Package: bowtie
Version: 0.12.7-3
Severity: wishlist
Tags: patch
Hi,
bowtie 1.0.0 is out and I've update debian/patches so that it compiles without
errors.
I'm a Debian Developer (account name: ogi) and since I'm working with various
NGS software, I plan to update Debian's packages. Could you give me repository
rights for updating the patches? Is it OK to go ahead and upload the new
version?
I've just finished with the patches and the names and descriptions need
improvement. I'll do it later.
Regards,
Ognyan Kulev
--- a/blockwise_sa.h
+++ b/blockwise_sa.h
@@ -448,8 +448,8 @@
try {
// Allocate and initialize containers for holding bucket
// sizes and representatives.
- fill(bucketSzs, numBuckets, 0, Exact());
- fill(bucketReps, numBuckets, 0xffffffff, Exact());
+ resize(bucketSzs, numBuckets, 0, Exact());
+ resize(bucketReps, numBuckets, 0xffffffff, Exact());
} catch(bad_alloc &e) {
if(this->_passMemExc) {
throw e; // rethrow immediately
@@ -806,7 +806,7 @@
// 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());
}
@@ -815,7 +815,7 @@
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
@@ -451,7 +451,7 @@
// 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)
@@ -531,7 +531,7 @@
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());
for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i;
}
@@ -652,7 +652,7 @@
VMSG_NL(" Doing sanity check");
uint32_t added = 0;
String<uint32_t> sorted;
- fill(sorted, length(_isaPrime), 0xffffffff, Exact());
+ resize(sorted, length(_isaPrime), 0xffffffff, Exact());
for(size_t di = 0; di < this->d(); di++) {
uint32_t d = _ds[di];
size_t i = 0;
@@ -713,7 +713,7 @@
assert_eq(length(_doffs), d+1);
// Size sPrime appropriately
reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
- fill(sPrime, sPrimeSz, 0xffffffff, Exact());
+ resize(sPrime, sPrimeSz, 0xffffffff, Exact());
// Slot suffixes from text into sPrime according to the mu
// mapping; where the mapping would leave a blank, insert a 0
uint32_t added = 0;
@@ -818,7 +818,7 @@
// arrays back into sPrime.
VMSG_NL(" Allocating rank array");
reserve(_isaPrime, length(sPrime)+1, Exact());
- fill(_isaPrime, length(sPrime), 0xffffffff, Exact());
+ resize(_isaPrime, length(sPrime), 0xffffffff, Exact());
assert_gt(length(_isaPrime), 0);
{
Timer timer(cout, " Ranking v-sort output time: ", this->verbose());
Description: Use build flags from environment (dpkg-buildflags).
Necessary for hardening flags.
Author: Simon Ruderich <si...@ruderich.org>
Last-Update: 2012-04-24
Bug-Closed: http://bugs.debian.org/670230
--- a/Makefile
+++ b/Makefile
@@ -173,7 +173,7 @@
$(MM_DEF) \
$(SHMEM_DEF)
-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
+ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
Note: This patch is deactivated because the Debian packaged version of SeqAn 1.2
is not compatible with the version included into this package
Author: Andreas Tille <tilleqdebian.org>
Date: 2011-01-30
Description: Use Debian packages SeqAn Librariy instead of copy in upstream source
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@
# Makefile for bowtie, bowtie-build, bowtie-inspect
#
-SEQAN_DIR = SeqAn-1.1
+SEQAN_DIR = /usr/include/seqan
SEQAN_INC = -I $(SEQAN_DIR)
INC = $(SEQAN_INC)
CPP = g++
@@ -133,7 +133,6 @@
$(wildcard genomes/NC_008253.fna) \
$(wildcard reads/e_coli_1000.*) \
$(wildcard reads/e_coli_1000_*) \
- SeqAn-1.1 \
doc/manual.html \
doc/README \
doc/style.css \
--- a/aligner.h
+++ b/aligner.h
@@ -337,7 +337,7 @@
bool verbose,
bool quiet,
int maxBts,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
int *btCnt = NULL,
AlignerMetrics *metrics = NULL) :
Aligner(true, rangeMode),
@@ -544,7 +544,7 @@
bool quiet_; // don't print informational/warning info
const int maxBts_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
int *btCnt_;
AlignerMetrics *metrics_;
};
@@ -585,7 +585,7 @@
bool verbose,
bool quiet,
int maxBts,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
@@ -1358,7 +1358,7 @@
bool quiet_;
int maxBts_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
int *btCnt_;
// Range-finding state for first mate
@@ -1482,7 +1482,7 @@
bool verbose,
bool quiet,
int maxBts,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
@@ -2035,7 +2035,7 @@
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 @@
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
@@ -124,7 +124,7 @@
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
bool maqPenalty_;
@@ -164,7 +164,7 @@
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -366,7 +366,7 @@
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 @@
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
@@ -161,7 +161,7 @@
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 @@
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -478,7 +478,7 @@
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 @@
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
@@ -231,7 +231,7 @@
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 @@
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -675,7 +675,7 @@
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 @@
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
@@ -554,7 +554,7 @@
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
- ChunkPool *pool_;
+ bowtieChunkPool *pool_;
BitPairReference* refs_;
vector<String<Dna5> >& os_;
bool strandFix_;
@@ -598,7 +598,7 @@
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
- ChunkPool *pool,
+ bowtieChunkPool *pool,
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
@@ -1375,7 +1375,7 @@
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
@@ -110,7 +110,7 @@
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;
@@ -221,7 +221,7 @@
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;
@@ -1202,7 +1202,7 @@
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,
@@ -1371,7 +1371,7 @@
// 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,
@@ -1668,7 +1668,7 @@
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,
@@ -2101,7 +2101,7 @@
// 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 @@
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 @@
bool verbose,
bool quiet,
bool mate1,
- ChunkPool* pool,
+ bowtieChunkPool* pool,
int *btCnt = NULL) :
params_(params),
rs_(rs),
@@ -2986,7 +2986,7 @@
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 @@
}
} 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 @@
/**
* Delete all the pools.
*/
- ~ChunkPool() {
+ ~bowtieChunkPool() {
if(pool_ != NULL) delete[] pool_;
}
@@ -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.
*/
- 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 @@
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 @@
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 @@
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 @@
bool quiet,
bool mate1,
uint32_t minCostAdjustment,
- ChunkPool* pool,
+ bowtieChunkPool* pool,
int *btCnt) :
RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
len_(0), mate1_(mate1),
--- a/pat.h
+++ b/pat.h
@@ -82,20 +82,20 @@
~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);
}
}
