Package: bowtie / 1.2.2+dfsg-4

seqan-rename-ChunkPool.patch Patch series | download
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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

--- bowtie.orig/aligner.h
+++ bowtie/aligner.h
@@ -391,7 +391,7 @@
 		bool verbose,
 		bool quiet,
 		int maxBts,
-		ChunkPool *pool,
+		bowtieChunkPool *pool,
 		int *btCnt = NULL,
 		AlignerMetrics *metrics = NULL) :
 		Aligner(true, rangeMode),
@@ -597,7 +597,7 @@
 	bool quiet_; // don't print informational/warning info
 
 	const int maxBts_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	int *btCnt_;
 	AlignerMetrics *metrics_;
 };
@@ -638,7 +638,7 @@
 		bool verbose,
 		bool quiet,
 		int maxBts,
-		ChunkPool *pool,
+		bowtieChunkPool *pool,
 		int *btCnt) :
 		Aligner(true, rangeMode),
 		refs_(refs),
@@ -1405,7 +1405,7 @@
 	bool quiet_;
 
 	int maxBts_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	int *btCnt_;
 
 	// Range-finding state for first mate
@@ -1529,7 +1529,7 @@
 		bool verbose,
 		bool quiet,
 		int maxBts,
-		ChunkPool *pool,
+		bowtieChunkPool *pool,
 		int *btCnt) :
 		Aligner(true, rangeMode),
 		refs_(refs),
@@ -2076,7 +2076,7 @@
 	TDriver* driver_;
 
 	// Pool for distributing chunks of best-first path descriptor memory
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 
 	bool verbose_;
 	bool quiet_;
--- bowtie.orig/aligner_0mm.h
+++ bowtie/aligner_0mm.h
@@ -32,7 +32,7 @@
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -123,7 +123,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	bool maqPenalty_;
@@ -162,7 +162,7 @@
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -363,7 +363,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- bowtie.orig/aligner_1mm.h
+++ bowtie/aligner_1mm.h
@@ -32,7 +32,7 @@
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -160,7 +160,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool maqPenalty_;
@@ -199,7 +199,7 @@
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -475,7 +475,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- bowtie.orig/aligner_23mm.h
+++ bowtie/aligner_23mm.h
@@ -33,7 +33,7 @@
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -230,7 +230,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool maqPenalty_;
@@ -271,7 +271,7 @@
 			RangeCache *cacheFw,
 			RangeCache *cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -672,7 +672,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- bowtie.orig/aligner_seed_mm.h
+++ bowtie/aligner_seed_mm.h
@@ -37,7 +37,7 @@
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
@@ -554,7 +554,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	bool strandFix_;
@@ -598,7 +598,7 @@
 			RangeCache* cacheFw,
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
-			ChunkPool *pool,
+			bowtieChunkPool *pool,
 			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool reportSe,
@@ -1375,7 +1375,7 @@
 	RangeCache *cacheFw_;
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
-	ChunkPool *pool_;
+	bowtieChunkPool *pool_;
 	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	const bool reportSe_;
--- bowtie.orig/ebwt_search.cpp
+++ bowtie/ebwt_search.cpp
@@ -125,7 +125,7 @@
 static bool strandFix;  // attempt to fix strand bias
 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 useV1;
 static bool reportSe;
@@ -232,7 +232,7 @@
 	strandFix				= true;  // attempt to fix strand bias
 	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?
 	useV1					= true;
 	reportSe				= false;
@@ -1340,7 +1340,7 @@
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
 
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 	UnpairedExactAlignerV1Factory alSEfact(
 			ebwt,
 			NULL,
@@ -1631,7 +1631,7 @@
 	// Global initialization
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 
 	Unpaired1mmAlignerV1Factory alSEfact(
 			ebwtFw,
@@ -2084,7 +2084,7 @@
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
 
-	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
 	Unpaired23mmAlignerV1Factory alSEfact(
 			ebwtFw,
 			&ebwtBw,
@@ -2756,7 +2756,7 @@
 	// Global initialization
 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
-	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) {
--- bowtie.orig/ebwt_search_backtrack.h
+++ bowtie/ebwt_search_backtrack.h
@@ -2703,7 +2703,7 @@
 			bool verbose,
 			bool quiet,
 			bool mate1,
-			ChunkPool* pool,
+			bowtieChunkPool* pool,
 			int *btCnt) :
 			SingleRangeSourceDriver<EbwtRangeSource>(
 					params, rs, fw, sink, sinkPt, os, verbose,
@@ -2877,7 +2877,7 @@
 			bool verbose,
 			bool quiet,
 			bool mate1,
-			ChunkPool* pool,
+			bowtieChunkPool* pool,
 			int *btCnt = NULL) :
 			params_(params),
 			rs_(rs),
@@ -2936,7 +2936,7 @@
 	bool verbose_;
 	bool quiet_;
 	bool mate1_;
-	ChunkPool* pool_;
+	bowtieChunkPool* pool_;
 	int *btCnt_;
 };
 
--- bowtie.orig/pool.h
+++ bowtie/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 @@
 			}
 		} 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 @@
 	/**
 	 * Delete all the pools.
 	 */
-	~ChunkPool() {
+	~bowtieChunkPool() {
 		if(pool_ != NULL) delete[] pool_;
 	}
 
@@ -189,7 +189,7 @@
 	 * 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 @@
 		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
--- bowtie.orig/range_source.h
+++ bowtie/range_source.h
@@ -1307,7 +1307,7 @@
 
 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"),
@@ -1556,7 +1556,7 @@
 
 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
@@ -1730,7 +1730,7 @@
 		bool quiet,
 		bool mate1,
 		uint32_t minCostAdjustment,
-		ChunkPool* pool,
+		bowtieChunkPool* pool,
 		int *btCnt) :
 		RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
 		len_(0), mate1_(mate1),