[med-svn] r23797 - in trunk/packages/bowtie/trunk/debian: . patches
Steffen Möller
moeller at moszumanska.debian.org
Thu Jun 8 14:26:04 UTC 2017
Author: moeller
Date: 2017-06-08 14:26:03 +0000 (Thu, 08 Jun 2017)
New Revision: 23797
Modified:
trunk/packages/bowtie/trunk/debian/changelog
trunk/packages/bowtie/trunk/debian/control
trunk/packages/bowtie/trunk/debian/copyright
trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
trunk/packages/bowtie/trunk/debian/patches/enable_arm64.patch
trunk/packages/bowtie/trunk/debian/patches/gcc-64bit.patch
trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch
trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch
trunk/packages/bowtie/trunk/debian/patches/reproducible.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch
trunk/packages/bowtie/trunk/debian/patches/series
trunk/packages/bowtie/trunk/debian/patches/spelling.patch
trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch
trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
trunk/packages/bowtie/trunk/debian/watch
Log:
Update to version 1.2
Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/changelog 2017-06-08 14:26:03 UTC (rev 23797)
@@ -1,3 +1,14 @@
+bowtie (1.2.0-1) unstable; urgency=medium
+
+ * New upstream version.
+ - Threading with tbb
+ - queue-based lock rather than spin/heavyweight lock
+ - reduced thread synchronization
+ * debian/watch: Adjusted for new distribution via github
+ * Team upload provided by new aspiring Debian Med member, sponsored by <moeller>
+
+ -- Stephan Struckmann <stephan.struckmann at gmail.com> Thu, 08 Jun 2017 15:24:17 +0200
+
bowtie (1.1.2-6) unstable; urgency=medium
* Enable build on all 64bit architectures (thanks for the patch to James
Modified: trunk/packages/bowtie/trunk/debian/control
===================================================================
--- trunk/packages/bowtie/trunk/debian/control 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/control 2017-06-08 14:26:03 UTC (rev 23797)
@@ -3,12 +3,14 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Ognyan Kulev <ogi at debian.org>
+ Stephan Struckmann <stephan.struckmann at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
help2man,
- seqan-dev (>= 1.4),
- python
+ libtbb-dev,
+ python,
+ seqan-dev (>= 1.4)
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/bowtie/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/
Modified: trunk/packages/bowtie/trunk/debian/copyright
===================================================================
--- trunk/packages/bowtie/trunk/debian/copyright 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/copyright 2017-06-08 14:26:03 UTC (rev 23797)
@@ -1,7 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Bowtie
Upstream-Contact: Ben Langmead <blangmea at jhsph.edu>
-Source: http://sourceforge.net/projects/bowtie-bio/files/bowtie/
+Source: https://github.com/BenLangmead/bowtie/
Files-Excluded: SeqAn*
Files: *
@@ -9,8 +9,9 @@
License: Artistic
Files: debian/*
-Copyright: © 2011 Steffen Moeller <moeller at debian.org>,
- Yask Gupta <yask.gupta87 at gmail.com>
+Copyright: © 2011 Steffen Moeller <moeller at debian.org>,
+ Yask Gupta <yask.gupta87 at gmail.com>
+ © 2017 Stephan Struckmann <stephan.struckmann at gmail.com>
© 2011-2014 Andreas Tille <tille at debian.org>
License: LGPL-3+
Modified: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -5,9 +5,11 @@
Forwarded: not-needed
Last-Update: 2014-08-13
---- a/Makefile
-+++ b/Makefile
-@@ -143,8 +143,8 @@ ifeq (32,$(BITS))
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
+@@ -175,8 +175,8 @@ ifeq (32,$(BITS))
$(error bowtie2 compilation requires a 64-bit platform )
endif
Modified: trunk/packages/bowtie/trunk/debian/patches/enable_arm64.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/enable_arm64.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/enable_arm64.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -4,9 +4,11 @@
Forwarded-Upstream: yes (http://bugs.debian.org/800548)
Description: Enable arm64 architecture
---- a/Makefile
-+++ b/Makefile
-@@ -125,7 +125,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
+@@ -155,7 +155,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
VERSION = $(shell cat VERSION)
BITS=32
Modified: trunk/packages/bowtie/trunk/debian/patches/gcc-64bit.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/gcc-64bit.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/gcc-64bit.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -10,9 +10,11 @@
Author: James Cowgill <jcowgill at debian.org>
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/Makefile
-+++ b/Makefile
-@@ -125,7 +125,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
+@@ -155,7 +155,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
VERSION = $(shell cat VERSION)
BITS=32
Modified: trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -1,20 +0,0 @@
-Description: Disable -Wl,--hash-style=both on mips machines.
