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gfm.h
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gfm.h
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/*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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.
*
* HISAT 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 HISAT 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef GFM_H_
#define GFM_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 <set>
#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"
#include "tokenize.h"
#include "repeat.h"
#include "repeat_kmer.h"
#ifdef POPCNT_CAPABILITY
#include "processor_support.h"
#endif
#include "gbwt_graph.h"
using namespace std;
// From ccnt_lut.cpp, automatically generated by gen_lookup_tables.pl
extern uint8_t cCntLUT_4[4][4][256];
extern uint8_t cCntLUT_4_rev[4][4][256];
extern uint8_t cCntBIT[8][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 GFM_FLAGS {
GFM_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.
*/
template <typename index_t = uint32_t>
class GFMParams {
public:
GFMParams() { }
GFMParams(
index_t len,
index_t gbwtLen,
index_t numNodes,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
index_t eftabLen,
bool entireReverse)
{
init(len, gbwtLen, numNodes, lineRate, offRate, ftabChars, eftabLen, entireReverse);
}
GFMParams(const GFMParams& gh) {
init(gh._len, gh._gbwtLen, gh._numNodes, gh._lineRate, gh._offRate,
gh._ftabChars, gh._eftabLen, gh._entireReverse);
}
void init(
index_t len,
index_t gbwtLen,
index_t numNodes,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
index_t eftabLen,
bool entireReverse)
{
_entireReverse = entireReverse;
_linearFM = (len + 1 == gbwtLen || gbwtLen == 0);
_len = len;
_gbwtLen = (gbwtLen == 0 ? len + 1 : gbwtLen);
_numNodes = (numNodes == 0 ? len + 1 : numNodes);
if(_linearFM) {
_sz = (len+3)/4;
_gbwtSz = _gbwtLen/4 + 1;
} else {
_sz = (len+1)/2;
_gbwtSz = _gbwtLen/2 + 1;
}
_lineRate = lineRate;
_origOffRate = offRate;
_offRate = offRate;
_offMask = std::numeric_limits<index_t>::max() << _offRate;
_ftabChars = ftabChars;
_eftabLen = eftabLen;
_eftabSz = _eftabLen*sizeof(index_t);
_ftabLen = (1 << (_ftabChars*2))+1;
_ftabSz = _ftabLen*sizeof(index_t);
_offsLen = (_numNodes + (1 << _offRate) - 1) >> _offRate;
_offsSz = _offsLen*sizeof(index_t);
_lineSz = 1 << _lineRate;
_sideSz = _lineSz * 1 /* lines per side */;
if(_linearFM) {
_sideGbwtSz = _sideSz - (sizeof(index_t) * 4);
_sideGbwtLen = _sideGbwtSz << 2;
} else {
_sideGbwtSz = _sideSz - (sizeof(index_t) * 6);
_sideGbwtLen = _sideGbwtSz << 1;
}
_numSides = (_gbwtSz+(_sideGbwtSz)-1)/(_sideGbwtSz);
_numLines = _numSides * 1 /* lines per side */;
_gbwtTotLen = _numSides * _sideSz;
_gbwtTotSz = _gbwtTotLen;
assert(repOk());
}
index_t len() const { return _len; }
index_t lenNucs() const { return _len; }
index_t gbwtLen() const { return _gbwtLen; }
index_t sz() const { return _sz; }
index_t gbwtSz() const { return _gbwtSz; }
int32_t lineRate() const { return _lineRate; }
int32_t origOffRate() const { return _origOffRate; }
int32_t offRate() const { return _offRate; }
index_t offMask() const { return _offMask; }
int32_t ftabChars() const { return _ftabChars; }
index_t eftabLen() const { return _eftabLen; }
index_t eftabSz() const { return _eftabSz; }
index_t ftabLen() const { return _ftabLen; }
index_t ftabSz() const { return _ftabSz; }
index_t offsLen() const { return _offsLen; }
index_t offsSz() const { return _offsSz; }
index_t lineSz() const { return _lineSz; }
index_t sideSz() const { return _sideSz; }
index_t sideGbtSz() const { return _sideGbwtSz; }
index_t sideGbwtLen() const { return _sideGbwtLen; }
index_t numSides() const { return _numSides; }
index_t numLines() const { return _numLines; }
index_t gbwtTotLen() const { return _gbwtTotLen; }
index_t gbwtTotSz() const { return _gbwtTotSz; }
bool entireReverse() const { return _entireReverse; }
bool linearFM() const { return _linearFM; }
index_t numNodes() const { return _numNodes; }
/**
* Set a new suffix-array sampling rate, which involves updating
* rate, mask, sample length, and sample size.
