diff options
Diffstat (limited to 'sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch')
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 |
1 files changed, 0 insertions, 382 deletions
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch deleted file mode 100644 index 171f9bab8fae..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch +++ /dev/null @@ -1,382 +0,0 @@ -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), |