[med-svn] [bowtie] 03/04: Refresh patches

Alex Mestiashvili malex-guest at moszumanska.debian.org
Mon Nov 27 13:13:41 UTC 2017


This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository bowtie.

commit bfa9399952ce045ad0b93baf5f58e1d471ddbf32
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Nov 27 13:49:43 2017 +0100

    Refresh patches
---
 debian/patches/build-as-Cpp03.patch              |  11 +--
 debian/patches/no_hash_style_both_for_mips.patch |   4 +-
 debian/patches/ppc64el.patch                     |  10 +-
 debian/patches/seqan-rename-ChunkPool.patch      | 112 +++++++++++------------
 debian/patches/seqan-rename-fill-to-resize.patch |  24 ++---
 debian/patches/use_debian_seqan.patch            |   8 +-
 6 files changed, 83 insertions(+), 86 deletions(-)

diff --git a/debian/patches/build-as-Cpp03.patch b/debian/patches/build-as-Cpp03.patch
index 69813a4..bc98b01 100644
--- a/debian/patches/build-as-Cpp03.patch
+++ b/debian/patches/build-as-Cpp03.patch
@@ -6,11 +6,9 @@ Subject: build as C++03
  Makefile | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 
-diff --git a/Makefile b/Makefile
-index cf8a1ab..f113317 100644
---- a/Makefile
-+++ b/Makefile
-@@ -17,7 +17,7 @@ BOWTIE_MM = 1
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -18,7 +18,7 @@
  BOWTIE_SHARED_MEM = 1
  EXTRA_FLAGS =
  EXTRA_CFLAGS =
@@ -18,5 +16,4 @@ index cf8a1ab..f113317 100644
 +EXTRA_CXXFLAGS = -std=c++03
  CFLAGS += $(EXTRA_CFLAGS)
  CXXFLAGS += $(EXTRA_CXXFLAGS)
- 
-
+ WARNING_FLAGS = -Wall -Wno-unused-private-field \
diff --git a/debian/patches/no_hash_style_both_for_mips.patch b/debian/patches/no_hash_style_both_for_mips.patch
index df0a02d..29a7598 100644
--- a/debian/patches/no_hash_style_both_for_mips.patch
+++ b/debian/patches/no_hash_style_both_for_mips.patch
@@ -8,8 +8,8 @@ Bug-Debian: https://bugs.debian.org/864439
 
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -59,7 +59,9 @@
- LINUX = 0
+@@ -63,7 +63,9 @@
+ LINUX =
  ifneq (,$(findstring Linux,$(shell uname)))
      LINUX = 1
 -    override EXTRA_FLAGS += -Wl,--hash-style=both
diff --git a/debian/patches/ppc64el.patch b/debian/patches/ppc64el.patch
index 38e6062..4424943 100644
--- a/debian/patches/ppc64el.patch
+++ b/debian/patches/ppc64el.patch
@@ -4,13 +4,13 @@ Author: Fernando Seiti Furusato <ferseiti at br.ibm.com>
 Last-Update: Fri, 12 Jun 2015 14:39:07 UTC
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -7,7 +7,7 @@
- 
+@@ -8,7 +8,7 @@
  SEQAN_DIR = /usr/include/seqan
- SEQAN_INC = -I $(SEQAN_DIR)
--INC = $(SEQAN_INC) -I third_party
+ # treat SeqAn as a sysdir to suppress warnings
+ SEQAN_INC = -isystem $(SEQAN_DIR)
+-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
 +INC = $(SEQAN_INC)
- CPP = g++ -w
+ CPP = g++
  CXX = $(CPP)
  CC = gcc
 @@ -104,11 +104,11 @@
diff --git a/debian/patches/seqan-rename-ChunkPool.patch b/debian/patches/seqan-rename-ChunkPool.patch
index a348bf0..77cb74a 100644
--- a/debian/patches/seqan-rename-ChunkPool.patch
+++ b/debian/patches/seqan-rename-ChunkPool.patch
@@ -4,9 +4,9 @@ Forwarded: no
 Author: Ognyan Kulev <ogi at debian.org>
 Last-Update: 2013-04-18
 
