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ebwt.h
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#ifndef EBWT_H_
#define EBWT_H_
#include <stdint.h>
#include <string.h>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <vector>
#include <set>
#include <sstream>
#include <fcntl.h>
#include <errno.h>
#include <stdexcept>
#include <seqan/sequence.h>
#include <seqan/index.h>
#include <sys/stat.h>
#ifdef BOWTIE_MM
#include <sys/mman.h>
#include <sys/shm.h>
#endif
#include "auto_array.h"
#include "shmem.h"
#include "alphabet.h"
#include "assert_helpers.h"
#include "bitpack.h"
#include "blockwise_sa.h"
#include "endian_swap.h"
#include "word_io.h"
#include "random_source.h"
#include "hit.h"
#include "ref_read.h"
#include "threading.h"
#include "bitset.h"
#include "str_util.h"
#include "mm.h"
#include "timer.h"
#include "refmap.h"
#include "color_dec.h"
#include "reference.h"
#ifdef POPCNT_CAPABILITY
#include "processor_support.h"
#endif
using namespace std;
using namespace seqan;
#ifndef PREFETCH_LOCALITY
// No locality by default
#define PREFETCH_LOCALITY 2
#endif
// From ccnt_lut.cpp, automatically generated by gen_lookup_tables.pl
extern uint8_t cCntLUT_4[4][4][256];
static const uint64_t c_table[4] = {
0xffffffffffffffffllu,
0xaaaaaaaaaaaaaaaallu,
0x5555555555555555llu,
0x0000000000000000llu
};
#ifndef VMSG_NL
#define VMSG_NL(args...) \
if(this->verbose()) { \
stringstream tmp; \
tmp << args << endl; \
this->verbose(tmp.str()); \
}
#endif
#ifndef VMSG
#define VMSG(args...) \
if(this->verbose()) { \
stringstream tmp; \
tmp << args; \
this->verbose(tmp.str()); \
}
#endif
/**
* Flags describing type of Ebwt.
*/
enum EBWT_FLAGS {
EBWT_COLOR = 2, // true -> Ebwt is colorspace
EBWT_ENTIRE_REV = 4 // true -> reverse Ebwt is the whole
// concatenated string reversed, rather than
// each stretch reversed
};
extern string gLastIOErrMsg;
inline bool is_read_err(int fdesc, ssize_t ret, size_t count){
if (ret < 0) {
std::stringstream sstm;
sstm << "ERRNO: " << errno << " ERR Msg:" << strerror(errno) << std::endl;
gLastIOErrMsg = sstm.str();
return true;
}
return false;
}
/* Checks whether a call to fread() failed or not. */
inline bool is_fread_err(FILE* file_hd, size_t ret, size_t count){
if (ferror(file_hd)) {
gLastIOErrMsg = "Error Reading File!";
return true;
}
return false;
}
/**
* Extended Burrows-Wheeler transform header. This together with the
* actual data arrays and other text-specific parameters defined in
* class Ebwt constitute the entire Ebwt.
*/
class EbwtParams {
public:
EbwtParams() { }
EbwtParams(TIndexOffU len,
int32_t lineRate,
int32_t linesPerSide,
int32_t offRate,
int32_t isaRate,
int32_t ftabChars,
bool color,
bool entireReverse)
{
init(len, lineRate, linesPerSide, offRate, isaRate, ftabChars, color, entireReverse);
}
EbwtParams(const EbwtParams& eh) {
init(eh._len, eh._lineRate, eh._linesPerSide, eh._offRate,
eh._isaRate, eh._ftabChars, eh._color, eh._entireReverse);
}
void init(TIndexOffU len, int32_t lineRate, int32_t linesPerSide,
int32_t offRate, int32_t isaRate, int32_t ftabChars,
bool color, bool entireReverse)
{
_color = color;
_entireReverse = entireReverse;
_len = len;
_bwtLen = _len + 1;
_sz = (len+3)/4;
_bwtSz = (len/4 + 1);
_lineRate = lineRate;
_linesPerSide = linesPerSide;
_origOffRate = offRate;
