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
--- diff_sample.h
+++ diff_sample.h
@@ -979,7 +979,7 @@ 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()),
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
--- pat.h
+++ pat.h
@@ -120,13 +120,13 @@
~Read() {
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);
}
#define RESET_BUF(str, buf, typ) _setBegin(str, (typ*)buf); _setLength(str, 0); _setCapacity(str, BUF_SIZE);
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/
--- diff_sample.h
+++ diff_sample.h
@@ -481,6 +481,8 @@ 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.
*/
@@ -493,6 +495,7 @@ static unsigned int popCount(T i) {
}
return cnt;
}
+#endif
/**
* Calculate log-base-2 of i
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
--- aligner.h
+++ aligner.h
@@ -391,7 +391,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
int *btCnt = NULL,
AlignerMetrics *metrics = NULL) :
Aligner(true, rangeMode),
@@ -597,7 +597,7 @@ protected:
bool quiet_; // don't print informational/warning info
const int maxBts_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
int *btCnt_;
AlignerMetrics *metrics_;
};
@@ -638,7 +638,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
@@ -1405,7 +1405,7 @@ protected:
bool quiet_;
int maxBts_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
int *btCnt_;
// Range-finding state for first mate
@@ -1529,7 +1529,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
@@ -2076,7 +2076,7 @@ protected:
TDriver* driver_;
// Pool for distributing chunks of best-first path descriptor memory
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
bool verbose_;
bool quiet_;
--- aligner_0mm.h
+++ 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,
@@ -123,7 +123,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
bool maqPenalty_;
@@ -162,7 +162,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -363,7 +363,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool reportSe_;
--- aligner_1mm.h
+++ 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,
@@ -160,7 +160,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool maqPenalty_;
@@ -199,7 +199,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -475,7 +475,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool reportSe_;
--- aligner_23mm.h
+++ 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,
@@ -230,7 +230,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool maqPenalty_;
@@ -271,7 +271,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -672,7 +672,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool reportSe_;
--- aligner_seed_mm.h
+++ 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_;
--- ebwt_search.cpp
+++ 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
-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 useV1;
static bool reportSe;
@@ -232,7 +232,7 @@ norc = false; // don't align rc orientation of read
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)
+ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB)
chunkVerbose = false; // have chunk allocator output status messages?
useV1 = true;
reportSe = false;
@@ -1343,7 +1343,7 @@ static void exactSearchWorkerStateful(vo
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
UnpairedExactAlignerV1Factory alSEfact(
ebwt,
NULL,
@@ -1632,7 +1632,7 @@ static void mismatchSearchWorkerFullStat
// Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
Unpaired1mmAlignerV1Factory alSEfact(
ebwtFw,
@@ -2083,7 +2083,7 @@ static void twoOrThreeMismatchSearchWork
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
Unpaired23mmAlignerV1Factory alSEfact(
ebwtFw,
&ebwtBw,
@@ -2753,7 +2753,7 @@ static void seededQualSearchWorkerFullSt
// Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
- 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) {
--- ebwt_search_backtrack.h
+++ ebwt_search_backtrack.h
@@ -2703,7 +2703,7 @@
bool verbose,
bool quiet,
bool mate1,
- ChunkPool* pool,
+ bowtieChunkPool* pool,
int *btCnt) :
SingleRangeSourceDriver<EbwtRangeSource>(
params, rs, fw, sink, sinkPt, os, verbose,
@@ -2877,7 +2877,7 @@
bool verbose,
bool quiet,
bool mate1,
- ChunkPool* pool,
+ bowtieChunkPool* pool,
int *btCnt = NULL) :
params_(params),
rs_(rs),
@@ -2936,7 +2936,7 @@
bool verbose_;
bool quiet_;
bool mate1_;
- ChunkPool* pool_;
+ bowtieChunkPool* pool_;
int *btCnt_;
};
--- pool.h
+++ 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
--- range_source.h
+++ range_source.h
@@ -1307,7 +1307,7 @@ 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"),
@@ -1556,7 +1556,7 @@
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
@@ -1730,7 +1730,7 @@
bool quiet,
bool mate1,
uint32_t minCostAdjustment,
- ChunkPool* pool,
+ bowtieChunkPool* pool,
int *btCnt) :
RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
len_(0), mate1_(mate1),
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
--- blockwise_sa.h
+++ blockwise_sa.h
@@ -673,8 +673,8 @@
try {
// Allocate and initialize containers for holding bucket
// sizes and representatives.
- fill(tparams[tid].bucketSzs, numBuckets, 0, Exact());
- fill(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
+ resize(tparams[tid].bucketSzs, numBuckets, 0, Exact());
+ resize(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
} catch(bad_alloc &e) {
if(this->_passMemExc) {
throw e; // rethrow immediately
@@ -1063,7 +1063,7 @@
hi = _sampleSuffs[cur_block];
//zHi.resizeExact(_dcV);
//zHi.fillZero();
- fill(zHi, _dcV, 0, Exact());
+ resize(zHi, _dcV, 0, Exact());
assert_eq(getValue(zHi, 0), 0);
calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
}
@@ -1074,7 +1074,7 @@
lo = _sampleSuffs[cur_block-1];
//zLo.resizeExact(_dcV);
//zLo.fillZero();
- fill(zLo, _dcV, 0, Exact());
+ resize(zLo, _dcV, 0, Exact());
assert_gt(_dcV, 3);
assert_eq(getValue(zLo, 0), 0);
calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
--- diff_sample.h
+++ diff_sample.h
@@ -457,7 +457,7 @@ 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)
@@ -540,7 +540,7 @@ 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;
@@ -664,7 +664,7 @@ 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;
@@ -728,7 +728,7 @@ void DifferenceCoverSample<TStr>::buildS
assert_eq(length(_doffs), d+1);
// Size sPrime appropriately
reserve(sPrime, sPrimeSz + padding, Exact()); // reserve extra slot for LS
- fill(sPrime, sPrimeSz + padding, OFF_MASK, Exact());
+ resize(sPrime, sPrimeSz + padding, 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;
@@ -952,7 +952,7 @@ void DifferenceCoverSample<TStr>::build(
// arrays back into sPrime.
VMSG_NL(" Allocating rank array");
reserve(_isaPrime, length(sPrime), 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());
--- Makefile.orig 2017-12-12 11:29:54.000000000 -0700
+++ Makefile 2019-01-27 04:46:19.000000000 -0700
@@ -7,10 +7,7 @@
prefix ?= /usr/local
bindir = $(prefix)/bin
-SEQAN_DIR = ./SeqAn-1.1
-# 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 = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include)
CXX ?= g++
CPP ?= $(CXX)
CC ?= gcc
@@ -178,7 +175,6 @@
$(wildcard genomes/NC_008253.fna) \
$(wildcard reads/e_coli_1000.*) \
$(wildcard reads/e_coli_1000_*) \
- SeqAn-1.1 \
bowtie \
bowtie-build \
bowtie-inspect \