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-rw-r--r--sci-biology/bowtie/Manifest1
-rw-r--r--sci-biology/bowtie/bowtie-1.1.2-r1.ebuild74
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch17
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch42
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch24
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch382
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch85
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch48
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch18
-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch27
10 files changed, 0 insertions, 718 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 824c7439adc1..50ad9715e984 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1 @@
-DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8
DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
deleted file mode 100644
index d8b607f870fc..000000000000
--- a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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
deleted file mode 100644
index 78b9c01a0462..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-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.fossdev@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
deleted file mode 100644
index af7f7f61cd5e..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Description: Proper type-casting in using seqan::_setBegin().
- Required by newer versions of GCC.
-Forwarded: no
-Author: Ognyan Kulev <ogi@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
deleted file mode 100644
index 52cb4f496521..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Description: Use SeqAn 1.4's seqan::popCount() function instead of own function
-Author: Ognyan Kulev <ogi@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
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),
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
deleted file mode 100644
index 38664aeee989..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-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@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
deleted file mode 100644
index ff484dfa3ebb..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-Author: Andreas Tille <tille@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 &quot;orphaned&quot; 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 &quot;NGS: QC and manipulation&quot;, then &quot;SOLiD-to-FASTQ&quot; 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 &quot;small&quot; and &quot;large&quot; 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 &quot;small&quot; and &quot;large&quot; 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 &quot;small&quot; index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a &quot;large&quot; 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-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
deleted file mode 100644
index bc0f1d09557d..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Fixes missing tinythread.cpp when using TBB:
-
-ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()'
-
---- bowtie-1.1.2/Makefile
-+++ bowtie-1.1.2/Makefile
-@@ -106,10 +106,7 @@
- endif
-
- OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
-- edit.cpp ebwt.cpp
--ifneq (1,$(WITH_TBB))
-- OTHER_CPPS += tinythread.cpp
--endif
-+ edit.cpp ebwt.cpp tinythread.cpp
-
- SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
- log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
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
deleted file mode 100644
index 54391ae415a3..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Use Debian packaged SeqAn library instead of copy in upstream source
-Author: Andreas Tille <tille@debian.org>
-Date: 2011-01-30
-Last-Update: 2013-04-18
-Reviewed-by: Ognyan Kulev <ogi@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 \