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bt2_idx.h
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bt2_idx.h
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/*
* Copyright 2011, Ben Langmead <[email protected]>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef EBWT_H_
#define EBWT_H_
#include <stdint.h>
#include <string.h>
#include <iostream>
#include <fstream>
#include <sstream>
#include <memory>
#include <fcntl.h>
#include <math.h>
#include <errno.h>
#include <stdexcept>
#include <sys/stat.h>
#ifdef BOWTIE_MM
#include <sys/mman.h>
#include <sys/shm.h>
#endif
#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 "ref_read.h"
#include "threading.h"
#include "str_util.h"
#include "mm.h"
#include "timer.h"
#include "reference.h"
#include "search_globals.h"
#include "ds.h"
#include "random_source.h"
#include "mem_ids.h"
#include "btypes.h"
#ifdef POPCNT_CAPABILITY
#include "processor_support.h"
#endif
using namespace std;
// 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] = {
0xffffffffffffffff,
0xaaaaaaaaaaaaaaaa,
0x5555555555555555,
0x0000000000000000
};
#ifndef VMSG_NL
#define VMSG_NL(...) \
if(this->verbose()) { \
stringstream tmp; \
tmp << __VA_ARGS__ << endl; \
this->verbose(tmp.str()); \
}
#endif
#ifndef VMSG
#define VMSG(...) \
if(this->verbose()) { \
stringstream tmp; \
tmp << __VA_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
};
/**
* 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 offRate,
int32_t ftabChars,
bool color,
bool entireReverse)
{
init(len, lineRate, offRate, ftabChars, color, entireReverse);
}
EbwtParams(const EbwtParams& eh) {
init(eh._len, eh._lineRate, eh._offRate,
eh._ftabChars, eh._color, eh._entireReverse);
}
void init(
TIndexOffU len,
int32_t lineRate,
int32_t offRate,
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;
_origOffRate = offRate;
_offRate = offRate;
_offMask = OFF_MASK << _offRate;
_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;
_lineSz = 1 << _lineRate;
_sideSz = _lineSz * 1 /* lines per side */;
_sideBwtSz = _sideSz - OFF_SIZE*4;
_sideBwtLen = _sideBwtSz*4;
_numSides = (_bwtSz+(_sideBwtSz)-1)/(_sideBwtSz);
_numLines = _numSides * 1 /* lines per side */;
_ebwtTotLen = _numSides * _sideSz;
_ebwtTotSz = _ebwtTotLen;
assert(repOk());
}
TIndexOffU len() const { return _len; }
TIndexOffU lenNucs() const { return _len + (_color ? 1 : 0); }
TIndexOffU bwtLen() const { return _bwtLen; }
TIndexOffU sz() const { return _sz; }
TIndexOffU bwtSz() const { return _bwtSz; }
int32_t lineRate() const { return _lineRate; }
int32_t origOffRate() const { return _origOffRate; }
int32_t offRate() const { return _offRate; }
TIndexOffU offMask() const { return _offMask; }
int32_t ftabChars() const { return _ftabChars; }
int32_t eftabLen() const { return _eftabLen; }
int32_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; }
int32_t lineSz() const { return _lineSz; }
int32_t sideSz() const { return _sideSz; }
int32_t sideBwtSz() const { return _sideBwtSz; }
int32_t sideBwtLen() const { return _sideBwtLen; }
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;
}
#ifndef NDEBUG
/// 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(_ftabChars, 32);
assert_eq(0, _ebwtTotSz % _lineSz);
return true;
}
#endif
