[med-svn] r13348 - in trunk/packages/bowtie/trunk/debian: . patches
Ognyan Kulev
ogi at alioth.debian.org
Thu Apr 18 09:56:33 UTC 2013
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 <ogi at debian.org> 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 <gregoa at debian.org>,
-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 <ogi at debian.org>
+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 <ogi at debian.org>
+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 <ogi at debian.org>
+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}' > .$@.md5
- 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 <tille at debian.org>
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 <ogi at debian.org>
+
+--- 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 \
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