* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: ddbfba3594bda0b32f359e057555d477ffbced1e
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 19:04:45 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct 14 12:47:58 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ddbfba35
sci-biology/bowtie: version bump, SLOT major version
sci-biology/bowtie is now SLOTed, in order to allow for a
parallel installation with bowtie2. In addition, the latest
bowtie now supports dev-cpp/tbb with 'tbb' USE flag.
sci-biology/bowtie/Manifest | 4 +-
sci-biology/bowtie/bowtie-0.12.8.ebuild | 44 ----------------
sci-biology/bowtie/bowtie-1.0.0.ebuild | 42 ----------------
sci-biology/bowtie/bowtie-1.1.2.ebuild | 58 ++++++++++++++++++++++
.../bowtie/files/bowtie-0.12.8-gcc-47.patch | 45 -----------------
.../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 ++++++
sci-biology/bowtie/metadata.xml | 5 ++
7 files changed, 79 insertions(+), 133 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 1345a9e..1291400 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1,2 @@
-DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
-DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1
+DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7
+DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
deleted file mode 100644
index c26c986..0000000
--- a/sci-biology/bowtie/bowtie-0.12.8.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86 ~x64-macos"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
-# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-gcc-47.patch
-}
-
-src_compile() {
- unset CFLAGS
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS=""
-}
-
-src_install() {
- dobin bowtie bowtie-*
- exeinto /usr/share/${PN}/scripts
- doexe scripts/*
- newman MANUAL bowtie.1
- dodoc AUTHORS NEWS TUTORIAL
-}
diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild
deleted file mode 100644
index b818119..0000000
--- a/sci-biology/bowtie/bowtie-1.0.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-src_compile() {
- unset CFLAGS
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS}"
-}
-
-src_install() {
- dobin bowtie bowtie-*
- exeinto /usr/share/${PN}/scripts
- doexe scripts/*
-
- insinto /usr/share/${PN}
- doins -r genomes indexes
-
- newman MANUAL bowtie.1
- dodoc AUTHORS NEWS TUTORIAL doc/README
- dohtml doc/{manual.html,style.css}
-}
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild
new file mode 100644
index 0000000..55eec50
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+IUSE="examples tbb"
+
+DEPEND="app-arch/unzip
+ tbb? ( dev-cpp/tbb )"
+RDEPEND=""
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+src_prepare() {
+ # Suppress useless -Wall pollution
+ sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
+
+ # always include tinythread.cpp
+ epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
+}
+
+src_compile() {
+ emake \
+ CC="$(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-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
deleted file mode 100644
index 3c8a1e1..0000000
--- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- alphabet.h | 24 ++++++++++++------------
- 1 files changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/alphabet.h b/alphabet.h
-index b464ddf..08d0281 100644
---- a/alphabet.h
-+++ b/alphabet.h
-@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
- return s_rc;
- }
-
-+/// Reverse a string in-place
-+template <typename TStr>
-+static inline void reverseInPlace(TStr& s) {
-+ typedef typename Value<TStr>::Type TVal;
-+ size_t len = length(s);
-+ for(size_t i = 0; i < (len>>1); i++) {
-+ TVal tmp = s[i];
-+ s[i] = s[len-i-1];
-+ s[len-i-1] = tmp;
-+ }
-+}
-+
- /**
- * Reverse-complement s in-place. Ns go to Ns.
- */
-@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
- }
- }
-
--/// Reverse a string in-place
--template <typename TStr>
--static inline void reverseInPlace(TStr& s) {
-- typedef typename Value<TStr>::Type TVal;
-- size_t len = length(s);
-- for(size_t i = 0; i < (len>>1); i++) {
-- TVal tmp = s[i];
-- s[i] = s[len-i-1];
-- s[len-i-1] = tmp;
-- }
--}
--
- /**
- * Return the reverse-complement of s.