*/
void setOffRate(int __offRate) {
_offRate = __offRate;
_offMask = std::numeric_limits<index_t>::max() << _offRate;
_offsLen = (_gbwtLen + (1 << _offRate) - 1) >> _offRate;
_offsSz = _offsLen * sizeof(index_t);
}
#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, _gbwtTotSz % _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
<< " gbwtLen: " << _gbwtLen << endl
<< " nodes: " << _numNodes << endl
<< " sz: " << _sz << endl
<< " gbwtSz: " << _gbwtSz << 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
<< " sideGbwtSz: " << _sideGbwtSz << endl
<< " sideGbwtLen: " << _sideGbwtLen << endl
<< " numSides: " << _numSides << endl
<< " numLines: " << _numLines << endl
<< " gbwtTotLen: " << _gbwtTotLen << endl
<< " gbwtTotSz: " << _gbwtTotSz << endl
<< " reverse: " << _entireReverse << endl
<< " linearFM: " << (_linearFM ? "Yes" : "No") << endl;
}
index_t _len;
index_t _gbwtLen;
index_t _sz;
index_t _gbwtSz;
int32_t _lineRate;
int32_t _origOffRate;
int32_t _offRate;
index_t _offMask;
int32_t _ftabChars;
index_t _eftabLen;
index_t _eftabSz;
index_t _ftabLen;
index_t _ftabSz;
index_t _offsLen;
index_t _offsSz;
index_t _lineSz;
index_t _sideSz;
index_t _sideGbwtSz;
index_t _sideGbwtLen;
index_t _numSides;
index_t _numLines;
index_t _gbwtTotLen;
index_t _gbwtTotSz;
bool _entireReverse;
bool _linearFM;
index_t _numNodes;
};
/**
* Exception to throw when a file-realted error occurs.
*/
class GFMFileOpenException : public std::runtime_error {
public:
GFMFileOpenException(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 gbwt text in terms of the side it
* occurs in and its offset within the side.
*/
template <typename index_t = uint32_t>
struct SideLocus {
SideLocus() :
_sideByteOff(0),
_sideNum(0),
_charOff(0),
_by(-1),
_bp(-1) { }
/**
* Construct from row and other relevant information about the Ebwt.
*/
SideLocus(index_t row, const GFMParams<index_t>& 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(
index_t top,
index_t bot,
const GFMParams<index_t>& gp,
const uint8_t* gfm,
SideLocus& ltop,
SideLocus& lbot)
{
const index_t sideGbwtLen = gp._sideGbwtLen;
assert_gt(bot, top);
ltop.initFromRow(top, gp, gfm);
index_t spread = bot - top;
// Many cache misses on the following lines
if(ltop._charOff + spread < sideGbwtLen) {
lbot._charOff = ltop._charOff + spread;
lbot._sideNum = ltop._sideNum;
lbot._sideByteOff = ltop._sideByteOff;
lbot._by = lbot._charOff >> 2;
assert_lt(lbot._by, (int)gp._sideGbwtSz);
lbot._bp = lbot._charOff & 0x3;
} else {
lbot.initFromRow(bot, gp, gfm);
}
}
/**
* Calculate SideLocus based on a row and other relevant
* information about the shape of the Ebwt.