/**
* 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
<< " offRate: " << _offRate << endl
<< " offMask: 0x" << hex << _offMask << dec << endl
<< " ftabChars: " << _ftabChars << endl
<< " eftabLen: " << _eftabLen << endl
<< " eftabSz: " << _eftabSz << endl
<< " ftabLen: " << _ftabLen << endl
<< " ftabSz: " << _ftabSz << endl
<< " offsLen: " << _offsLen << endl
<< " offsSz: " << _offsSz << endl
<< " lineSz: " << _lineSz << endl
<< " sideSz: " << _sideSz << endl
<< " sideBwtSz: " << _sideBwtSz << endl
<< " sideBwtLen: " << _sideBwtLen << endl
<< " numSides: " << _numSides << endl
<< " numLines: " << _numLines << endl
<< " ebwtTotLen: " << _ebwtTotLen << endl
<< " ebwtTotSz: " << _ebwtTotSz << endl
<< " color: " << _color << endl
<< " reverse: " << _entireReverse << endl;
}
TIndexOffU _len;
TIndexOffU _bwtLen;
TIndexOffU _sz;
TIndexOffU _bwtSz;
int32_t _lineRate;
int32_t _origOffRate;
int32_t _offRate;
TIndexOffU _offMask;
int32_t _ftabChars;
uint32_t _eftabLen;
uint32_t _eftabSz;
TIndexOffU _ftabLen;
TIndexOffU _ftabSz;
TIndexOffU _offsLen;
uint64_t _offsSz;
uint32_t _lineSz;
uint32_t _sideSz;
uint32_t _sideBwtSz;
uint32_t _sideBwtLen;
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);
}
/**
* Encapsulates a location in the bwt text in terms of the side it
* occurs in and its offset within the side.
*/
struct SideLocus {
SideLocus() :
_sideByteOff(0),
_sideNum(0),
_charOff(0),
_by(-1),
_bp(-1) { }
/**
* Construct from row and other relevant information about the Ebwt.
*/
SideLocus(TIndexOffU row, const EbwtParams& ep, const uint8_t* ebwt) {
initFromRow(row, ep, ebwt);
}
/**
* Init two SideLocus objects from a top/bot pair, using the result
* from one call to initFromRow to possibly avoid a second call.
*/
static void initFromTopBot(
TIndexOffU top,
TIndexOffU bot,
const EbwtParams& ep,
const uint8_t* ebwt,
SideLocus& ltop,
SideLocus& lbot)
{
const TIndexOffU sideBwtLen = ep._sideBwtLen;
assert_gt(bot, top);
ltop.initFromRow(top, ep, ebwt);
TIndexOffU spread = bot - top;
// Many cache misses on the following lines
if(ltop._charOff + spread < sideBwtLen) {
lbot._charOff = (uint32_t)(ltop._charOff + spread);
lbot._sideNum = ltop._sideNum;
lbot._sideByteOff = ltop._sideByteOff;
lbot._by = lbot._charOff >> 2;
assert_lt(lbot._by, (int)ep._sideBwtSz);
lbot._bp = lbot._charOff & 3;
} else {
lbot.initFromRow(bot, ep, ebwt);
}
}
/**
* Calculate SideLocus based on a row and other relevant
* information about the shape of the Ebwt.
*/
void initFromRow(TIndexOffU row, const EbwtParams& ep, const uint8_t* ebwt) {
const int32_t sideSz = ep._sideSz;
// Side length is hard-coded for now; this allows the compiler
// to do clever things to accelerate / and %.
_sideNum = row / (48*OFF_SIZE);
assert_lt(_sideNum, ep._numSides);
_charOff = row % (48*OFF_SIZE);
_sideByteOff = _sideNum * sideSz;
assert_leq(row, ep._len);
assert_leq(_sideByteOff + sideSz, ep._ebwtTotSz);
// Tons of cache misses on the next line
_by = _charOff >> 2; // byte within side
assert_lt(_by, (int)ep._sideBwtSz);
_bp = _charOff & 3; // bit-pair within byte
}
/**
* Transform this SideLocus to refer to the next side (i.e. the one
* corresponding to the next side downstream). Set all cursors to
* point to the beginning of the side.