- */
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
new file mode 100644
index 0000000..2a081ff
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
@@ -0,0 +1,14 @@
+--- 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/metadata.xml b/sci-biology/bowtie/metadata.xml
index e493417..58f2d36 100644
--- a/sci-biology/bowtie/metadata.xml
+++ b/sci-biology/bowtie/metadata.xml
@@ -5,4 +5,9 @@
<upstream>
<remote-id type="sourceforge">bowtie-bio</remote-id>
</upstream>
+ <use>
+ <flag name='tbb'>Enables building bowtie with the Intel
+ Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This
+ flag is recommended.</flag>
+ </use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2015-12-26 18:05 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-12-26 18:05 UTC (permalink / raw
To: gentoo-commits
commit: 369678cffc9f7ecae414f3800f01a2c2251e8669
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 26 18:02:47 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 26 18:02:47 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=369678cf
sci-biology/bowtie: Drop old
obsoletes:
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/bowtie/Manifest | 1 -
sci-biology/bowtie/bowtie-0.12.8.ebuild | 44 ---------------------
.../bowtie/files/bowtie-0.12.8-gcc-47.patch | 45 ----------------------
3 files changed, 90 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index c692c89..1291400 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,3 +1,2 @@
-DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7
DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
deleted file mode 100644
index c26c986..0000000
--- a/sci-biology/bowtie/bowtie-0.12.8.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86 ~x64-macos"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
-# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-gcc-47.patch
-}
-
-src_compile() {
- unset CFLAGS
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS=""
-}
-
-src_install() {
- dobin bowtie bowtie-*
- exeinto /usr/share/${PN}/scripts
- doexe scripts/*
- newman MANUAL bowtie.1
- dodoc AUTHORS NEWS TUTORIAL
-}
diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
deleted file mode 100644
index 3c8a1e1..0000000
--- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- alphabet.h | 24 ++++++++++++------------
- 1 files changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/alphabet.h b/alphabet.h
-index b464ddf..08d0281 100644
---- a/alphabet.h
-+++ b/alphabet.h
-@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
- return s_rc;
- }
-
-+/// Reverse a string in-place
-+template <typename TStr>
-+static inline void reverseInPlace(TStr& s) {
-+ typedef typename Value<TStr>::Type TVal;
-+ size_t len = length(s);
-+ for(size_t i = 0; i < (len>>1); i++) {
-+ TVal tmp = s[i];
-+ s[i] = s[len-i-1];
-+ s[len-i-1] = tmp;
-+ }
-+}
-+
- /**
- * Reverse-complement s in-place. Ns go to Ns.
- */
-@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
- }
- }
-
--/// Reverse a string in-place
--template <typename TStr>
--static inline void reverseInPlace(TStr& s) {
-- typedef typename Value<TStr>::Type TVal;
-- size_t len = length(s);
-- for(size_t i = 0; i < (len>>1); i++) {
-- TVal tmp = s[i];
-- s[i] = s[len-i-1];
-- s[len-i-1] = tmp;
-- }
--}
--
- /**
- * Return the reverse-complement of s.
- */
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2020-09-09 10:36 Michał Górny
0 siblings, 0 replies; 3+ messages in thread
From: Michał Górny @ 2020-09-09 10:36 UTC (permalink / raw
To: gentoo-commits
commit: 72b619bb3a27ec63f571afbf73ec75893fcc2d99
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 9 10:26:34 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Sep 9 10:34:29 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=72b619bb
sci-biology/bowtie: Remove old
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-biology/bowtie/Manifest | 1 -
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, 718 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 824c7439adc..50ad9715e98 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 d8b607f870f..00000000000
--- 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 78b9c01a046..00000000000
--- 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 af7f7f61cd5..00000000000
--- 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 52cb4f49652..00000000000
--- 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 171f9bab8fa..00000000000
--- 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 38664aeee98..00000000000
--- 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 ff484dfa3eb..00000000000
--- 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 "orphaned" mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click "NGS: QC and manipulation", then "SOLiD-to-FASTQ" in the left-hand sidebar).</p>
- <h2 id="wrapper-scripts">Wrapper scripts</h2>
--<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p>
-+<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p>
- <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p>
- <h2 id="small-and-large-indexes">Small and large indexes</h2>
- <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a "large" index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p>
---- a/ref_read.cpp
-+++ b/ref_read.cpp
-@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in,
- << "reference into smaller chunks and index each independently." << endl;
- #else
- cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl
-- << "build a large index instead using the appropiate options." << endl;
-+ << "build a large index instead using the appropriate options." << endl;
- #endif
- throw 1;
- }
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
deleted file mode 100644
index bc0f1d09557..00000000000
--- 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 54391ae415a..00000000000
--- 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 \
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2015-12-26 18:05 [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/ Justin Lecher
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