_offRate = offRate;
_offMask = OFF_MASK << _offRate;
_isaRate = isaRate;
_isaMask = OFF_MASK << ((_isaRate >= 0) ? _isaRate : 0);
_ftabChars = ftabChars;
_eftabLen = _ftabChars*2;
_eftabSz = _eftabLen*OFF_SIZE;
_ftabLen = (1 << (_ftabChars*2))+1;
_ftabSz = _ftabLen*OFF_SIZE;
_offsLen = (_bwtLen + (1 << _offRate) - 1) >> _offRate;
_offsSz = (uint64_t)_offsLen*OFF_SIZE;
_isaLen = (_isaRate == -1)? 0 : ((_bwtLen + (1 << _isaRate) - 1) >> _isaRate);
_isaSz = _isaLen*OFF_SIZE;
_lineSz = 1 << _lineRate;
_sideSz = _lineSz * _linesPerSide;
_sideBwtSz = _sideSz - 2*OFF_SIZE;
_sideBwtLen = _sideBwtSz*4;
_numSidePairs = (_bwtSz+(2*_sideBwtSz)-1)/(2*_sideBwtSz);
_numSides = _numSidePairs*2;
_numLines = _numSides * _linesPerSide;
_ebwtTotLen = _numSidePairs * (2*_sideSz);
_ebwtTotSz = _ebwtTotLen;
assert(repOk());
}
TIndexOffU len() const { return _len; }
TIndexOffU bwtLen() const { return _bwtLen; }
TIndexOffU sz() const { return _sz; }
TIndexOffU bwtSz() const { return _bwtSz; }
int32_t lineRate() const { return _lineRate; }
int32_t linesPerSide() const { return _linesPerSide; }
int32_t origOffRate() const { return _origOffRate; }
int32_t offRate() const { return _offRate; }
TIndexOffU offMask() const { return _offMask; }
int32_t isaRate() const { return _isaRate; }
uint32_t isaMask() const { return _isaMask; }
int32_t ftabChars() const { return _ftabChars; }
uint32_t eftabLen() const { return _eftabLen; }
uint32_t eftabSz() const { return _eftabSz; }
TIndexOffU ftabLen() const { return _ftabLen; }
TIndexOffU ftabSz() const { return _ftabSz; }
TIndexOffU offsLen() const { return _offsLen; }
uint64_t offsSz() const { return _offsSz; }
TIndexOffU isaLen() const { return _isaLen; }
uint64_t isaSz() const { return _isaSz; }
uint32_t lineSz() const { return _lineSz; }
uint32_t sideSz() const { return _sideSz; }
uint32_t sideBwtSz() const { return _sideBwtSz; }
uint32_t sideBwtLen() const { return _sideBwtLen; }
uint32_t numSidePairs() const { return _numSidePairs; } /* check */
TIndexOffU numSides() const { return _numSides; }
TIndexOffU numLines() const { return _numLines; }
TIndexOffU ebwtTotLen() const { return _ebwtTotLen; }
TIndexOffU ebwtTotSz() const { return _ebwtTotSz; }
bool color() const { return _color; }
bool entireReverse() const { return _entireReverse; }
/**
* Set a new suffix-array sampling rate, which involves updating
* rate, mask, sample length, and sample size.
*/
void setOffRate(int __offRate) {
_offRate = __offRate;
_offMask = OFF_MASK << _offRate;
_offsLen = (_bwtLen + (1 << _offRate) - 1) >> _offRate;
_offsSz = (uint64_t) _offsLen*OFF_SIZE;
}
/**
* Set a new inverse suffix-array sampling rate, which involves
* updating rate, mask, sample length, and sample size.
*/
void setIsaRate(int __isaRate) {
_isaRate = __isaRate;
_isaMask = OFF_MASK << _isaRate;
_isaLen = (_bwtLen + (1 << _isaRate) - 1) >> _isaRate;
_isaSz = (uint64_t)_isaLen*OFF_SIZE;
}
/// Check that this EbwtParams is internally consistent
bool repOk() const {
assert_gt(_len, 0);
assert_gt(_lineRate, 3);
assert_geq(_offRate, 0);
assert_leq(_ftabChars, 16);
assert_geq(_ftabChars, 1);
assert_lt(_lineRate, 32);
assert_lt(_linesPerSide, 32);
assert_lt(_ftabChars, 32);
assert_eq(0, _ebwtTotSz % (2*_lineSz));
return true;
}
/**
* Pretty-print the header contents to the given output stream.