*/
void nextSide(const EbwtParams& ep) {
assert(valid());
_sideByteOff += ep.sideSz();
_sideNum++;
_by = _bp = _charOff = 0;
assert(valid());
}
/**
* Return true iff this is an initialized SideLocus
*/
bool valid() const {
if(_bp != -1) {
return true;
}
return false;
}
/**
* Convert locus to BW row it corresponds to.
*/
TIndexOffU toBWRow() const {
return _sideNum * 48*OFF_SIZE + _charOff;
}
#ifndef NDEBUG
/**
* Check that SideLocus is internally consistent and consistent
* with the (provided) EbwtParams.
*/
bool repOk(const EbwtParams& ep) const {
ASSERT_ONLY(TIndexOffU row = _sideNum * 48*OFF_SIZE + _charOff);
assert_leq(row, ep._len);
assert_range(-1, 3, _bp);
assert_range(0, (int)ep._sideBwtSz, _by);
return true;
}
#endif
/// Make this look like an invalid SideLocus
void invalidate() {
_bp = -1;
}
/**
* Return a read-only pointer to the beginning of the top side.
*/
const uint8_t *side(const uint8_t* ebwt) const {
return ebwt + _sideByteOff;
}
TIndexOffU _sideByteOff; // offset of top side within ebwt[]
TIndexOffU _sideNum; // index of side
uint32_t _charOff; // character offset within side
int32_t _by; // byte within side (not adjusted for bw sides)
int32_t _bp; // bitpair within byte (not adjusted for bw sides)
};
#ifdef POPCNT_CAPABILITY // wrapping of "struct"
struct USE_POPCNT_GENERIC {
#endif
// Use this standard bit-bashing population count
inline static int pop64(uint64_t x) {
// Lots of cache misses on following lines (>10K)
x = x - ((x >> 1) & 0x5555555555555555llu);
x = (x & 0x3333333333333333llu) + ((x >> 2) & 0x3333333333333333llu);
x = (x + (x >> 4)) & 0x0F0F0F0F0F0F0F0Fllu;
x = x + (x >> 8);
x = x + (x >> 16);
x = x + (x >> 32);
return (int)(x & 0x3Fllu);
}
#ifdef POPCNT_CAPABILITY // wrapping a "struct"
};
#endif
#ifdef POPCNT_CAPABILITY
struct USE_POPCNT_INSTRUCTION {
inline static int pop64(uint64_t x) {
int64_t count;
asm ("popcnt %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
return count;
}
};
#endif
/**
* Tricky-bit-bashing bitpair counting for given two-bit value (0-3)
* within a 64-bit argument.
*/
#ifdef POPCNT_CAPABILITY
template<typename Operation>
#endif
inline static int countInU64(int c, uint64_t dw) {
uint64_t c0 = c_table[c];
uint64_t x0 = dw ^ c0;
uint64_t x1 = (x0 >> 1);
uint64_t x2 = x1 & (0x5555555555555555);
uint64_t x3 = x0 & x2;
#ifdef POPCNT_CAPABILITY
uint64_t tmp = Operation().pop64(x3);
#else
uint64_t tmp = pop64(x3);
#endif
return (int) tmp;
}
// Forward declarations for Ebwt class
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().
*/
class Ebwt {
public:
#define Ebwt_INITS \
_toBigEndian(currentlyBigEndian()), \
_overrideOffRate(overrideOffRate), \
_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(EBWT_CAT), \
_rstarts(EBWT_CAT), \
_fchr(EBWT_CAT), \
_ftab(EBWT_CAT), \
_eftab(EBWT_CAT), \
_offs(EBWT_CAT), \
_ebwt(EBWT_CAT), \
_useMm(false), \
useShmem_(false), \
_refnames(EBWT_CAT), \
mmFile1_(NULL), \
mmFile2_(NULL)
/// Construct an Ebwt from the given input file
Ebwt(const string& in,
int color,
int needEntireReverse,
bool fw,
int32_t overrideOffRate, // = -1,
int32_t offRatePlus, // = -1,
bool useMm, // = false,
bool useShmem, // = false,
bool mmSweep, // = false,
bool loadNames, // = false,
bool loadSASamp, // = true,
bool loadFtab, // = true,
bool loadRstarts, // = true,
bool verbose, // = false,
bool startVerbose, // = false,
bool passMemExc, // = false,
bool sanityCheck) : // = false) :
Ebwt_INITS
{
assert(!useMm || !useShmem);
#ifdef POPCNT_CAPABILITY
ProcessorSupport ps;
_usePOPCNTinstruction = ps.POPCNTenabled();
#endif
packed_ = false;
_useMm = useMm;
useShmem_ = useShmem;
_in1Str = in + ".1." + gEbwt_ext;
_in2Str = in + ".2." + gEbwt_ext;
readIntoMemory(
color, // expect index to be colorspace?
