commit: 1e3f5d88f730c5d04b64095114d2e48c1ec4ba58 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Apr 9 18:26:28 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Apr 9 18:57:05 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e3f5d88
sci-biology/bowtie: unbundle SeqAn, import Debian patches * EAPI=6 Package-Manager: portage-2.2.28 sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 75 ++++ .../files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch | 17 + .../files/bowtie-1.1.2-fix-setBegin-call.patch | 42 +++ .../bowtie/files/bowtie-1.1.2-seqan-popcount.patch | 24 ++ .../bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 +++++++++++++++++++++ .../bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 +++++ .../bowtie/files/bowtie-1.1.2-spelling.patch | 48 +++ .../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 ++ 8 files changed, 700 insertions(+) diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild new file mode 100644 index 0000000..e0b4358 --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + sci-biology/seqan:1.4 + app-arch/unzip" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( + "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" + "${FILESDIR}/${P}-fix-setBegin-call.patch" + "${FILESDIR}/${P}-seqan-popcount.patch" + "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" + "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" + "${FILESDIR}/${P}-spelling.patch" + "${FILESDIR}/${P}-tbb-tinythread-missing.patch" + "${FILESDIR}/${P}-unbundle-seqan.patch" +) + +src_prepare() { + default + + # remove bundled libraries, use system seqan 1.4 + rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch new file mode 100644 index 0000000..78b9c01 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch @@ -0,0 +1,17 @@ +Description: Change class name of _Context_LSS + New version 1.4 of SeQan uses a different name of the class. +Forwarded: no +Author: Gert Wollny <gw.foss...@gmail.com> +Last-Update: 2014-100-06 + +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -856,7 +856,7 @@ void DifferenceCoverSample<TStr>::build( + { + Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); + VMSG_NL(" Invoking Larsson-Sadakane on ranks"); +- _Context_LSS<TIndexOff> c; ++ ContextLss_<TIndexOff> c; + c.suffixsort( + (TIndexOff*)begin(_isaPrime, Standard()), + (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch new file mode 100644 index 0000000..af7f7f6 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch @@ -0,0 +1,42 @@ +Description: Proper type-casting in using seqan::_setBegin(). + Required by newer versions of GCC. +Forwarded: no +Author: Ognyan Kulev <o...@debian.org> +Last-Update: 2013-04-18 + +--- a/pat.h ++++ b/pat.h +@@ -82,20 +82,20 @@ struct ReadBuf { + ~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); + } + } + diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch new file mode 100644 index 0000000..52cb4f4 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch @@ -0,0 +1,24 @@ +Description: Use SeqAn 1.4's seqan::popCount() function instead of own function +Author: Ognyan Kulev <o...@debian.org> +Last-Update: 2014-03-08 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -476,6 +476,8 @@ static String<T> getDeltaMap(T v, const + return amap; + } + ++// Debian: Use seqan::popCount ++#if 0 + /** + * Return population count (count of all bits set to 1) of i. + */ +@@ -488,6 +490,7 @@ static unsigned int popCount(T i) { + } + return cnt; + } ++#endif + + /** + * Calculate log-base-2 of i 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 0000000..171f9ba --- /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 <o...@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), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch new file mode 100644 index 0000000..38664ae --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch @@ -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 <o...@debian.org> +Last-Update: 2014-08-13 + +--- a/blockwise_sa.h ++++ b/blockwise_sa.h +@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS + try { + // Allocate and initialize containers for holding bucket + // sizes and representatives. +- fill(bucketSzs, numBuckets, 0, Exact()); +- fill(bucketReps, numBuckets, OFF_MASK, Exact()); ++ resize(bucketSzs, numBuckets, 0, Exact()); ++ resize(bucketReps, numBuckets, OFF_MASK, Exact()); + } catch(bad_alloc &e) { + if(this->_passMemExc) { + throw e; // rethrow immediately +@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl + // 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()); + } +@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl + 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 +@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const + // 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) +@@ -532,7 +532,7 @@ public: + 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()); + uint32_t lim = (uint32_t)length(_ds); + for(uint32_t i = 0; i < lim; i++) { + _dInv[_ds[i]] = i; +@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil + VMSG_NL(" Doing sanity check"); + TIndexOffU added = 0; + String<TIndexOffU> sorted; +- fill(sorted, length(_isaPrime), OFF_MASK, Exact()); ++ resize(sorted, length(_isaPrime), OFF_MASK, Exact()); + for(size_t di = 0; di < this->d(); di++) { + uint32_t d = _ds[di]; + size_t i = 0; +@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS + assert_eq(length(_doffs), d+1); + // Size sPrime appropriately + reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS +- fill(sPrime, sPrimeSz, OFF_MASK, Exact()); ++ resize(sPrime, sPrimeSz, OFF_MASK, Exact()); + // Slot suffixes from text into sPrime according to the mu + // mapping; where the mapping would leave a blank, insert a 0 + TIndexOffU added = 0; +@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build( + // arrays back into sPrime. + VMSG_NL(" Allocating rank array"); + reserve(_isaPrime, length(sPrime)+1, Exact()); +- fill(_isaPrime, length(sPrime), OFF_MASK, Exact()); ++ resize(_isaPrime, length(sPrime), OFF_MASK, Exact()); + assert_gt(length(_isaPrime), 0); + { + Timer timer(cout, " Ranking v-sort output time: ", this->verbose()); diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch new file mode 100644 index 0000000..ff484df --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch @@ -0,0 +1,48 @@ +Author: Andreas Tille <ti...@debian.org> +Last-Update: Thu, 01 Oct 2015 09:47:23 +0200 +Description: Fix spelling + +--- a/MANUAL ++++ b/MANUAL +@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie + actually wrapper scripts that call binary programs as appropriate. The + wrappers shield users from having to distinguish between "small" and + "large" index formats, discussed briefly in the following section. The +-appropiate index type is selected based on the input size. ++appropriate index type is selected based on the input size. + + It is recommended that you always run the bowtie wrappers and not run + the binaries directly. +--- a/MANUAL.markdown ++++ b/MANUAL.markdown +@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie + actually wrapper scripts that call binary programs as appropriate. The + wrappers shield users from having to distinguish between "small" and + "large" index formats, discussed briefly in the following section. The +-appropiate index type is selected based on the input size. ++appropriate index type is selected based on the input size. + + It is recommended that you always run the bowtie wrappers and not run + the binaries directly. +--- a/doc/manual.html ++++ b/doc/manual.html +@@ -201,7 +201,7 @@ T2302111203131231130300111123220 + <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p> + <p>Note that SOLiD-generated read files can have "orphaned" mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click "NGS: QC and manipulation", then "SOLiD-to-FASTQ" in the left-hand sidebar).</p> + <h2 id="wrapper-scripts">Wrapper scripts</h2> +-<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p> ++<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p> + <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p> + <h2 id="small-and-large-indexes">Small and large indexes</h2> + <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a "large" index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p> +--- a/ref_read.cpp ++++ b/ref_read.cpp +@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in, + << "reference into smaller chunks and index each independently." << endl; + #else + cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl +- << "build a large index instead using the appropiate options." << endl; ++ << "build a large index instead using the appropriate options." << endl; + #endif + throw 1; + } diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch new file mode 100644 index 0000000..54391ae --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch @@ -0,0 +1,27 @@ +Description: Use Debian packaged SeqAn library instead of copy in upstream source +Author: Andreas Tille <ti...@debian.org> +Date: 2011-01-30 +Last-Update: 2013-04-18 +Reviewed-by: Ognyan Kulev <o...@debian.org> + +--- a/Makefile ++++ b/Makefile +@@ -5,9 +5,7 @@ + prefix = /usr/local + bindir = $(prefix)/bin + +-SEQAN_DIR = SeqAn-1.1 +-SEQAN_INC = -I $(SEQAN_DIR) +-INC = $(SEQAN_INC) -I third_party ++INC = `pkg-config --cflags seqan-1.4` + CPP = g++ + CXX = $(CPP) + CC = gcc +@@ -168,7 +166,6 @@ + $(wildcard genomes/NC_008253.fna) \ + $(wildcard reads/e_coli_1000.*) \ + $(wildcard reads/e_coli_1000_*) \ +- SeqAn-1.1 \ + bowtie \ + bowtie-build \ + bowtie-inspect \