*/
void print(ostream& out) const {
out << "Headers:" << endl
<< " len: " << _len << endl
<< " bwtLen: " << _bwtLen << endl
<< " sz: " << _sz << endl
<< " bwtSz: " << _bwtSz << endl
<< " lineRate: " << _lineRate << endl
<< " linesPerSide: " << _linesPerSide << endl
<< " offRate: " << _offRate << endl
<< " offMask: 0x" << hex << _offMask << dec << endl
<< " isaRate: " << _isaRate << endl
<< " isaMask: 0x" << hex << _isaMask << dec << endl
<< " ftabChars: " << _ftabChars << endl
<< " eftabLen: " << _eftabLen << endl
<< " eftabSz: " << _eftabSz << endl
<< " ftabLen: " << _ftabLen << endl
<< " ftabSz: " << _ftabSz << endl
<< " offsLen: " << _offsLen << endl
<< " offsSz: " << _offsSz << endl
<< " isaLen: " << _isaLen << endl
<< " isaSz: " << _isaSz << endl
<< " lineSz: " << _lineSz << endl
<< " sideSz: " << _sideSz << endl
<< " sideBwtSz: " << _sideBwtSz << endl
<< " sideBwtLen: " << _sideBwtLen << endl
<< " numSidePairs: " << _numSidePairs << endl
<< " numSides: " << _numSides << endl
<< " numLines: " << _numLines << endl
<< " ebwtTotLen: " << _ebwtTotLen << endl
<< " ebwtTotSz: " << _ebwtTotSz << endl
<< " reverse: " << _entireReverse << endl;
}
TIndexOffU _len;
TIndexOffU _bwtLen;
TIndexOffU _sz;
TIndexOffU _bwtSz;
int32_t _lineRate;
int32_t _linesPerSide;
int32_t _origOffRate;
int32_t _offRate;
TIndexOffU _offMask;
int32_t _isaRate;
uint32_t _isaMask;
int32_t _ftabChars;
uint32_t _eftabLen;
uint32_t _eftabSz;
TIndexOffU _ftabLen;
TIndexOffU _ftabSz;
TIndexOffU _offsLen;
uint64_t _offsSz;
TIndexOffU _isaLen;
uint64_t _isaSz;
uint32_t _lineSz;
uint32_t _sideSz;
uint32_t _sideBwtSz;
uint32_t _sideBwtLen;
uint32_t _numSidePairs;
TIndexOffU _numSides;
TIndexOffU _numLines;
TIndexOffU _ebwtTotLen;
TIndexOffU _ebwtTotSz;
bool _color;
bool _entireReverse;
};
/**
* Exception to throw when a file-realted error occurs.
*/
class EbwtFileOpenException : public std::runtime_error {
public:
EbwtFileOpenException(const std::string& msg = "") :
std::runtime_error(msg) { }
};
/**
* Calculate size of file with given name.
*/
static inline int64_t fileSize(const char* name) {
std::ifstream f;
f.open(name, std::ios_base::binary | std::ios_base::in);
if (!f.good() || f.eof() || !f.is_open()) { return 0; }
f.seekg(0, std::ios_base::beg);
std::ifstream::pos_type begin_pos = f.tellg();
f.seekg(0, std::ios_base::end);
return static_cast<int64_t>(f.tellg() - begin_pos);
}
// Forward declarations for Ebwt class
struct SideLocus;
template<typename TStr> class EbwtSearchParams;
/**
* Extended Burrows-Wheeler transform data.
*
* An Ebwt may be transferred to and from RAM with calls to
* evictFromMemory() and loadIntoMemory(). By default, a newly-created
* Ebwt is not loaded into memory; if the user would like to use a
* newly-created Ebwt to answer queries, they must first call
* loadIntoMemory().