---- a/aligner.h
-+++ b/aligner.h
-@@ -385,7 +385,7 @@ public:
+--- bowtie.orig/aligner.h
++++ bowtie/aligner.h
+@@ -391,7 +391,7 @@
  		bool verbose,
  		bool quiet,
  		int maxBts,
@@ -15,7 +15,7 @@ Last-Update: 2013-04-18
  		int *btCnt = NULL,
  		AlignerMetrics *metrics = NULL) :
  		Aligner(true, rangeMode),
-@@ -592,7 +592,7 @@ protected:
+@@ -597,7 +597,7 @@
  	bool quiet_; // don't print informational/warning info
  
  	const int maxBts_;
@@ -24,7 +24,7 @@ Last-Update: 2013-04-18
  	int *btCnt_;
  	AlignerMetrics *metrics_;
  };
-@@ -633,7 +633,7 @@ public:
+@@ -638,7 +638,7 @@
  		bool verbose,
  		bool quiet,
  		int maxBts,
@@ -33,7 +33,7 @@ Last-Update: 2013-04-18
  		int *btCnt) :
  		Aligner(true, rangeMode),
  		refs_(refs),
-@@ -1405,7 +1405,7 @@ protected:
+@@ -1405,7 +1405,7 @@
  	bool quiet_;
  
  	int maxBts_;
@@ -42,7 +42,7 @@ Last-Update: 2013-04-18
  	int *btCnt_;
  
  	// Range-finding state for first mate
-@@ -1529,7 +1529,7 @@ public:
+@@ -1529,7 +1529,7 @@
  		bool verbose,
  		bool quiet,
  		int maxBts,
@@ -51,7 +51,7 @@ Last-Update: 2013-04-18
  		int *btCnt) :
  		Aligner(true, rangeMode),
  		refs_(refs),
-@@ -2081,7 +2081,7 @@ protected:
+@@ -2076,7 +2076,7 @@
  	TDriver* driver_;
  
  	// Pool for distributing chunks of best-first path descriptor memory
@@ -60,9 +60,9 @@ Last-Update: 2013-04-18
  