*/
void initFromRow(
index_t row,
const GFMParams<index_t>& gp,
const uint8_t* gfm) {
const index_t sideSz = gp._sideSz;
// Side length is hard-coded for now; this allows the compiler
// to do clever things to accelerate / and %.
_sideNum = row / gp._sideGbwtLen;
assert_lt(_sideNum, gp._numSides);
_charOff = row % gp._sideGbwtLen;
_sideByteOff = _sideNum * sideSz;
assert_leq(row, gp._gbwtLen);
assert_leq(_sideByteOff + sideSz, gp._gbwtTotSz);
// Tons of cache misses on the next line
_by = _charOff >> 2; // byte within side
assert_lt(_by, (int)gp._sideGbwtSz);
_bp = _charOff & 0x3; // bit-pair within byte
}
/**
* 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_bit(
index_t top,
index_t bot,
const GFMParams<index_t>& gp,
const uint8_t* gfm,
SideLocus& ltop,
SideLocus& lbot)
{
const index_t sideGbwtLen = gp._sideGbwtLen;
// assert_gt(bot, top);
ltop.initFromRow_bit(top, gp, gfm);
index_t spread = bot - top;
// Many cache misses on the following lines
if(ltop._charOff + spread < sideGbwtLen) {
lbot._charOff = ltop._charOff + spread;
lbot._sideNum = ltop._sideNum;
lbot._sideByteOff = ltop._sideByteOff;
lbot._by = lbot._charOff >> 3;
assert_lt(lbot._by, (int)gp._sideGbwtSz);
lbot._bp = lbot._charOff & 0x7;
} else {
lbot.initFromRow_bit(bot, gp, gfm);
}
}
/**
* Calculate SideLocus based on a row and other relevant
* information about the shape of the Ebwt.
*/
void initFromRow_bit(
index_t row,
const GFMParams<index_t>& gp,
const uint8_t* gfm) {
const index_t sideSz = gp._sideSz;
// Side length is hard-coded for now; this allows the compiler
// to do clever things to accelerate / and %.
_sideNum = row / gp._sideGbwtLen;
assert_lt(_sideNum, gp._numSides);
_charOff = row % gp._sideGbwtLen;
_sideByteOff = _sideNum * sideSz;
assert_lt(row, gp._gbwtLen);
assert_leq(_sideByteOff + sideSz, gp._gbwtTotSz);
// Tons of cache misses on the next line
_by = _charOff >> 3; // byte within side
assert_lt(_by, (int)gp._sideGbwtSz);
_bp = _charOff & 0x7; // 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 GFMParams<index_t>& gp) {
assert(valid());
_sideByteOff += gp.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.
*/
index_t toBWRow(const GFMParams<index_t>& gp) const;
#ifndef NDEBUG
/**
* Check that SideLocus is internally consistent and consistent
* with the (provided) EbwtParams.
*/
bool repOk(const GFMParams<index_t>& gp) const {
ASSERT_ONLY(index_t row = toBWRow(gp));
assert_leq(row, gp._gbwtLen);
assert_range(-1, 3, _bp);
assert_range(0, (int)gp._sideGbwtSz, _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* gbwt) const {
return gbwt + _sideByteOff;
}
/**
* Return a read-only pointer to the beginning of the top side.
*/
const uint8_t *next_side(const GFMParams<index_t>& gp, const uint8_t* gbwt) const {
if(_sideByteOff + gp._sideSz < gp._ebwtTotSz) {
return gbwt + _sideByteOff + gp._sideSz;
} else {
return NULL;
}
}
index_t _sideByteOff; // offset of top side within ebwt[]
index_t _sideNum; // index of side
index_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)
};
/**
* Convert locus to BW row it corresponds to.