*/
template <typename TStr>
class Ebwt {
public:
typedef typename Value<TStr>::Type TAlphabet;
#define Ebwt_INITS \
_toBigEndian(currentlyBigEndian()), \
_overrideOffRate(__overrideOffRate), \
_overrideIsaRate(__overrideIsaRate), \
_verbose(verbose), \
_passMemExc(passMemExc), \
_sanity(sanityCheck), \
_fw(__fw), \
_in1(NULL), \
_in2(NULL), \
_zOff(OFF_MASK), \
_zEbwtByteOff(OFF_MASK), \
_zEbwtBpOff(-1), \
_nPat(0), \
_nFrag(0), \
_plen(NULL), \
_rstarts(NULL), \
_fchr(NULL), \
_ftab(NULL), \
_eftab(NULL), \
_offs(NULL), \
_isa(NULL), \
_ebwt(NULL), \
_useMm(false), \
useShmem_(false), \
_refnames(), \
rmap_(NULL), \
mmFile1_(NULL), \
mmFile2_(NULL)
#ifdef EBWT_STATS
#define Ebwt_STAT_INITS \
,mapLFExs_(0llu), \
mapLFs_(0llu), \
mapLFcs_(0llu), \
mapLF1cs_(0llu), \
mapLF1s_(0llu)
#else
#define Ebwt_STAT_INITS
#endif
/// Construct an Ebwt from the given input file
Ebwt(const string& in,
int color,
int needEntireReverse,
bool __fw,
int32_t __overrideOffRate = -1,
int32_t __overrideIsaRate = -1,
bool useMm = false,
bool useShmem = false,
bool mmSweep = false,
bool loadNames = false,
const ReferenceMap* rmap = NULL,
bool verbose = false,
bool startVerbose = false,
bool passMemExc = false,
bool sanityCheck = false) :
Ebwt_INITS
Ebwt_STAT_INITS
{
assert(!useMm || !useShmem);
#ifdef POPCNT_CAPABILITY
ProcessorSupport ps;
_usePOPCNTinstruction = ps.POPCNTenabled();
#endif
rmap_ = rmap;
_useMm = useMm;
useShmem_ = useShmem;
_in1Str = in + ".1." + gEbwt_ext;
_in2Str = in + ".2." + gEbwt_ext;
readIntoMemory(
color, // expect colorspace reference?
__fw ? -1 : needEntireReverse, // need REF_READ_REVERSE
true, // stop after loading the header portion?
&_eh, // params structure to fill in
mmSweep, // mmSweep
loadNames, // loadNames
startVerbose); // startVerbose
// If the offRate has been overridden, reflect that in the
// _eh._offRate field
if(_overrideOffRate > _eh._offRate) {
_eh.setOffRate(_overrideOffRate);
assert_eq(_overrideOffRate, _eh._offRate);
}
// Same with isaRate
if(_overrideIsaRate > _eh._isaRate) {
_eh.setIsaRate(_overrideIsaRate);
assert_eq(_overrideIsaRate, _eh._isaRate);
}
assert(repOk());
}
/// Construct an Ebwt from the given header parameters and string
/// vector, optionally using a blockwise suffix sorter with the
/// given 'bmax' and 'dcv' parameters. The string vector is
/// ultimately joined and the joined string is passed to buildToDisk().
Ebwt(int color,
int32_t lineRate,
int32_t linesPerSide,
int32_t offRate,
int32_t isaRate,
int32_t ftabChars,
int nthreads,
const string& file, // base filename for EBWT files
bool __fw,
bool useBlockwise,
TIndexOffU bmax,
TIndexOffU bmaxSqrtMult,
TIndexOffU bmaxDivN,
int dcv,
vector<FileBuf*>& is,
vector<RefRecord>& szs,
vector<uint32_t>& plens,
TIndexOffU sztot,
const RefReadInParams& refparams,
uint32_t seed,
int32_t __overrideOffRate = -1,
int32_t __overrideIsaRate = -1,
bool verbose = false,
bool passMemExc = false,
bool sanityCheck = false) :
Ebwt_INITS
Ebwt_STAT_INITS,
_eh(joinedLen(szs),
lineRate,
linesPerSide,
offRate,
isaRate,
ftabChars,
color,
refparams.reverse == REF_READ_REVERSE)
{
#ifdef POPCNT_CAPABILITY
ProcessorSupport ps;
_usePOPCNTinstruction = ps.POPCNTenabled();
#endif
_in1Str = file + ".1." + gEbwt_ext;
_in2Str = file + ".2." + gEbwt_ext;