  	bool verbose_;
  	bool quiet_;
---- a/aligner_0mm.h
-+++ b/aligner_0mm.h
-@@ -32,7 +32,7 @@ public:
+--- bowtie.orig/aligner_0mm.h
++++ bowtie/aligner_0mm.h
+@@ -32,7 +32,7 @@
  			RangeCache* cacheFw,
  			RangeCache* cacheBw,
  			uint32_t cacheLimit,
@@ -71,7 +71,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool maqPenalty,
-@@ -123,7 +123,7 @@ private:
+@@ -123,7 +123,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -80,7 +80,7 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	bool maqPenalty_;
-@@ -162,7 +162,7 @@ public:
+@@ -162,7 +162,7 @@
  			RangeCache* cacheFw,
  			RangeCache* cacheBw,
  			uint32_t cacheLimit,
@@ -89,7 +89,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool reportSe,
-@@ -363,7 +363,7 @@ private:
+@@ -363,7 +363,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -98,9 +98,9 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	const bool reportSe_;
---- a/aligner_1mm.h
-+++ b/aligner_1mm.h
-@@ -32,7 +32,7 @@ public:
+--- bowtie.orig/aligner_1mm.h
++++ bowtie/aligner_1mm.h
+@@ -32,7 +32,7 @@
  			RangeCache *cacheFw,
  			RangeCache *cacheBw,
  			uint32_t cacheLimit,
@@ -109,7 +109,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool maqPenalty,
-@@ -160,7 +160,7 @@ private:
+@@ -160,7 +160,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -118,7 +118,7 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	const bool maqPenalty_;
-@@ -199,7 +199,7 @@ public:
+@@ -199,7 +199,7 @@
  			RangeCache *cacheFw,
  			RangeCache *cacheBw,
  			uint32_t cacheLimit,
@@ -127,7 +127,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool reportSe,
-@@ -475,7 +475,7 @@ private:
+@@ -475,7 +475,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -136,9 +136,9 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	const bool reportSe_;
---- a/aligner_23mm.h
-+++ b/aligner_23mm.h
-@@ -33,7 +33,7 @@ public:
+--- bowtie.orig/aligner_23mm.h
++++ bowtie/aligner_23mm.h
+@@ -33,7 +33,7 @@
  			RangeCache *cacheFw,
  			RangeCache *cacheBw,
  			uint32_t cacheLimit,
@@ -147,7 +147,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool maqPenalty,
-@@ -230,7 +230,7 @@ private:
+@@ -230,7 +230,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -156,7 +156,7 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	const bool maqPenalty_;
-@@ -271,7 +271,7 @@ public:
+@@ -271,7 +271,7 @@
  			RangeCache *cacheFw,
  			RangeCache *cacheBw,
  			uint32_t cacheLimit,
@@ -165,7 +165,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool reportSe,
-@@ -672,7 +672,7 @@ private:
+@@ -672,7 +672,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -174,9 +174,9 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	const bool reportSe_;
---- a/aligner_seed_mm.h
-+++ b/aligner_seed_mm.h
-@@ -37,7 +37,7 @@ public:
+--- bowtie.orig/aligner_seed_mm.h
++++ bowtie/aligner_seed_mm.h
+@@ -37,7 +37,7 @@
  			RangeCache* cacheFw,
  			RangeCache* cacheBw,
  			uint32_t cacheLimit,
@@ -185,7 +185,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool maqPenalty,
-@@ -554,7 +554,7 @@ private:
+@@ -554,7 +554,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -194,7 +194,7 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	bool strandFix_;
-@@ -598,7 +598,7 @@ public:
+@@ -598,7 +598,7 @@
  			RangeCache* cacheFw,
  			RangeCache* cacheBw,
  			uint32_t cacheLimit,
@@ -203,7 +203,7 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			vector<String<Dna5> >& os,
  			bool reportSe,
-@@ -1375,7 +1375,7 @@ private:
+@@ -1375,7 +1375,7 @@
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;
  	const uint32_t cacheLimit_;
@@ -212,9 +212,9 @@ Last-Update: 2013-04-18
  	BitPairReference* refs_;
  	vector<String<Dna5> >& os_;
  	const bool reportSe_;
---- a/ebwt_search.cpp
-+++ b/ebwt_search.cpp
-@@ -117,7 +117,7 @@ static bool norc; // don't align rc orie
+--- bowtie.orig/ebwt_search.cpp
++++ bowtie/ebwt_search.cpp
+@@ -125,7 +125,7 @@
  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
@@ -223,7 +223,7 @@ Last-Update: 2013-04-18
  static bool chunkVerbose; // have chunk allocator output status messages?
  static bool useV1;
  static bool reportSe;
-@@ -226,7 +226,7 @@ static void resetOptions() {
+@@ -232,7 +232,7 @@
  	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
@@ -232,7 +232,7 @@ Last-Update: 2013-04-18
  	chunkVerbose			= false; // have chunk allocator output status messages?
  	useV1					= true;
  	reportSe				= false;
-@@ -1220,7 +1220,7 @@ static void exactSearchWorkerStateful(vo
+@@ -1342,7 +1342,7 @@
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
  
@@ -241,7 +241,7 @@ Last-Update: 2013-04-18
  	UnpairedExactAlignerV1Factory alSEfact(
  			ebwt,
  			NULL,
-@@ -1426,7 +1426,7 @@ static void mismatchSearchWorkerFullStat
+@@ -1630,7 +1630,7 @@
  	// Global initialization
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
@@ -250,7 +250,7 @@ Last-Update: 2013-04-18
  
  	Unpaired1mmAlignerV1Factory alSEfact(
  			ebwtFw,
-@@ -1790,7 +1790,7 @@ static void twoOrThreeMismatchSearchWork
+@@ -2082,7 +2082,7 @@
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
  
@@ -259,7 +259,7 @@ Last-Update: 2013-04-18
  	Unpaired23mmAlignerV1Factory alSEfact(
  			ebwtFw,
  			&ebwtBw,
-@@ -2364,7 +2364,7 @@ static void seededQualSearchWorkerFullSt
+@@ -2753,7 +2753,7 @@
  	// Global initialization
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
@@ -268,9 +268,9 @@ Last-Update: 2013-04-18
  