*/
template <typename index_t>
inline index_t SideLocus<index_t>::toBWRow(const GFMParams<index_t>& gp) const {
return _sideNum * (gp._sideGbwtSz << (gp.linearFM() ? 2 : 1)) + _charOff;
}
#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;
#ifdef USING_MSC_COMPILER
count = __popcnt64(x);
#else
asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
#endif
return (int)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;
}
#ifdef POPCNT_CAPABILITY // wrapping of "struct"
struct USE_POPCNT_GENERIC_BITS {
// Use this standard bit-bashing population count
inline static uint64_t pop64(uint64_t x) {
#else
// Use this standard bit-bashing population count
inline static uint64_t pop6464(uint64_t x) {
#endif
x -= (x >> 1) & 0x5555555555555555ULL;
x = (x & 0x3333333333333333ULL) + ((x >> 2) & 0x3333333333333333ULL);
x = (x + (x >> 4)) & 0x0f0f0f0f0f0f0f0fULL;
return int((x * 0x0101010101010101ULL) >> 56);
}
#ifdef POPCNT_CAPABILITY // wrapping a "struct"
};
#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_bits(uint64_t dw) {
#ifdef POPCNT_CAPABILITY
uint64_t tmp = Operation().pop64(dw);
#else
uint64_t tmp = pop6464(dw);
#endif
return (int) tmp;
}
// Forward declarations for Ebwt class
class GFMSearchParams;
/**
* 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 <class index_t = uint32_t>
class GFM {
public:
#define GFM_INITS \
_toBigEndian(currentlyBigEndian()), \
_overrideOffRate(overrideOffRate), \
_verbose(verbose), \
_passMemExc(passMemExc), \
_sanity(sanityCheck), \
fw_(fw), \
_in1(NULL), \
_in2(NULL), \
_nPat(0), \
_nFrag(0), \
_plen(EBWT_CAT), \
_rstarts(EBWT_CAT), \
_fchr(EBWT_CAT), \
_ftab(EBWT_CAT), \
_eftab(EBWT_CAT), \
_offs(EBWT_CAT), \
_gfm(EBWT_CAT), \
_useMm(false), \
useShmem_(false), \
_refnames(EBWT_CAT), \
mmFile1_(NULL), \
mmFile2_(NULL), \
_nthreads(1)
/// Construct a GFM from the given input file
GFM(const string& in,
ALTDB<index_t>* altdb,
RepeatDB<index_t>* repeatdb,
EList<size_t>* readLens,
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 loadSpliceSites, // = true,
bool verbose, // = false,
bool startVerbose, // = false,
bool passMemExc, // = false,
bool sanityCheck, // = false)
bool useHaplotype, // = false
bool skipLoading = false) :
GFM_INITS
{
assert(!useMm || !useShmem);
#ifdef POPCNT_CAPABILITY
ProcessorSupport ps;
_usePOPCNTinstruction = ps.POPCNTenabled();
#endif
packed_ = false;
_useMm = useMm;
useShmem_ = useShmem;
_in1Str = in + ".1." + gfm_ext;
_in2Str = in + ".2." + gfm_ext;
if(skipLoading) return;
if(repeatdb == NULL) {
readIntoMemory(
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?