// Open output files
ofstream fout1(_in1Str.c_str(), ios::binary);
if(!fout1.good()) {
cerr << "Could not open index file for writing: \"" << _in1Str << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
}
ofstream fout2(_in2Str.c_str(), ios::binary);
if(!fout2.good()) {
cerr << "Could not open index file for writing: \"" << _in2Str << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
}
// Build
initFromVector(
is,
szs,
plens,
sztot,
refparams,
fout1,
fout2,
file,
nthreads,
useBlockwise,
bmax,
bmaxSqrtMult,
bmaxDivN,
dcv,
seed);
// Close output files
fout1.flush();
int64_t tellpSz1 = (int64_t)fout1.tellp();
VMSG_NL("Wrote " << fout1.tellp() << " bytes to primary EBWT file: " << _in1Str);
fout1.close();
bool err = false;
if(tellpSz1 > fileSize(_in1Str.c_str())) {
err = true;
cerr << "Index is corrupt: File size for " << _in1Str << " should have been " << tellpSz1
<< " but is actually " << fileSize(_in1Str.c_str()) << "." << endl;
}
fout2.flush();
int64_t tellpSz2 = (int64_t)fout2.tellp();
VMSG_NL("Wrote " << fout2.tellp() << " bytes to secondary EBWT file: " << _in2Str);
fout2.close();
if(tellpSz2 > fileSize(_in2Str.c_str())) {
err = true;
cerr << "Index is corrupt: File size for " << _in2Str << " should have been " << tellpSz2
<< " but is actually " << fileSize(_in2Str.c_str()) << "." << endl;
}
if(err) {
cerr << "Please check if there is a problem with the disk or if disk is full." << endl;
throw 1;
}
// Reopen as input streams
VMSG_NL("Re-opening _in1 and _in2 as input streams");
if(_sanity) {
VMSG_NL("Sanity-checking Ebwt");
assert(!isInMemory());
readIntoMemory(
color,
__fw ? -1 : refparams.reverse == REF_READ_REVERSE,
false,
NULL,
false,
true,
false);
sanityCheckAll(refparams.reverse);
evictFromMemory();
assert(!isInMemory());
}
VMSG_NL("Returning from Ebwt constructor");
}
bool isPacked();
/**
* Write the rstarts array given the szs array for the reference.
*/
void szsToDisk(const vector<RefRecord>& szs, ostream& os, int reverse) {
TIndexOffU seq = 0;
TIndexOffU off = 0;
TIndexOffU totlen = 0;
for(unsigned int i = 0; i < szs.size(); i++) {
if(szs[i].len == 0) continue;
if(szs[i].first) off = 0;
off += szs[i].off;
#ifdef ACCOUNT_FOR_ALL_GAP_REFS
if(szs[i].first && szs[i].len > 0) seq++;
#else
if(szs[i].first) seq++;
#endif
TIndexOffU seqm1 = seq-1;
assert_lt(seqm1, _nPat);
TIndexOffU fwoff = off;
if(reverse == REF_READ_REVERSE) {
// Invert pattern idxs
seqm1 = _nPat - seqm1 - 1;
// Invert pattern idxs
assert_leq(off + szs[i].len, _plen[seqm1]);
fwoff = _plen[seqm1] - (off + szs[i].len);
}
writeU<TIndexOffU>(os, totlen, this->toBe()); // offset from beginning of joined string
writeU<TIndexOffU>(os, seqm1, this->toBe()); // sequence id
writeU<TIndexOffU>(os, fwoff, this->toBe()); // offset into sequence
totlen += szs[i].len;
off += szs[i].len;
}
}
/**
* Helper for the constructors above. Takes a vector of text
* strings and joins them into a single string with a call to
* joinToDisk, which does a join (with padding) and writes some of
* the resulting data directly to disk rather than keep it in
* memory. It then constructs a suffix-array producer (what kind
* depends on 'useBlockwise') for the resulting sequence. The
* suffix-array producer can then be used to obtain chunks of the
* joined string's suffix array.