  	AlignerMetrics *metrics = NULL;
  	if(stats) {
---- a/ebwt_search_backtrack.h
-+++ b/ebwt_search_backtrack.h
-@@ -2703,7 +2703,7 @@ public:
+--- bowtie.orig/ebwt_search_backtrack.h
++++ bowtie/ebwt_search_backtrack.h
+@@ -2703,7 +2703,7 @@
  			bool verbose,
  			bool quiet,
  			bool mate1,
@@ -279,7 +279,7 @@ Last-Update: 2013-04-18
  			int *btCnt) :
  			SingleRangeSourceDriver<EbwtRangeSource>(
  					params, rs, fw, sink, sinkPt, os, verbose,
-@@ -2877,7 +2877,7 @@ public:
+@@ -2877,7 +2877,7 @@
  			bool verbose,
  			bool quiet,
  			bool mate1,
@@ -288,7 +288,7 @@ Last-Update: 2013-04-18
  			int *btCnt = NULL) :
  			params_(params),
  			rs_(rs),
-@@ -2936,7 +2936,7 @@ protected:
+@@ -2936,7 +2936,7 @@
  	bool verbose_;
  	bool quiet_;
  	bool mate1_;
@@ -297,8 +297,8 @@ Last-Update: 2013-04-18
  	int *btCnt_;
  };
  
---- a/pool.h
-+++ b/pool.h
+--- bowtie.orig/pool.h
++++ bowtie/pool.h
 @@ -19,13 +19,13 @@
   * is set at construction time.  Heap memory is only allocated at
   * construction and deallocated at destruction.
@@ -315,7 +315,7 @@ Last-Update: 2013-04-18
  		verbose(verbose_), patid(0), pool_(NULL), cur_(0),
  		chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz),
  		bits_(lim_), exhaustCrash_(false),
-@@ -38,7 +38,7 @@ public:
+@@ -38,7 +38,7 @@
  			}
  		} catch(std::bad_alloc& e) {
  			ThreadSafe _ts(&gLock);
@@ -324,7 +324,7 @@ Last-Update: 2013-04-18
  			          << totSz << " bytes" << std::endl;
  			exhausted();
  			throw 1; // Exit if we haven't already
-@@ -48,7 +48,7 @@ public:
+@@ -48,7 +48,7 @@
  	/**
  	 * Delete all the pools.
  	 */
@@ -333,7 +333,7 @@ Last-Update: 2013-04-18
  		if(pool_ != NULL) delete[] pool_;
  	}
  
-@@ -189,7 +189,7 @@ public:
+@@ -189,7 +189,7 @@
  	 * Initialize a new pool with an initial size of about 'bytes'
  	 * bytes.  Exit with an error message if we can't allocate it.
  	 */
@@ -342,7 +342,7 @@ Last-Update: 2013-04-18
  		pool_(pool), name_(name), curPool_(0), cur_(0)
  	{
  		assert(pool != NULL);
-@@ -388,7 +388,7 @@ protected:
+@@ -388,7 +388,7 @@
  		lastCurInPool_.pop_back();
  	}
  
@@ -351,9 +351,9 @@ Last-Update: 2013-04-18
  	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
-@@ -1307,7 +1307,7 @@ class PathManager {
+--- bowtie.orig/range_source.h
++++ bowtie/range_source.h
+@@ -1307,7 +1307,7 @@
  
  public:
  
@@ -362,7 +362,7 @@ Last-Update: 2013-04-18
  		branchQ_(verbose, quiet),
  		cpool(cpool_),
  		bpool(cpool, "branch"),
-@@ -1556,7 +1556,7 @@ protected:
+@@ -1556,7 +1556,7 @@
  
  public:
  
@@ -371,7 +371,7 @@ Last-Update: 2013-04-18
  	AllocOnlyPool<Branch> bpool; // pool for allocating Branches
  	AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates
  	AllocOnlyPool<Edit> epool; // pool for allocating Edits
-@@ -1730,7 +1730,7 @@ public:
+@@ -1730,7 +1730,7 @@
  		bool quiet,
  		bool mate1,
  		uint32_t minCostAdjustment,
diff --git a/debian/patches/seqan-rename-fill-to-resize.patch b/debian/patches/seqan-rename-fill-to-resize.patch
index e4da969..b078686 100644
--- a/debian/patches/seqan-rename-fill-to-resize.patch
+++ b/debian/patches/seqan-rename-fill-to-resize.patch
@@ -5,9 +5,9 @@ Forwarded: no
 Author: Ognyan Kulev <ogi at debian.org>
 Last-Update: 2014-08-13
 
