From 9ee6d97c2883d42f204a533a8bc1f4562df778fb Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 16 Sep 2020 09:32:48 +0100 Subject: gentoo resync : 16.09.2020 --- sci-biology/bowtie/Manifest | 10 - sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 74 ---- .../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-1.1.2-tbb-tinythread-missing.patch | 18 - .../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 -- 10 files changed, 727 deletions(-) delete mode 100644 sci-biology/bowtie/bowtie-1.1.2-r1.ebuild delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch (limited to 'sci-biology/bowtie') 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 -Last-Update: 2014-100-06 - ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -856,7 +856,7 @@ void DifferenceCoverSample::build( - { - Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); - VMSG_NL(" Invoking Larsson-Sadakane on ranks"); -- _Context_LSS c; -+ ContextLss_ 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 -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 -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 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 -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 >& os, - bool maqPenalty, -@@ -124,7 +124,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - bool maqPenalty_; -@@ -164,7 +164,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -366,7 +366,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& 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 >& os, - bool maqPenalty, -@@ -161,7 +161,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool maqPenalty_; -@@ -201,7 +201,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -478,7 +478,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& 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 >& os, - bool maqPenalty, -@@ -231,7 +231,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool maqPenalty_; -@@ -273,7 +273,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -675,7 +675,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& 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 >& os, - bool maqPenalty, -@@ -554,7 +554,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - bool strandFix_; -@@ -598,7 +598,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -1375,7 +1375,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& 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( - 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 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 bpool; // pool for allocating Branches - AllocOnlyPool rpool; // pool for allocating RangeStates - AllocOnlyPool epool; // pool for allocating Edits -@@ -1811,7 +1811,7 @@ public: - bool quiet, - bool mate1, - uint32_t minCostAdjustment, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt) : - RangeSourceDriver(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 -Last-Update: 2014-08-13 - ---- a/blockwise_sa.h -+++ b/blockwise_sa.h -@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA::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::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::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 getDeltaMap(T v, const - // Declare anchor-map-related items - String 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::doBuil - VMSG_NL(" Doing sanity check"); - TIndexOffU added = 0; - String 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::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::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 -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 -

Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is --ff. This is because most SOLiD datasets have that orientation.

-

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 .csfastq 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).

-

Wrapper scripts

--

The bowtie, bowtie-build and bowtie-inspect 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.

-+

The bowtie, bowtie-build and bowtie-inspect 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.

-

It is recommended that you always run the bowtie wrappers and not run the binaries directly.

-

Small and large indexes

-

bowtie-build can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, bowtie-build builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, bowtie-build builds a "large" index using 64-bit numbers. Small indexes are stored in files with the .ebwt extension, and large indexes are stored in files with the .ebwtl 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.

---- a/ref_read.cpp -+++ b/ref_read.cpp -@@ -263,7 +263,7 @@ fastaRefReadSizes(vector& 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 -Date: 2011-01-30 -Last-Update: 2013-04-18 -Reviewed-by: Ognyan Kulev - ---- 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 \ -- cgit v1.2.3