*/
void initFromVector(
vector<FileBuf*>& is,
vector<RefRecord>& szs,
vector<uint32_t>& plens,
TIndexOffU sztot,
const RefReadInParams& refparams,
ofstream& out1,
ofstream& out2,
const string& outfile,
int nthreads,
bool useBlockwise,
TIndexOffU bmax,
TIndexOffU bmaxSqrtMult,
TIndexOffU bmaxDivN,
int dcv,
uint32_t seed)
{
// Compose text strings into single string
VMSG_NL("Calculating joined length");
TStr s; // holds the entire joined reference after call to joinToDisk
TIndexOffU jlen;
jlen = joinedLen(szs);
assert_geq(jlen, sztot);
VMSG_NL("Writing header");
writeFromMemory(true, out1, out2);
try {
VMSG_NL("Reserving space for joined string");
seqan::reserve(s, jlen, Exact());
VMSG_NL("Joining reference sequences");
if(refparams.reverse == REF_READ_REVERSE) {
{
Timer timer(cout, " Time to join reference sequences: ", _verbose);
joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
} {
Timer timer(cout, " Time to reverse reference sequence: ", _verbose);
vector<RefRecord> tmp;
reverseInPlace(s);
reverseRefRecords(szs, tmp, false, false);
szsToDisk(tmp, out1, refparams.reverse);
}
} else {
Timer timer(cout, " Time to join reference sequences: ", _verbose);
joinToDisk(is, szs, plens, sztot, refparams, s, out1, out2, seed);
szsToDisk(szs, out1, refparams.reverse);
}
// Joined reference sequence now in 's'
} catch(bad_alloc& e) {
// If we throw an allocation exception in the try block,
// that means that the joined version of the reference
// string itself is too larger to fit in memory. The only
// alternatives are to tell the user to give us more memory
// or to try again with a packed representation of the
// reference (if we haven't tried that already).
cerr << "Could not allocate space for a joined string of " << jlen << " elements." << endl;
if(!isPacked() && _passMemExc) {
// Pass the exception up so that we can retry using a
// packed string representation
throw e;
}
// There's no point passing this exception on. The fact
// that we couldn't allocate the joined string means that
// --bmax is irrelevant - the user should re-run with
// ebwt-build-packed
if(isPacked()) {
cerr << "Please try running bowtie-build on a computer with more memory." << endl;
} else {
cerr << "Please try running bowtie-build in packed mode (-p/--packed) or in automatic" << endl
<< "mode (-a/--auto), or try again on a computer with more memory." << endl;
}
if(sizeof(void*) == 4) {
cerr << "If this computer has more than 4 GB of memory, try using a 64-bit executable;" << endl
<< "this executable is 32-bit." << endl;
}
throw 1;
}
// Succesfully obtained joined reference string
assert_geq(length(s), jlen);
if(bmax != OFF_MASK) {
VMSG_NL("bmax according to bmax setting: " << bmax);
}
else if(bmaxSqrtMult != OFF_MASK) {
bmax *= bmaxSqrtMult;
VMSG_NL("bmax according to bmaxSqrtMult setting: " << bmax);
}
else if(bmaxDivN != OFF_MASK) {
bmax = max<TIndexOffU>(jlen / bmaxDivN, 1);
VMSG_NL("bmax according to bmaxDivN setting: " << bmax);
}
else {
bmax = (TIndexOffU)sqrt(length(s));
VMSG_NL("bmax defaulted to: " << bmax);
}
int iter = 0;
bool first = true;
// Look for bmax/dcv parameters that work.
while(true) {
if(!first && bmax < 40 && _passMemExc) {
cerr << "Could not find approrpiate bmax/dcv settings for building this index." << endl;
if(!isPacked()) {
// Throw an exception exception so that we can
// retry using a packed string representation
throw bad_alloc();
} else {
cerr << "Already tried a packed string representation." << endl;
}