---- a/diff_sample.h
-+++ b/diff_sample.h
-@@ -457,7 +457,7 @@ static String<T> getDeltaMap(T v, const
+--- bowtie.orig/diff_sample.h
++++ bowtie/diff_sample.h
+@@ -457,7 +457,7 @@
  	// Declare anchor-map-related items
  	String<T> amap;
  	size_t amapEnts = 1;
@@ -16,7 +16,7 @@ Last-Update: 2014-08-13
  	amap[0] = 0;
  	// Print out difference cover (and optionally calculate
  	// anchor map)
-@@ -537,7 +537,7 @@ public:
+@@ -537,7 +537,7 @@
  		assert_gt(_d, 0);
  		assert_eq(1, popCount(_v)); // must be power of 2
  		// Build map from d's to idx's
@@ -25,7 +25,7 @@ Last-Update: 2014-08-13
  		uint32_t lim = (uint32_t)length(_ds);
  		for(uint32_t i = 0; i < lim; i++) {
  			_dInv[_ds[i]] = i;
-@@ -661,7 +661,7 @@ void DifferenceCoverSample<TStr>::doBuil
+@@ -661,7 +661,7 @@
  	VMSG_NL("  Doing sanity check");
  	TIndexOffU added = 0;
  	String<TIndexOffU> sorted;
@@ -34,7 +34,7 @@ Last-Update: 2014-08-13
  	for(size_t di = 0; di < this->d(); di++) {
  		uint32_t d = _ds[di];
  		size_t i = 0;
-@@ -725,7 +725,7 @@ void DifferenceCoverSample<TStr>::buildS
+@@ -725,7 +725,7 @@
  	assert_eq(length(_doffs), d+1);
  	// Size sPrime appropriately
  	reserve(sPrime, sPrimeSz + padding, Exact()); // reserve extra slot for LS
@@ -43,7 +43,7 @@ Last-Update: 2014-08-13
  	// Slot suffixes from text into sPrime according to the mu
  	// mapping; where the mapping would leave a blank, insert a 0
  	TIndexOffU added = 0;
-@@ -949,7 +949,7 @@ void DifferenceCoverSample<TStr>::build(
+@@ -949,7 +949,7 @@
  		// arrays back into sPrime.
  		VMSG_NL("  Allocating rank array");
  		reserve(_isaPrime, length(sPrime), Exact());
@@ -52,9 +52,9 @@ Last-Update: 2014-08-13
  		assert_gt(length(_isaPrime), 0);
  		{
  			Timer timer(cout, "  Ranking v-sort output time: ", this->verbose());
---- a/blockwise_sa.h
-+++ b/blockwise_sa.h
-@@ -670,8 +670,8 @@ class BinarySorting_worker {
+--- bowtie.orig/blockwise_sa.h
++++ bowtie/blockwise_sa.h
+@@ -665,8 +665,8 @@
  					try {
  						// Allocate and initialize containers for holding bucket
  						// sizes and representatives.
@@ -65,7 +65,7 @@ Last-Update: 2014-08-13
  					} catch(bad_alloc &e) {
  						if(this->_passMemExc) {
  							throw e; // rethrow immediately
-@@ -1060,7 +1060,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
+@@ -1055,7 +1055,7 @@
  				hi = _sampleSuffs[cur_block];
  				//zHi.resizeExact(_dcV);
  				//zHi.fillZero();
@@ -74,7 +74,7 @@ Last-Update: 2014-08-13
  				assert_eq(getValue(zHi, 0), 0);
  				calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
  			}
-@@ -1071,7 +1071,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
+@@ -1066,7 +1066,7 @@
  				lo = _sampleSuffs[cur_block-1];
  				//zLo.resizeExact(_dcV);
  				//zLo.fillZero();
diff --git a/debian/patches/use_debian_seqan.patch b/debian/patches/use_debian_seqan.patch
index 115124c..ca18f17 100644
--- a/debian/patches/use_debian_seqan.patch
+++ b/debian/patches/use_debian_seqan.patch
@@ -10,11 +10,11 @@ Reviewed-by: Ognyan Kulev <ogi at debian.org>
  prefix = /usr/local
  bindir = $(prefix)/bin
  
--SEQAN_DIR = SeqAn-1.1
+-SEQAN_DIR = ./SeqAn-1.1
 +SEQAN_DIR = /usr/include/seqan
- SEQAN_INC = -I $(SEQAN_DIR)
- INC = $(SEQAN_INC) -I third_party
- CPP = g++ -w
+ # treat SeqAn as a sysdir to suppress warnings
+ SEQAN_INC = -isystem $(SEQAN_DIR)
+ INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
 @@ -208,7 +208,6 @@
                 $(wildcard genomes/NC_008253.fna) \
                 $(wildcard reads/e_coli_1000.*) \

-- 
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