- It's not supported on mips and mipsel ports and leads to build errors.
-Author: Ognyan Kulev <ogi at debian.org>
-Forwarded: not-needed
-Last-Update: 2013-04-24
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/Makefile
-+++ b/Makefile
-@@ -58,7 +58,9 @@ endif
- LINUX = 0
- ifneq (,$(findstring Linux,$(shell uname)))
- LINUX = 1
-- EXTRA_FLAGS += -Wl,--hash-style=both
-+ ifeq (,$(findstring mips,$(shell uname -m)))
-+ EXTRA_FLAGS += -Wl,--hash-style=both
-+ endif
- endif
-
- MM_DEF =
Modified: trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -3,44 +3,37 @@
Bug-Debian: http://bugs.debian.org/788537
Description: enable for ppc64el
---- a/Makefile
-+++ b/Makefile
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
@@ -7,7 +7,7 @@ bindir = $(prefix)/bin
SEQAN_DIR = /usr/include/seqan
SEQAN_INC = -I $(SEQAN_DIR)
-INC = $(SEQAN_INC) -I third_party
+INC = $(SEQAN_INC)
- CPP = g++
+ CPP = g++ -w
CXX = $(CPP)
CC = gcc
-@@ -43,7 +43,7 @@ endif
- MACOS = 0
- ifneq (,$(findstring Darwin,$(shell uname)))
- MACOS = 1
-- ifneq (,$(findstring 13,$(shell uname -r)))
-+ ifneq (,$(findstring 12,$(shell uname -r)))
- CPP = clang++
- CC = clang
- EXTRA_FLAGS += -stdlib=libstdc++
-@@ -82,11 +82,11 @@ else
- PTHREAD_LIB = -lpthread
+@@ -94,11 +94,11 @@ else
+ LIBS = $(PTHREAD_LIB)
endif
-POPCNT_CAPABILITY ?= 1
-ifeq (1, $(POPCNT_CAPABILITY))
-- EXTRA_FLAGS += -DPOPCNT_CAPABILITY
+- override EXTRA_FLAGS += -DPOPCNT_CAPABILITY
- INC += -I third_party
-endif
+#POPCNT_CAPABILITY ?= 1
+#ifeq (1, $(POPCNT_CAPABILITY))
-+# EXTRA_FLAGS += -DPOPCNT_CAPABILITY
++# override EXTRA_FLAGS += -DPOPCNT_CAPABILITY
+# INC += -I third_party
+#endif
PREFETCH_LOCALITY = 2
PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
-@@ -125,7 +125,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+@@ -155,7 +155,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
VERSION = $(shell cat VERSION)
BITS=32
Modified: trunk/packages/bowtie/trunk/debian/patches/reproducible.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/reproducible.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/reproducible.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -1,8 +1,10 @@
Description: make build reproducible
Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/Makefile
-+++ b/Makefile
-@@ -207,9 +207,9 @@
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
+@@ -237,9 +237,9 @@ allall: $(BIN_LIST) $(BIN_LIST_AUX)
DEFS=-fno-strict-aliasing \
-DBOWTIE_VERSION="\"`cat VERSION`\"" \
@@ -15,7 +17,7 @@
$(FILE_FLAGS) \
$(PTHREAD_DEF) \
$(PREF_DEF) \
-@@ -217,8 +217,8 @@
+@@ -247,8 +247,8 @@ DEFS=-fno-strict-aliasing \
$(SHMEM_DEF)
ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -4,10 +4,12 @@
Author: Ognyan Kulev <ogi at debian.org>
Last-Update: 2013-04-18
---- a/pat.h
-+++ b/pat.h
-@@ -82,20 +82,20 @@ struct ReadBuf {
- ~ReadBuf() {
+Index: bowtie-1.2.0/pat.h
+===================================================================
+--- bowtie-1.2.0.orig/pat.h
++++ bowtie-1.2.0/pat.h
+@@ -118,13 +118,13 @@ struct Read {
+ ~Read() {
clearAll(); reset();
// Prevent seqan from trying to free buffers
- _setBegin(patFw, NULL);
@@ -24,19 +26,6 @@
+ _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);
- }
}
+ #define RESET_BUF(str, buf, typ) _setBegin(str, (typ*)buf); _setLength(str, 0); _setCapacity(str, BUF_SIZE);
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -4,9 +4,11 @@
Author: Ognyan Kulev <ogi at debian.org>
