gentoo resync : 16.09.2020

10 files changed, 0 insertions, 727 deletions

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index bbf916477036..f9a42acddbb3 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,14 +1,4 @@
-AUX bowtie-1.1.2-_ContextLss-1.1-1.4.patch 601 BLAKE2B 36de166ef2f22d6a6cf9a5773d62f74bd69241b2a788f376108f847f09be0811b4c0156e8a5ded0e0f724cdffa77ed0b79ade064c0268b91ff966319ac2c0d0d SHA512 e39ec6323cc6fee49a6ecf3565066d9cb8f8001af2701de292025f268d57dcfa3d4c35f3e2aed56b7e3835a955e5bfb595214ac232309fcc46c6d51f83cd9f2e
-AUX bowtie-1.1.2-fix-setBegin-call.patch 1269 BLAKE2B 3bfa4fca8a94c600f6d405c4824cc83ac5838c0353f3e36417bdb1e88222902f786fe6f8e3e5099f577ca5044b2caf5d9eaf64876311ea9df4a5d4314bd22f03 SHA512 8838a0d8b35c9ceb4be1ef3439eab5e3478dcfe11c5e59e327717676eceab413b07ec97dbda9fb3527ab61653a8a6e2d651b5bb4c24114288d3b07922348c5d3
-AUX bowtie-1.1.2-seqan-popcount.patch 566 BLAKE2B 6d9d109fbbba2b85d22c923959ca0726cb9bb2da950b0b0b9aa84106c9b74c24d5bf997d1339273f92cffc5bf42c9852bf376dce260c1374c3374f8f230e395d SHA512 07b70a1941b98033967b8a7303fab94aa3a047bd5da9355f58f03af04f4515903cbf2698700fb3e987546998ebb28225672aa8fbfc65dd8bc202be8a26290838
-AUX bowtie-1.1.2-seqan-rename-ChunkPool.patch 11618 BLAKE2B bc4e9610bdde7dba741c7963c59f0361cca43e6224d1c4f2448d53111cbb0ac2d0cbd45a8d90948689bf0af1c511f180839a0b981c1588dda2f52f3a2e06a0d6 SHA512 3d05ea37c753c780163123ab8fdf8d149f0daddf4c52fcf81b1380951f132edf312b13505ea9afc2ff34ee4f3188b5251beb9e71e3c78f2eeabfadd4ab1ae5a1
-AUX bowtie-1.1.2-seqan-rename-fill-to-resize.patch 3280 BLAKE2B 00815454c116bc8b64a96668508fdddbf9909aefea84353031524eef479e60a540ed74512ca7c4e62d41e6bea4bed60cf102621390070b4f45bc63abcb2b20dd SHA512 e0a96c870670c6c38b48da0c0e0f3dc4f5e9b0654ecb1d55c22484472192cc926168a333625a582c470e2781f6e062d6704723feb29d7f32f2a19eb229622aa0
-AUX bowtie-1.1.2-spelling.patch 4157 BLAKE2B 2a48f2da1e68df166230fe35f9858b34b86962d97ec7d36a9bc0b19615961623ff2403dc630dae4cb2d4ade439b4b487762ac7be32efb7947dee3b2bb919d7a1 SHA512 1679ecdaffa55adb2c1e206a77eba6052e4d9e65e476f73df795bf1fc9e323d34c20f4673a285701b067c65477b3804cd44a4c30b36ae5502f534a4cf191af18
-AUX bowtie-1.1.2-tbb-tinythread-missing.patch 554 BLAKE2B 745629aa93f2e74191b944345b95b4d2e4e399a9e5c5a0f48690d3abe411076e4f71603333ff70050af8c63c2a9dcb753d1e9ceb1fa2ec066b9002a7f71ea96f SHA512 04cc9dad3a6c2598bde41975604a75ca5f0b1490144d2a9f91c049b04b8af80d95e8842aaf1b551ec3d9ca842981e72aa692f00b80971c067d7464776c1e78c9
-AUX bowtie-1.1.2-unbundle-seqan.patch 751 BLAKE2B d9689b298f21f4619dbbed96b58d8ae7fc5f646539ae33291222d282153b545ad6fb3e30fe1ba5f0f452e2f3e7e9706b6761f5d4184dcd5ad96a55ccc7b246be SHA512 9a68ccc98774a2c9ddb8f45b5ed009230d14d3e29837c6dd8aac34e298f57208361ef45d0e7d9d074495f3465b58f08606cced9e4fccb549785591ff954cb2b8
 AUX bowtie-2.2.9-fix-c++14.patch 687 BLAKE2B a75f473f429379789a97142d7820fb19fc1a64b764236c6fa1c068cefb03e37a58b41b0a515a62d42e85b3131f0dfe8f2bb856126528099277394674a0e53248 SHA512 3aa6e7a30fdf93ae564091ce9b87338ab9feccbd0c873f4130af71dc94fd3b27527b42a93f13471a2613bad44dbacd639d17515000f03856695a0021ce14dfc5
-DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8
 DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
-EBUILD bowtie-1.1.2-r1.ebuild 1643 BLAKE2B 81f79b8b8d9b9a56061bf92df193a21e2db03bdacb6290020e8fb2426e3e1cf9e5a6a802cb6fa5f5f68be8d7f92f749e14c0c3528ebad5825d3927bcf33ca483 SHA512 8b5c22f29aafb5977313ea002fcd654ac991015f7808f02f8e02c2105dd9a6fa77b5f5342e82d38b07674c93dbe397333be78f6d1ca9a24a60531d6a40efe382
 EBUILD bowtie-2.2.9.ebuild 1277 BLAKE2B b9cf9edc34af3f01eb1cde1510637bbcbaf7206d9a24135d859d14dcefe793abd0b78dd19dbcd1835840514e754061aee86a79d5992ca68d316c64c98bb4891c SHA512 40e22698d5df241b8b98c601f8ed22276d39f4c9818bb23afec0a39b625fd38a0fdb3f4b4d6f8c01b458e2b6b3464a7ee8a135bd446f3488354eeca9934daa85
 MISC metadata.xml 528 BLAKE2B 310fb406a0dbe56b194ae13cf521264e105f9d849b09e10d5d7e556c7d00a9cc7a0f9546a91e43f30344c9ec14a76e0d8a3f037fb4cb91bba68999d9f45b69e0 SHA512 1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301
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 \