Author: ogi Date: 2013-04-18 09:56:32 +0000 (Thu, 18 Apr 2013) New Revision: 13348
Added: trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch Removed: trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch Modified: trunk/packages/bowtie/trunk/debian/changelog trunk/packages/bowtie/trunk/debian/patches/series trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch Log: Preparation for bowtie 1.0.0: refreshed patches and usage of Debian's SeqAn library. Modified: trunk/packages/bowtie/trunk/debian/changelog =================================================================== --- trunk/packages/bowtie/trunk/debian/changelog 2013-04-17 15:55:58 UTC (rev 13347) +++ trunk/packages/bowtie/trunk/debian/changelog 2013-04-18 09:56:32 UTC (rev 13348) @@ -1,3 +1,15 @@ +bowtie (1.0.0-1) UNRELEASED; urgency=low + + * New upstream version. + * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch. + * Removed patch gcc-4.7.patch (fixed upstream). + * Activated use_debian_seqan.patch and added the following patches: + - seqan-fix-setBegin-call.patch + - seqan-rename-ChunkPool.patch + - seqan-rename-fill-to-resize.patch + + -- Ognyan Kulev <[email protected]> Thu, 18 Apr 2013 13:00:04 +0300 + bowtie (0.12.7-3) unstable; urgency=low * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS Deleted: trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch 2013-04-17 15:55:58 UTC (rev 13347) +++ trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch 2013-04-18 09:56:32 UTC (rev 13348) @@ -1,49 +0,0 @@ -Author: gregor herrmann <[email protected]>, -Date: Sun, 22 Apr 2012 22:27:51 +0200 -Bug-Closed: http://bugs.debian.org/667120 -Description: function "reverseInPlace" is declared after the function is used - For more detailed information see - http://lists.debian.org/debian-mentors/2012/04/msg00409.html - and other mails in this thread. - ---- bowtie-0.12.7.orig/alphabet.h -+++ bowtie-0.12.7/alphabet.h -@@ -41,6 +41,19 @@ - /** - * Reverse-complement s in-place. Ns go to Ns. - */ -+ -+/// Reverse a string in-place -+template <typename TStr> -+static inline void reverseInPlace(TStr& s) { -+ typedef typename Value<TStr>::Type TVal; -+ size_t len = length(s); -+ for(size_t i = 0; i < (len>>1); i++) { -+ TVal tmp = s[i]; -+ s[i] = s[len-i-1]; -+ s[len-i-1] = tmp; -+ } -+} -+ - template<typename TStr> - static inline void reverseComplementInPlace(TStr& s, bool color) { - typedef typename Value<TStr>::Type TVal; -@@ -69,18 +82,6 @@ - } - } - --/// Reverse a string in-place --template <typename TStr> --static inline void reverseInPlace(TStr& s) { -- typedef typename Value<TStr>::Type TVal; -- size_t len = length(s); -- for(size_t i = 0; i < (len>>1); i++) { -- TVal tmp = s[i]; -- s[i] = s[len-i-1]; -- s[len-i-1] = tmp; -- } --} -- - /** - * Return the reverse-complement of s. - */ Added: trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch (rev 0) +++ trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch 2013-04-18 09:56:32 UTC (rev 13348) @@ -0,0 +1,42 @@ +Description: Proper type-casting in using seqan::_setBegin(). + Required by newer versions of GCC. +Forwarded: no +Author: Ognyan Kulev <[email protected]> +Last-Update: 2013-04-18 + +--- a/pat.h ++++ b/pat.h +@@ -82,20 +82,20 @@ + ~ReadBuf() { + clearAll(); reset(); + // Prevent seqan from trying to free buffers +- _setBegin(patFw, NULL); +- _setBegin(patRc, NULL); +- _setBegin(qual, NULL); +- _setBegin(patFwRev, NULL); +- _setBegin(patRcRev, NULL); +- _setBegin(qualRev, NULL); +- _setBegin(name, NULL); ++ _setBegin(patFw, (Dna5*)NULL); ++ _setBegin(patRc, (Dna5*)NULL); ++ _setBegin(qual, (char*)NULL); ++ _setBegin(patFwRev, (Dna5*)NULL); ++ _setBegin(patRcRev, (Dna5*)NULL); ++ _setBegin(qualRev, (char*)NULL); ++ _setBegin(name, (char*)NULL); + for(int j = 0; j < 3; j++) { +- _setBegin(altPatFw[j], NULL); +- _setBegin(altPatFwRev[j], NULL); +- _setBegin(altPatRc[j], NULL); +- _setBegin(altPatRcRev[j], NULL); +- _setBegin(altQual[j], NULL); +- _setBegin(altQualRev[j], NULL); ++ _setBegin(altPatFw[j], (Dna5*)NULL); ++ _setBegin(altPatFwRev[j], (Dna5*)NULL); ++ _setBegin(altPatRc[j], (Dna5*)NULL); ++ _setBegin(altPatRcRev[j], (Dna5*)NULL); ++ _setBegin(altQual[j], (char*)NULL); ++ _setBegin(altQualRev[j], (char*)NULL); + } + } + Added: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch (rev 0) +++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2013-04-18 09:56:32 UTC (rev 13348) @@ -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 <[email protected]> +Last-Update: 2013-04-18 + +--- a/aligner.h ++++ b/aligner.h +@@ -337,7 +337,7 @@ + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt = NULL, + AlignerMetrics *metrics = NULL) : + Aligner(true, rangeMode), +@@ -544,7 +544,7 @@ + bool quiet_; // don't print informational/warning info + + const int maxBts_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + int *btCnt_; + AlignerMetrics *metrics_; + }; +@@ -585,7 +585,7 @@ + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt) : + Aligner(true, rangeMode), + refs_(refs), +@@ -1358,7 +1358,7 @@ + bool quiet_; + + int maxBts_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + int *btCnt_; + + // Range-finding state for first mate +@@ -1482,7 +1482,7 @@ + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt) : + Aligner(true, rangeMode), + refs_(refs), +@@ -2035,7 +2035,7 @@ + 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 @@ + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -124,7 +124,7 @@ + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + bool maqPenalty_; +@@ -164,7 +164,7 @@ + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -366,7 +366,7 @@ + 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 @@ + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -161,7 +161,7 @@ + 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 @@ + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -478,7 +478,7 @@ + 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 @@ + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -231,7 +231,7 @@ + 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 @@ + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -675,7 +675,7 @@ + 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 @@ + 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_; +--- a/ebwt_search.cpp ++++ b/ebwt_search.cpp +@@ -110,7 +110,7 @@ + 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; +@@ -221,7 +221,7 @@ + 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; +@@ -1202,7 +1202,7 @@ + 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, +@@ -1371,7 +1371,7 @@ + // 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, +@@ -1668,7 +1668,7 @@ + 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, +@@ -2101,7 +2101,7 @@ + // 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 @@ + 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 @@ + bool verbose, + bool quiet, + bool mate1, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt = NULL) : + params_(params), + rs_(rs), +@@ -2986,7 +2986,7 @@ + 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 @@ + } + } 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 +--- a/range_source.h ++++ b/range_source.h +@@ -1388,7 +1388,7 @@ + + 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"), +@@ -1637,7 +1637,7 @@ + + 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 +@@ -1811,7 +1811,7 @@ + bool quiet, + bool mate1, + uint32_t minCostAdjustment, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt) : + RangeSourceDriver<TRangeSource>(true, minCostAdjustment), + len_(0), mate1_(mate1), Added: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch (rev 0) +++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch 2013-04-18 09:56:32 UTC (rev 13348) @@ -0,0 +1,85 @@ +Description: Renamed seqan::fill function calls to use seqan::resize. + SeqAn 1.3 renamed seqan::fill() to seqan::resize(). + SeqAn ticket: http://trac.seqan.de/ticket/77 +Forwarded: no +Author: Ognyan Kulev <[email protected]> +Last-Update: 2013-04-18 + +--- a/blockwise_sa.h ++++ b/blockwise_sa.h +@@ -448,8 +448,8 @@ + try { + // Allocate and initialize containers for holding bucket + // sizes and representatives. +- fill(bucketSzs, numBuckets, 0, Exact()); +- fill(bucketReps, numBuckets, 0xffffffff, Exact()); ++ resize(bucketSzs, numBuckets, 0, Exact()); ++ resize(bucketReps, numBuckets, 0xffffffff, Exact()); + } catch(bad_alloc &e) { + if(this->_passMemExc) { + throw e; // rethrow immediately +@@ -806,7 +806,7 @@ + // Not the last bucket + assert_lt(_cur, length(_sampleSuffs)); + hi = _sampleSuffs[_cur]; +- fill(zHi, _dcV, 0, Exact()); ++ resize(zHi, _dcV, 0, Exact()); + assert_eq(zHi[0], 0); + calcZ(t, hi, zHi, this->verbose(), this->sanityCheck()); + } +@@ -815,7 +815,7 @@ + assert_gt(_cur, 0); + assert_leq(_cur, length(_sampleSuffs)); + lo = _sampleSuffs[_cur-1]; +- fill(zLo, _dcV, 0, Exact()); ++ resize(zLo, _dcV, 0, Exact()); + assert_gt(_dcV, 3); + assert_eq(zLo[0], 0); + calcZ(t, lo, zLo, this->verbose(), this->sanityCheck()); +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -451,7 +451,7 @@ + // Declare anchor-map-related items + String<T> amap; + size_t amapEnts = 1; +- fill(amap, v, 0xffffffff, Exact()); ++ resize(amap, v, 0xffffffff, Exact()); + amap[0] = 0; + // Print out difference cover (and optionally calculate + // anchor map) +@@ -531,7 +531,7 @@ + assert_gt(_d, 0); + assert_eq(1, popCount(_v)); // must be power of 2 + // Build map from d's to idx's +- fill(_dInv, _v, 0xffffffff, Exact()); ++ resize(_dInv, _v, 0xffffffff, Exact()); + for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i; + } + +@@ -652,7 +652,7 @@ + VMSG_NL(" Doing sanity check"); + uint32_t added = 0; + String<uint32_t> sorted; +- fill(sorted, length(_isaPrime), 0xffffffff, Exact()); ++ resize(sorted, length(_isaPrime), 0xffffffff, Exact()); + for(size_t di = 0; di < this->d(); di++) { + uint32_t d = _ds[di]; + size_t i = 0; +@@ -713,7 +713,7 @@ + assert_eq(length(_doffs), d+1); + // Size sPrime appropriately + reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS +- fill(sPrime, sPrimeSz, 0xffffffff, Exact()); ++ resize(sPrime, sPrimeSz, 0xffffffff, Exact()); + // Slot suffixes from text into sPrime according to the mu + // mapping; where the mapping would leave a blank, insert a 0 + uint32_t added = 0; +@@ -818,7 +818,7 @@ + // arrays back into sPrime. + VMSG_NL(" Allocating rank array"); + reserve(_isaPrime, length(sPrime)+1, Exact()); +- fill(_isaPrime, length(sPrime), 0xffffffff, Exact()); ++ resize(_isaPrime, length(sPrime), 0xffffffff, Exact()); + assert_gt(length(_isaPrime), 0); + { + Timer timer(cout, " Ranking v-sort output time: ", this->verbose()); Modified: trunk/packages/bowtie/trunk/debian/patches/series =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/series 2013-04-17 15:55:58 UTC (rev 13347) +++ trunk/packages/bowtie/trunk/debian/patches/series 2013-04-18 09:56:32 UTC (rev 13348) @@ -1,2 +1,5 @@ -gcc-4.7.patch use-dpkg-buildflags.patch +use_debian_seqan.patch +seqan-fix-setBegin-call.patch +seqan-rename-ChunkPool.patch +seqan-rename-fill-to-resize.patch Modified: trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2013-04-17 15:55:58 UTC (rev 13347) +++ trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2013-04-18 09:56:32 UTC (rev 13348) @@ -4,14 +4,14 @@ Last-Update: 2012-04-24 Bug-Closed: http://bugs.debian.org/670230 ---- bowtie-0.12.7.orig/Makefile -+++ bowtie-0.12.7/Makefile -@@ -177,7 +177,7 @@ - cat $^ | md5sum | awk '{print $$1}' > [email protected] - endef +--- a/Makefile ++++ b/Makefile +@@ -173,7 +173,7 @@ + $(MM_DEF) \ + $(SHMEM_DEF) --ALL_FLAGS=$(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) -+ALL_FLAGS=$(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) +-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) ++ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" Modified: trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2013-04-17 15:55:58 UTC (rev 13347) +++ trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2013-04-18 09:56:32 UTC (rev 13348) @@ -1,11 +1,11 @@ -Note: This patch is deactivated because the Debian packaged version of SeqAn 1.2 - is not compatible with the version included into this package - -Author: Andreas Tille <tilleqdebian.org> +Description: Use Debian packaged SeqAn library instead of copy in upstream source +Author: Andreas Tille <[email protected]> Date: 2011-01-30 -Description: Use Debian packages SeqAn Librariy instead of copy in upstream source ---- bowtie-0.12.7.orig/Makefile -+++ bowtie-0.12.7/Makefile +Last-Update: 2013-04-18 +Reviewed-by: Ognyan Kulev <[email protected]> + +--- a/Makefile ++++ b/Makefile @@ -2,7 +2,7 @@ # Makefile for bowtie, bowtie-build, bowtie-inspect # @@ -14,13 +14,12 @@ +SEQAN_DIR = /usr/include/seqan SEQAN_INC = -I $(SEQAN_DIR) INC = $(SEQAN_INC) - GCC_PREFIX = $(shell dirname `which gcc`) -@@ -149,8 +149,6 @@ - $(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) + CPP = g++ +@@ -133,7 +133,6 @@ + $(wildcard genomes/NC_008253.fna) \ + $(wildcard reads/e_coli_1000.*) \ + $(wildcard reads/e_coli_1000_*) \ +- SeqAn-1.1 \ + doc/manual.html \ + doc/README \ + doc/style.css \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