Last-Update: 2013-04-18
---- a/aligner.h
-+++ b/aligner.h
-@@ -337,7 +337,7 @@ public:
+Index: bowtie-1.2.0/aligner.h
+===================================================================
+--- bowtie-1.2.0.orig/aligner.h
++++ bowtie-1.2.0/aligner.h
+@@ -385,7 +385,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
@@ -15,7 +17,7 @@
int *btCnt = NULL,
AlignerMetrics *metrics = NULL) :
Aligner(true, rangeMode),
-@@ -544,7 +544,7 @@ protected:
+@@ -592,7 +592,7 @@ protected:
bool quiet_; // don't print informational/warning info
const int maxBts_;
@@ -24,7 +26,7 @@
int *btCnt_;
AlignerMetrics *metrics_;
};
-@@ -585,7 +585,7 @@ public:
+@@ -633,7 +633,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
@@ -33,7 +35,7 @@
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
-@@ -1358,7 +1358,7 @@ protected:
+@@ -1405,7 +1405,7 @@ protected:
bool quiet_;
int maxBts_;
@@ -42,7 +44,7 @@
int *btCnt_;
// Range-finding state for first mate
-@@ -1482,7 +1482,7 @@ public:
+@@ -1529,7 +1529,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
@@ -51,7 +53,7 @@
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
-@@ -2035,7 +2035,7 @@ protected:
+@@ -2081,7 +2081,7 @@ protected:
TDriver* driver_;
// Pool for distributing chunks of best-first path descriptor memory
@@ -60,8 +62,10 @@
bool verbose_;
bool quiet_;
---- a/aligner_0mm.h
-+++ b/aligner_0mm.h
+Index: bowtie-1.2.0/aligner_0mm.h
+===================================================================
+--- bowtie-1.2.0.orig/aligner_0mm.h
++++ bowtie-1.2.0/aligner_0mm.h
@@ -32,7 +32,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
@@ -71,7 +75,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -124,7 +124,7 @@ private:
+@@ -123,7 +123,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -80,7 +84,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
bool maqPenalty_;
-@@ -164,7 +164,7 @@ public:
+@@ -162,7 +162,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
@@ -89,7 +93,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -366,7 +366,7 @@ private:
+@@ -363,7 +363,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -98,8 +102,10 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool reportSe_;
---- a/aligner_1mm.h
-+++ b/aligner_1mm.h
+Index: bowtie-1.2.0/aligner_1mm.h
+===================================================================
+--- bowtie-1.2.0.orig/aligner_1mm.h
++++ bowtie-1.2.0/aligner_1mm.h
@@ -32,7 +32,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
@@ -109,7 +115,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -161,7 +161,7 @@ private:
+@@ -160,7 +160,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -118,7 +124,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool maqPenalty_;
-@@ -201,7 +201,7 @@ public:
+@@ -199,7 +199,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
@@ -127,7 +133,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -478,7 +478,7 @@ private:
+@@ -475,7 +475,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -136,8 +142,10 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool reportSe_;
---- a/aligner_23mm.h
-+++ b/aligner_23mm.h
+Index: bowtie-1.2.0/aligner_23mm.h
+===================================================================
+--- bowtie-1.2.0.orig/aligner_23mm.h
++++ bowtie-1.2.0/aligner_23mm.h
@@ -33,7 +33,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
@@ -147,7 +155,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -231,7 +231,7 @@ private:
+@@ -230,7 +230,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -156,7 +164,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool maqPenalty_;
-@@ -273,7 +273,7 @@ public:
+@@ -271,7 +271,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
@@ -165,7 +173,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -675,7 +675,7 @@ private:
+@@ -672,7 +672,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -174,8 +182,10 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool reportSe_;
---- a/aligner_seed_mm.h
-+++ b/aligner_seed_mm.h
+Index: bowtie-1.2.0/aligner_seed_mm.h
+===================================================================
+--- bowtie-1.2.0.orig/aligner_seed_mm.h
++++ bowtie-1.2.0/aligner_seed_mm.h
@@ -37,7 +37,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
@@ -212,10 +222,12 @@
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
+Index: bowtie-1.2.0/ebwt_search.cpp
+===================================================================
+--- bowtie-1.2.0.orig/ebwt_search.cpp
++++ bowtie-1.2.0/ebwt_search.cpp
+@@ -111,7 +111,7 @@ static bool norc; // don't align rc orie
+ static bool strandFix; // attempt to fix strand bias
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
@@ -223,8 +235,8 @@
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
+@@ -222,7 +222,7 @@ static void resetOptions() {
+ strandFix = true; // attempt to fix strand bias
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)
@@ -232,8 +244,8 @@
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);
+@@ -1204,7 +1204,7 @@ static void exactSearchWorkerStateful(vo
+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
@@ -241,17 +253,17 @@
UnpairedExactAlignerV1Factory alSEfact(
ebwt,
NULL,
-@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat
+@@ -1388,7 +1388,7 @@ static void mismatchSearchWorkerFullStat
// Global initialization
- PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
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);
+@@ -1723,7 +1723,7 @@ static void twoOrThreeMismatchSearchWork
+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
@@ -259,18 +271,20 @@
Unpaired23mmAlignerV1Factory alSEfact(
ebwtFw,
&ebwtBw,
-@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt
+@@ -2258,7 +2258,7 @@ static void seededQualSearchWorkerFullSt
// Global initialization
- PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
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:
+Index: bowtie-1.2.0/ebwt_search_backtrack.h
+===================================================================
+--- bowtie-1.2.0.orig/ebwt_search_backtrack.h
++++ bowtie-1.2.0/ebwt_search_backtrack.h
+@@ -2703,7 +2703,7 @@ public:
bool verbose,
bool quiet,
bool mate1,
@@ -279,7 +293,7 @@
int *btCnt) :
SingleRangeSourceDriver<EbwtRangeSource>(
params, rs, fw, sink, sinkPt, os, verbose,
-@@ -2927,7 +2927,7 @@ public:
+@@ -2877,7 +2877,7 @@ public:
bool verbose,
bool quiet,
bool mate1,
@@ -288,7 +302,7 @@
int *btCnt = NULL) :
params_(params),
rs_(rs),
-@@ -2986,7 +2986,7 @@ protected:
+@@ -2936,7 +2936,7 @@ protected:
bool verbose_;
bool quiet_;
bool mate1_;
@@ -297,8 +311,10 @@
int *btCnt_;
};
---- a/pool.h
-+++ b/pool.h
+Index: bowtie-1.2.0/pool.h
+===================================================================
+--- bowtie-1.2.0.orig/pool.h
++++ bowtie-1.2.0/pool.h
@@ -19,13 +19,13 @@
* is set at construction time. Heap memory is only allocated at
* construction and deallocated at destruction.
