NULL) delete[] pool_;
 	}
 
@@ -189,7 +189,7 @@ public:
 	 * Initialize a new pool with an initial size of about 'bytes'
 	 * bytes.  Exit with an error message if we can't allocate it.
 	 */
-	AllocOnlyPool(ChunkPool* pool, const char *name) :
+	AllocOnlyPool(bowtieChunkPool* pool, const char *name) :
 		pool_(pool), name_(name), curPool_(0), cur_(0)
 	{
 		assert(pool != NULL);
@@ -388,7 +388,7 @@ protected:
 		lastCurInPool_.pop_back();
 	}
 
-	ChunkPool*      pool_;
+	bowtieChunkPool*      pool_;
 	const char     *name_;
 	std::vector<T*> pools_; /// the memory pools
 	uint32_t        curPool_; /// pool we're current allocating from
--- a/range_source.h
+++ b/range_source.h
@@ -1388,7 +1388,7 @@ class PathManager {
 
 public:
 
-	PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
+	PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
 		branchQ_(verbose, quiet),
 		cpool(cpool_),
 		bpool(cpool, "branch"),
@@ -1637,7 +1637,7 @@ protected:
 
 public:
 
-	ChunkPool *cpool; // pool for generic chunks of memory
+	bowtieChunkPool *cpool; // pool for generic chunks of memory
 	AllocOnlyPool<Branch> bpool; // pool for allocating Branches
 	AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates
 	AllocOnlyPool<Edit> epool; // pool for allocating Edits
@@ -1811,7 +1811,7 @@ public:
 		bool quiet,
 		bool mate1,
 		uint32_t minCostAdjustment,
-		ChunkPool* pool,
+		bowtieChunkPool* pool,
 		int *btCnt) :
 		RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
 		len_(0), mate1_(mate1),