cerr << "Please try indexing this reference on a computer with more memory." << endl;
if(sizeof(void*) == 4) {
cerr << "If this computer has more than 4 GB of memory, try using a 64-bit executable;" << endl
<< "this executable is 32-bit." << endl;
}
throw 1;
}
if(dcv > 4096) dcv = 4096;
if((iter % 6) == 5 && dcv < 4096 && dcv != 0) {
dcv <<= 1; // double difference-cover period
} else {
bmax -= (bmax >> 2); // reduce by 25%
}
VMSG("Using parameters --bmax " << bmax);
if(dcv == 0) {
VMSG_NL(" and *no difference cover*");
} else {
VMSG_NL(" --dcv " << dcv);
}
iter++;
try {
{
VMSG_NL(" Doing ahead-of-time memory usage test");
// Make a quick-and-dirty attempt to force a bad_alloc iff
// we would have thrown one eventually as part of
// constructing the DifferenceCoverSample
dcv <<= 1;
TIndexOffU sz = (TIndexOffU)DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
if(nthreads > 1) sz *= (nthreads + 1);
AutoArray<uint8_t> tmp(sz);
dcv >>= 1;
// Likewise with the KarkkainenBlockwiseSA
sz = (TIndexOffU)KarkkainenBlockwiseSA<TStr>::simulateAllocs(s, bmax);
AutoArray<uint8_t> tmp2(sz);
// Now throw in the 'ftab' and 'isaSample' structures
// that we'll eventually allocate in buildToDisk
AutoArray<TIndexOffU> ftab(_eh._ftabLen * 2);
AutoArray<uint8_t> side(_eh._sideSz);
// Grab another 20 MB out of caution
AutoArray<uint32_t> extra(20*1024*1024);
// If we made it here without throwing bad_alloc, then we
// passed the memory-usage stress test
VMSG(" Passed! Constructing with these parameters: --bmax " << bmax << " --dcv " << dcv);
if(isPacked()) {
VMSG(" --packed");
}
VMSG_NL("");
}
VMSG_NL("Constructing suffix-array element generator");
KarkkainenBlockwiseSA<TStr> bsa(s, bmax, nthreads, dcv, seed, _sanity, _passMemExc, _verbose, outfile);
assert(bsa.suffixItrIsReset());
assert_eq(bsa.size(), length(s)+1);
VMSG_NL("Converting suffix-array elements to index image");
buildToDisk(bsa, s, out1, out2);
out1.flush(); out2.flush();
if(out1.fail() || out2.fail()) {
cerr << "An error occurred writing the index to disk. Please check if the disk is full." << endl;
throw 1;
}
break;
} catch(bad_alloc& e) {
if(_passMemExc) {
VMSG_NL(" Ran out of memory; automatically trying more memory-economical parameters.");
} else {
cerr << "Out of memory while constructing suffix array. Please try using a smaller" << endl
<< "number of blocks by specifying a smaller --bmax or a larger --bmaxdivn" << endl;
throw 1;
}
}
first = false;
}
assert(repOk());
// Now write reference sequence names on the end
#ifdef ACCOUNT_FOR_ALL_GAP_REFS
assert_geq(this->_refnames.size(), this->_nPat);
#else
assert_eq(this->_refnames.size(), this->_nPat);
#endif
for(TIndexOffU i = 0; i < this->_refnames.size(); i++) {
out1 << this->_refnames[i] << endl;
}
out1 << '\0';
out1.flush(); out2.flush();
if(out1.fail() || out2.fail()) {
cerr << "An error occurred writing the index to disk. Please check if the disk is full." << endl;
throw 1;
}
VMSG_NL("Returning from initFromVector");
}
/**
* Return the length that the joined string of the given string
* list will have. Note that this is indifferent to how the text
* fragments correspond to input sequences - it just cares about
* the lengths of the fragments.
*/
TIndexOffU joinedLen(vector<RefRecord>& szs) {
TIndexOffU ret = 0;
for(unsigned int i = 0; i < szs.size(); i++) {
ret += szs[i].len;
}
return ret;
}
/// Destruct an Ebwt
~Ebwt() {
// Only free buffers if we're *not* using memory-mapped files
if(!_useMm) {
// Delete everything that was allocated in read(false, ...)