fw ? -1 : needEntireReverse, // need REF_READ_REVERSE
loadSASamp, // load the SA sample portion?
loadFtab, // load the ftab & eftab?
loadRstarts, // load the rstarts array?
true, // stop after loading the header portion?
&_eh, // params
mmSweep, // mmSweep
loadNames, // loadNames
startVerbose); // startVerbose
// If the offRate has been overridden, reflect that in the
// _eh._offRate field
if(offRatePlus > 0 && _overrideOffRate == -1) {
_overrideOffRate = _eh._offRate + offRatePlus;
}
if(_overrideOffRate > _eh._offRate) {
_eh.setOffRate(_overrideOffRate);
assert_eq(_overrideOffRate, _eh._offRate);
}
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().
template<typename TStr>
Ebwt(
TStr exampleStr,
bool packed,
int color,
int needEntireReverse,
int32_t lineRate,
int32_t offRate,
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,
EList<FileBuf*>& is,
EList<RefRecord>& szs,
TIndexOffU sztot,
const RefReadInParams& refparams,
uint32_t seed,
int32_t overrideOffRate = -1,
bool doSaFile = false,
bool doBwtFile = false,
bool verbose = false,
bool passMemExc = false,
bool sanityCheck = false) :
Ebwt_INITS,
_eh(
joinedLen(szs),
lineRate,
offRate,
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;
packed_ = packed;
// Open output files
ofstream fout1(_in1Str.c_str(), ios::binary);
if(!fout1.good()) {
cerr << "Could not open index file for writing: \"" << _in1Str.c_str() << "\"" << 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.c_str() << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
}
_inSaStr = file + ".sa";
_inBwtStr = file + ".bwt";
ofstream *saOut = NULL, *bwtOut = NULL;
if(doSaFile) {
saOut = new ofstream(_inSaStr.c_str(), ios::binary);
if(!saOut->good()) {
cerr << "Could not open suffix-array file for writing: \"" << _inSaStr.c_str() << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
}
}
if(doBwtFile) {
bwtOut = new ofstream(_inBwtStr.c_str(), ios::binary);
if(!bwtOut->good()) {
cerr << "Could not open suffix-array file for writing: \"" << _inBwtStr.c_str() << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
}
}
// Build SA(T) and BWT(T) block by block
initFromVector<TStr>(
is,
szs,
sztot,
refparams,
fout1,
fout2,
file,
saOut,
bwtOut,
nthreads,
useBlockwise,
bmax,
bmaxSqrtMult,
bmaxDivN,
dcv,
seed,
verbose);
// Close output files
fout1.flush();
int64_t tellpSz1 = (int64_t)fout1.tellp();
VMSG_NL("Wrote " << fout1.tellp() << " bytes to primary EBWT file: " << _in1Str.c_str());
fout1.close();
bool err = false;
if(tellpSz1 > fileSize(_in1Str.c_str())) {
err = true;
cerr << "Index is corrupt: File size for " << _in1Str.c_str() << " 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.c_str());
fout2.close();
if(tellpSz2 > fileSize(_in2Str.c_str())) {
err = true;
cerr << "Index is corrupt: File size for " << _in2Str.c_str() << " should have been " << tellpSz2
<< " but is actually " << fileSize(_in2Str.c_str()) << "." << endl;
}
if(saOut != NULL) {
// Check on suffix array output file size
int64_t tellpSzSa = (int64_t)saOut->tellp();
VMSG_NL("Wrote " << tellpSzSa << " bytes to suffix-array file: " << _inSaStr.c_str());
