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, 382 insertions, 0 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 new file mode 100644 index 000000000000..171f9bab8fae --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch @@ -0,0 +1,382 @@ +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), |