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
if(_offs != NULL && !useShmem_) {
delete[] _offs; _offs = NULL;
} else if(_offs != NULL && useShmem_) {
FREE_SHARED(_offs);
}
if(_isa != NULL) delete[] _isa; _isa = NULL;
if(_plen != NULL) delete[] _plen; _plen = NULL;
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
if(_ebwt != NULL && !useShmem_) {
delete[] _ebwt; _ebwt = NULL;
} else if(_ebwt != NULL && useShmem_) {
FREE_SHARED(_ebwt);
}
}
if (_in1 != NULL) fclose(_in1);
if (_in2 != NULL) fclose(_in2);
#ifdef EBWT_STATS
cout << (_fw ? "Forward index:" : "Mirror index:") << endl;
cout << " mapLFEx: " << mapLFExs_ << endl;
cout << " mapLF: " << mapLFs_ << endl;
cout << " mapLF(c): " << mapLFcs_ << endl;
cout << " mapLF1(c): " << mapLF1cs_ << endl;
cout << " mapLF(c): " << mapLF1s_ << endl;
#endif
}
/// Accessors
const EbwtParams& eh() const { return _eh; }
TIndexOffU zOff() const { return _zOff; }
TIndexOffU zEbwtByteOff() const { return _zEbwtByteOff; }
TIndexOff zEbwtBpOff() const { return _zEbwtBpOff; }
TIndexOffU nPat() const { return _nPat; }
TIndexOffU nFrag() const { return _nFrag; }
TIndexOffU* fchr() const { return _fchr; }
TIndexOffU* ftab() const { return _ftab; }
TIndexOffU* eftab() const { return _eftab; }
TIndexOffU* offs() const { return _offs; }
uint32_t* isa() const { return _isa; } /* check */
TIndexOffU* plen() const { return _plen; }
TIndexOffU* rstarts() const { return _rstarts; }
uint8_t* ebwt() const { return _ebwt; }
const ReferenceMap* rmap() const { return rmap_; }
bool toBe() const { return _toBigEndian; }
bool verbose() const { return _verbose; }
bool sanityCheck() const { return _sanity; }
vector<string>& refnames() { return _refnames; }
bool fw() const { return _fw; }
#ifdef POPCNT_CAPABILITY
bool _usePOPCNTinstruction;
#endif
/// Return true iff the Ebwt is currently in memory
bool isInMemory() const {
if(_ebwt != NULL) {
assert(_eh.repOk());
assert(_ftab != NULL);
assert(_eftab != NULL);
assert(_fchr != NULL);
assert(_offs != NULL);
assert(_isa != NULL);
assert(_rstarts != NULL);
assert_neq(_zEbwtByteOff, OFF_MASK);
assert_neq(_zEbwtBpOff, -1);
return true;
} else {
assert(_ftab == NULL);
assert(_eftab == NULL);
assert(_fchr == NULL);
assert(_offs == NULL);
assert(_rstarts == NULL);
assert_eq(_zEbwtByteOff, OFF_MASK);
assert_eq(_zEbwtBpOff, -1);
return false;
}
}
/// Return true iff the Ebwt is currently stored on disk
bool isEvicted() const {
return !isInMemory();
}
/**
* Load this Ebwt into memory by reading it in from the _in1 and
* _in2 streams.
*/
void loadIntoMemory(
int color,
int needEntireReverse,
bool loadNames,
bool verbose)
{
readIntoMemory(
color, // expect index to be colorspace?
needEntireReverse, // require reverse index to be concatenated reference reversed
false, // stop after loading the header portion?
NULL, // params
false, // mmSweep
loadNames, // loadNames
verbose); // startVerbose
}
/**
* Frees memory associated with the Ebwt.
*/
void evictFromMemory() {
assert(isInMemory());
if(!_useMm) {
delete[] _fchr;
delete[] _ftab;
delete[] _eftab;
if(!useShmem_) delete[] _offs;
delete[] _isa;
// Keep plen; it's small and the client may want to query it
// even when the others are evicted.
//delete[] _plen;
delete[] _rstarts;
if(!useShmem_) delete[] _ebwt;
}
_fchr = NULL;
_ftab = NULL;
_eftab = NULL;
_offs = NULL;
_isa = NULL;
// Keep plen; it's small and the client may want to query it
// even when the others are evicted.
//_plen = NULL;
_rstarts = NULL;
_ebwt = NULL;
_zEbwtByteOff = OFF_MASK;
_zEbwtBpOff = -1;
}
/**
* Non-static facade for static function ftabHi.
*/
TIndexOffU ftabHi(TIndexOffU i) const {
return Ebwt::ftabHi(_ftab, _eftab, _eh._len, _eh._ftabLen,
_eh._eftabLen, i);
}
/**
* Get "high interpretation" of ftab entry at index i. The high
* interpretation of a regular ftab entry is just the entry
* itself. The high interpretation of an extended entry is the
* second correpsonding ui32 in the eftab.
*
* It's a static member because it's convenient to ask this
* question before the Ebwt is fully initialized.
*/
static TIndexOffU ftabHi(TIndexOffU *ftab,
TIndexOffU *eftab,
TIndexOffU len,
TIndexOffU ftabLen,
TIndexOffU eftabLen,
TIndexOffU i)
{
assert_lt(i, ftabLen);
if(ftab[i] <= len) {
return ftab[i];
} else {
TIndexOffU efIdx = ftab[i] ^ OFF_MASK;
assert_lt(efIdx*2+1, eftabLen);
return eftab[efIdx*2+1];
}
}
/**
* Non-static facade for static function ftabLo.
*/