@@ -351,9 +367,11 @@
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 {
+Index: bowtie-1.2.0/range_source.h
+===================================================================
+--- bowtie-1.2.0.orig/range_source.h
++++ bowtie-1.2.0/range_source.h
+@@ -1307,7 +1307,7 @@ class PathManager {
public:
@@ -362,7 +380,7 @@
branchQ_(verbose, quiet),
cpool(cpool_),
bpool(cpool, "branch"),
-@@ -1637,7 +1637,7 @@ protected:
+@@ -1556,7 +1556,7 @@ protected:
public:
@@ -371,7 +389,7 @@
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:
+@@ -1730,7 +1730,7 @@ public:
bool quiet,
bool mate1,
uint32_t minCostAdjustment,
Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/series 2017-06-08 14:26:03 UTC (rev 23797)
@@ -4,7 +4,6 @@
seqan-rename-ChunkPool.patch
seqan-rename-fill-to-resize.patch
disable_bits_flag.patch
-no_hash_style_both_for_mips.patch
seqan-popcount.patch
# do_not_use_outdated_copy_of_cpuid_h.patch
bowtie_ContextLss-1.1-1.4.patch
Modified: trunk/packages/bowtie/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/spelling.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/spelling.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -2,8 +2,10 @@
Last-Update: Thu, 01 Oct 2015 09:47:23 +0200
Description: Fix spelling
---- a/MANUAL
-+++ b/MANUAL
+Index: bowtie-1.2.0/MANUAL
+===================================================================
+--- bowtie-1.2.0.orig/MANUAL
++++ bowtie-1.2.0/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
@@ -13,8 +15,10 @@
It is recommended that you always run the bowtie wrappers and not run
the binaries directly.
---- a/MANUAL.markdown
-+++ b/MANUAL.markdown
+Index: bowtie-1.2.0/MANUAL.markdown
+===================================================================
+--- bowtie-1.2.0.orig/MANUAL.markdown
++++ bowtie-1.2.0/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
@@ -24,9 +28,11 @@
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
+Index: bowtie-1.2.0/doc/manual.html
+===================================================================
+--- bowtie-1.2.0.orig/doc/manual.html
++++ bowtie-1.2.0/doc/manual.html
+@@ -200,7 +200,7 @@ 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>
@@ -35,8 +41,10 @@
<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
+Index: bowtie-1.2.0/ref_read.cpp
+===================================================================
+--- bowtie-1.2.0.orig/ref_read.cpp
++++ bowtie-1.2.0/ref_read.cpp
@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in,
<< "reference into smaller chunks and index each independently." << endl;
#else
Modified: trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -4,9 +4,11 @@
Last-Update: 2012-04-24
Bug-Closed: http://bugs.debian.org/670230
---- a/Makefile
-+++ b/Makefile
-@@ -215,7 +215,7 @@ DEFS=-fno-strict-aliasing \
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
+@@ -247,7 +247,7 @@ DEFS=-fno-strict-aliasing \
$(MM_DEF) \
$(SHMEM_DEF)
Modified: trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -4,8 +4,10 @@
Last-Update: 2013-04-18
Reviewed-by: Ognyan Kulev <ogi at debian.org>
---- a/Makefile
-+++ b/Makefile
+Index: bowtie-1.2.0/Makefile
+===================================================================
+--- bowtie-1.2.0.orig/Makefile
++++ bowtie-1.2.0/Makefile
@@ -5,7 +5,7 @@
prefix = /usr/local
bindir = $(prefix)/bin
@@ -14,8 +16,8 @@
+SEQAN_DIR = /usr/include/seqan
SEQAN_INC = -I $(SEQAN_DIR)
INC = $(SEQAN_INC) -I third_party
- CPP = g++
-@@ -168,7 +168,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh)
+ CPP = g++ -w
+@@ -200,7 +200,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh)
$(wildcard genomes/NC_008253.fna) \
$(wildcard reads/e_coli_1000.*) \
$(wildcard reads/e_coli_1000_*) \
Modified: trunk/packages/bowtie/trunk/debian/watch
===================================================================
--- trunk/packages/bowtie/trunk/debian/watch 2017-06-08 13:29:12 UTC (rev 23796)
+++ trunk/packages/bowtie/trunk/debian/watch 2017-06-08 14:26:03 UTC (rev 23797)
@@ -1,2 +1,8 @@
-version=3
-http://sf.net/bowtie-bio/bowtie-([\d\.]+)-src\.zip
+version=4
+# only active up to version 1.1.x
+#http://sf.net/bowtie-bio/bowtie-([\d\.]+)-src\.zip
+# since 1.2.0
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%bowtie-$1.tar.gz%" \
+ https://github.com/BenLangmead/bowtie/tags \
+ (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
+
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