saOut->close();
if(tellpSzSa > fileSize(_inSaStr.c_str())) {
err = true;
cerr << "Index is corrupt: File size for " << _inSaStr.c_str() << " should have been " << tellpSzSa
<< " but is actually " << fileSize(_inSaStr.c_str()) << "." << endl;
}
}
if(bwtOut != NULL) {
// Check on suffix array output file size
int64_t tellpSzBwt = (int64_t)bwtOut->tellp();
VMSG_NL("Wrote " << tellpSzBwt << " bytes to BWT file: " << _inBwtStr.c_str());
bwtOut->close();
if(tellpSzBwt > fileSize(_inBwtStr.c_str())) {
err = true;
cerr << "Index is corrupt: File size for " << _inBwtStr.c_str() << " should have been " << tellpSzBwt
<< " but is actually " << fileSize(_inBwtStr.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 Bt2");
assert(!isInMemory());
readIntoMemory(
color, // colorspace?
fw ? -1 : needEntireReverse, // 1 -> need the reverse to be reverse-of-concat
true, // load SA sample (_offs[])?
true, // load ftab (_ftab[] & _eftab[])?
true, // load r-starts (_rstarts[])?
false, // just load header?
NULL, // Params object to fill
false, // mm sweep?
true, // load names?
false); // verbose startup?
sanityCheckAll(refparams.reverse);
evictFromMemory();
assert(!isInMemory());
}
VMSG_NL("Returning from Ebwt constructor");
}
/**
* Static constructor for a pair of forward/reverse indexes for the
* given reference string.
*/
template<typename TStr>
static pair<Ebwt*, Ebwt*>
fromString(
const char* str,
bool packed,
int color,
int reverse,
bool bigEndian,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
const string& file,
bool useBlockwise,
TIndexOffU bmax,
TIndexOffU bmaxSqrtMult,
TIndexOffU bmaxDivN,
int dcv,
uint32_t seed,
bool verbose,
bool autoMem,
bool sanity)
{
EList<std::string> strs(EBWT_CAT);
strs.push_back(std::string(str));
return fromStrings<TStr>(
strs,
packed,
color,
reverse,
bigEndian,
lineRate,
offRate,
ftabChars,
file,
useBlockwise,
bmax,
bmaxSqrtMult,
bmaxDivN,
dcv,
seed,
verbose,
autoMem,
sanity);
}
/**
* Static constructor for a pair of forward/reverse indexes for the
* given list of reference strings.
*/
template<typename TStr>
static pair<Ebwt*, Ebwt*>
fromStrings(
const EList<std::string>& strs,
bool packed,
int color,
int reverse,
bool bigEndian,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
const string& file,
bool useBlockwise,
TIndexOffU bmax,
TIndexOffU bmaxSqrtMult,
TIndexOffU bmaxDivN,
int dcv,
uint32_t seed,
bool verbose,
bool autoMem,
bool sanity)
{
assert(!strs.empty());
EList<FileBuf*> is(EBWT_CAT);
RefReadInParams refparams(color, REF_READ_FORWARD, false, false);
// Adapt sequence strings to stringstreams open for input
auto_ptr<stringstream> ss(new stringstream());
for(TIndexOffU i = 0; i < strs.size(); i++) {
(*ss) << ">" << i << endl << strs[i] << endl;
}
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
assert(!fb->eof());
assert(fb->get() == '>');
ASSERT_ONLY(fb->reset());
assert(!fb->eof());
is.push_back(fb.get());
// Vector for the ordered list of "records" comprising the input
// sequences. A record represents a stretch of unambiguous
// characters in one of the input sequences.