&_gh, // 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 = _gh._offRate + offRatePlus;
}
if(_overrideOffRate > _gh._offRate) {
_gh.setOffRate(_overrideOffRate);
assert_eq(_overrideOffRate, _gh._offRate);
}
}
// Read ALTs
EList<ALT<index_t> >& alts = altdb->alts();
EList<Haplotype<index_t> >& haplotypes = altdb->haplotypes();
EList<string>& altnames = altdb->altnames();
alts.clear(); altnames.clear();
string in7Str = in + ".7." + gfm_ext;
string in8Str = in + ".8." + gfm_ext;
// open alts
if(verbose || startVerbose) cerr << "Opening \"" << in7Str.c_str() << "\"" << endl;
ifstream in7(in7Str.c_str(), ios::binary);
if(!in7.good()) {
cerr << "Could not open index file " << in7Str.c_str() << endl;
}
EList<index_t> to_alti;
index_t to_alti_far = 0;
readI32(in7, this->toBe());
index_t numAlts = readIndex<index_t>(in7, this->toBe());
// open altnames
if(verbose || startVerbose) cerr << "Opening \"" << in8Str.c_str() << "\"" << endl;
ifstream in8(in8Str.c_str(), ios::binary);
if(!in8.good()) {
cerr << "Could not open index file " << in8Str.c_str() << endl;
}
readI32(in8, this->toBe());
index_t numAltnames = readIndex<index_t>(in8, this->toBe());
assert_eq(numAlts, numAltnames);
if(numAlts > 0) {
alts.resizeExact(numAlts); alts.clear();
to_alti.resizeExact(numAlts); to_alti.clear();
while(!in7.eof() && !in8.eof()) {
alts.expand();
alts.back().read(in7, this->toBe());
to_alti.push_back(to_alti_far);
to_alti_far++;
altnames.expand();
in8 >> altnames.back();
if(!loadSpliceSites) {
if(alts.back().splicesite()) {
alts.pop_back();
assert_gt(numAlts, 0);
altnames.pop_back();
assert_gt(numAltnames, 0);
numAlts--;
numAltnames--;
to_alti.back() = std::numeric_limits<index_t>::max();
to_alti_far--;
}
}
if(alts.size() == numAlts) break;
}
}
assert_eq(alts.size(), numAlts);
assert_eq(to_alti_far, numAlts);
assert_eq(alts.size(), altnames.size());
// Check if it hits the end of file, and this routine is needed for backward compatibility
if(in7.peek() != std::ifstream::traits_type::eof()) {
index_t numHaplotypes = readIndex<index_t>(in7, this->toBe());
if(numHaplotypes > 0) {
haplotypes.resizeExact(numHaplotypes);
haplotypes.clear();
while(!in7.eof()) {
haplotypes.expand();
haplotypes.back().read(in7, this->toBe());
Haplotype<index_t>& ht = haplotypes.back();
for(index_t h = 0; h < ht.alts.size(); h++) {
ht.alts[h] = to_alti[ht.alts[h]];
}
if(haplotypes.size() == numHaplotypes) break;
}
}
if(!useHaplotype) {
haplotypes.nullify();
}
}
// Read repeats
_repeat = false;
if(repeatdb != NULL) {
_repeat = true;
// Number of repeat groups in the index
index_t numRepeatIndex = readIndex<index_t>(in7, this->toBe());
assert_gt(numRepeatIndex, 0);
EList<pair<index_t, index_t> > repeatLens; repeatLens.resizeExact(numRepeatIndex);
for(size_t k = 0; k < numRepeatIndex; k++) {
repeatLens[k].first = readIndex<index_t>(in7, this->toBe());
repeatLens[k].second = readIndex<index_t>(in7, this->toBe());
}
if (readLens != NULL && !readLens->empty()) {
// Load subset of repeat groups.
size_t k = 0;
size_t k2 = 0;
_repeatIncluded.resizeExact(numRepeatIndex);
_repeatIncluded.fillZero();
while(k < numRepeatIndex && k2 < readLens->size()) {
if (repeatLens[k].first >= (*readLens)[k2]) {
_repeatIncluded[k] = true;
k2++;
} else {
k++;
}
}
// at least last repeat group is included
_repeatIncluded[numRepeatIndex - 1] = true;
_repeatLens.clear();
for(size_t i = 0; i < numRepeatIndex; i++) {
if (_repeatIncluded[i]) {
_repeatLens.push_back(repeatLens[i]);
}
}
} else {
// Load all repeat groups
_repeatLens = repeatLens;
_repeatIncluded.resizeExact(numRepeatIndex);
_repeatIncluded.fill(true);
}
repeatdb->read(in7, this->toBe(), _repeatIncluded);
index_t numKmertables = readIndex<index_t>(in7, this->toBe());
EList<streampos> filePos; filePos.resizeExact(numKmertables);
for(size_t k = 0; k < numKmertables; k++) {
filePos[k] = readIndex<uint64_t>(in7, this->toBe());
}
for(size_t k = 0; k < numKmertables; k++) {
if(!_repeatIncluded[k])
continue;
if(k > 0) {
in7.seekg(filePos[k-1]);
}
_repeat_kmertables.expand();
_repeat_kmertables.back().read(in7, this->toBe());
}
in7.seekg(filePos.back());
}
in7.close();
in8.close();
// Sort SNPs and Splice Sites based on positions
index_t nalts = (index_t)alts.size();
for(index_t s = 0; s < nalts; s++) {
ALT<index_t> alt = alts[s];
if(alt.snp()) altdb->setSNPs(true);
if(alt.exon()) altdb->setExons(true);
if(alt.splicesite()) {
altdb->setSpliceSites(true);
alts.push_back(alt);
alts.back().left = alt.right;
alts.back().right = alt.left;
altnames.push_back("ssr");
} else if(alt.deletion()) {
alts.push_back(alt);
alts.back().pos = alt.pos + alt.len - 1;
alts.back().reversed = true;
string altname = altnames[s];
altnames.push_back(altname);
}
}
if(alts.size() > 1 && alts.size() > nalts) {
assert_eq(alts.size(), altnames.size());
EList<pair<ALT<index_t>, index_t> > buf; buf.resize(alts.size());
EList<string> buf2; buf2.resize(alts.size());
for(size_t i = 0; i < alts.size(); i++) {
buf[i].first = alts[i];
buf[i].second = (index_t)i;
buf2[i] = altnames[i];
}
buf.sort();
for(size_t i = 0; i < alts.size(); i++) {
alts[i] = buf[i].first;
altnames[i] = buf2[buf[i].second];
if(buf[i].second < numAlts) {
to_alti[buf[i].second] = i;
}
}
}
if(useHaplotype) {
EList<index_t>& haplotype_maxrights = altdb->haplotype_maxrights();
haplotype_maxrights.resizeExact(haplotypes.size());
for(index_t h = 0; h < haplotypes.size(); h++) {
Haplotype<index_t>& ht = haplotypes[h];
for(index_t h2 = 0; h2 < ht.alts.size(); h2++) {
ht.alts[h2] = to_alti[ht.alts[h2]];
}
if(h == 0) {
haplotype_maxrights[h] = ht.right;
} else {
haplotype_maxrights[h] = std::max<index_t>(haplotype_maxrights[h - 1], ht.right);
}
}
}
assert(repeatdb != NULL || 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().
GFM(
bool packed,
int needEntireReverse,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
const string& file, // base filename for GFM files
bool fw,
int dcv,
EList<RefRecord>& szs,
index_t sztot,
const RefReadInParams& refparams,
uint32_t seed,
int32_t overrideOffRate = -1,
bool verbose = false,
bool passMemExc = false,
bool sanityCheck = false) :
GFM_INITS,
_gh(
joinedLen(szs),
0,
0,
lineRate,
offRate,
ftabChars,
0,
refparams.reverse == REF_READ_REVERSE)
{
#ifdef POPCNT_CAPABILITY
ProcessorSupport ps;
_usePOPCNTinstruction = ps.POPCNTenabled();
#endif
packed_ = packed;
}
/// 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>
GFM(
TStr& s,
bool packed,
int needEntireReverse,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
int nthreads,
const string& snpfile,
const string& htfile,
const string& ssfile,
const string& exonfile,
const string& svfile,
const string& repeatfile,
const string& outfile, // base filename for GFM files
bool fw,
bool useBlockwise,
index_t bmax,
index_t bmaxSqrtMult,
index_t bmaxDivN,
int dcv,
EList<FileBuf*>& is,
EList<RefRecord>& szs,
index_t sztot,
const RefReadInParams& refparams,
EList<RefRecord>* parent_szs,
EList<string>* parent_refnames,
uint32_t seed,
int32_t overrideOffRate = -1,
bool verbose = false,
bool passMemExc = false,