EList<RefRecord> szs(EBWT_CAT);
std::pair<TIndexOffU, TIndexOffU> sztot;
sztot = BitPairReference::szsFromFasta(is, file, bigEndian, refparams, szs, sanity);
// Construct Ebwt from input strings and parameters
Ebwt *ebwtFw = new Ebwt(
TStr(),
packed,
refparams.color ? 1 : 0,
-1, // fw
lineRate,
offRate, // suffix-array sampling rate
ftabChars, // number of chars in initial arrow-pair calc
file, // basename for .?.ebwt files
true, // fw?
useBlockwise, // useBlockwise
bmax, // block size for blockwise SA builder
bmaxSqrtMult, // block size as multiplier of sqrt(len)
bmaxDivN, // block size as divisor of len
dcv, // difference-cover period
is, // list of input streams
szs, // list of reference sizes
sztot.first, // total size of all unambiguous ref chars
refparams, // reference read-in parameters
seed, // pseudo-random number generator seed
-1, // override offRate
verbose, // be talkative
autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically
sanity); // verify results and internal consistency
refparams.reverse = reverse;
szs.clear();
sztot = BitPairReference::szsFromFasta(is, file, bigEndian, refparams, szs, sanity);
// Construct Ebwt from input strings and parameters
Ebwt *ebwtBw = new Ebwt(
TStr(),
packed,
refparams.color ? 1 : 0,
reverse == REF_READ_REVERSE,
lineRate,
offRate, // suffix-array sampling rate
ftabChars, // number of chars in initial arrow-pair calc
file + ".rev",// basename for .?.ebwt files
false, // fw?
useBlockwise, // useBlockwise
bmax, // block size for blockwise SA builder
bmaxSqrtMult, // block size as multiplier of sqrt(len)
bmaxDivN, // block size as divisor of len
dcv, // difference-cover period
is, // list of input streams
szs, // list of reference sizes
sztot.first, // total size of all unambiguous ref chars
refparams, // reference read-in parameters
seed, // pseudo-random number generator seed
-1, // override offRate
verbose, // be talkative
autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically
sanity); // verify results and internal consistency
return make_pair(ebwtFw, ebwtBw);
}
/// Return true iff the Ebwt is packed
bool isPacked() { return packed_; }
/**
* Write the rstarts array given the szs array for the reference.
*/
void szsToDisk(const EList<RefRecord>& szs, ostream& os, int reverse);
/**
* 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.
*/
template <typename TStr>
void initFromVector(EList<FileBuf*>& is,
EList<RefRecord>& szs,
TIndexOffU sztot,
const RefReadInParams& refparams,
ofstream& out1,
ofstream& out2,
const string& outfile,
ofstream* saOut,
ofstream* bwtOut,
int nthreads,
bool useBlockwise,
TIndexOffU bmax,
TIndexOffU bmaxSqrtMult,
TIndexOffU bmaxDivN,
int dcv,
uint32_t seed,
bool verbose)
{
// 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");
s.resize(jlen);
VMSG_NL("Joining reference sequences");
if(refparams.reverse == REF_READ_REVERSE) {
{
Timer timer(cout, " Time to join reference sequences: ", _verbose);
joinToDisk(is, szs, sztot, refparams, s, out1, out2);
} {
Timer timer(cout, " Time to reverse reference sequence: ", _verbose);
EList<RefRecord> tmp(EBWT_CAT);
s.reverse();
reverseRefRecords(szs, tmp, false, verbose);
szsToDisk(tmp, out1, refparams.reverse);
}
} else {
Timer timer(cout, " Time to join reference sequences: ", _verbose);
joinToDisk(is, szs, sztot, refparams, s, out1, out2);
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(s.length(), jlen);
if(bmax != OFF_MASK) {
VMSG_NL("bmax according to bmax setting: " << bmax);
}
else if(bmaxSqrtMult != OFF_MASK) {
bmax *= bmaxSqrtMult;