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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>
#include <map>
#include <set>
#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 "taxonomy.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];
extern uint8_t cCntLUT_4_rev[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.
*/
template <typename index_t = uint32_t>
class EbwtParams {
public:
EbwtParams() { }
EbwtParams(
index_t 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(
index_t 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 = std::numeric_limits<index_t>::max() << _offRate;
_ftabChars = ftabChars;
_eftabLen = _ftabChars*2;
_eftabSz = _eftabLen*sizeof(index_t);
_ftabLen = (1 << (_ftabChars*2))+1;
_ftabSz = _ftabLen*sizeof(index_t);
_offsLen = (_bwtLen + (1 << _offRate) - 1) >> _offRate;
_offsSz = _offsLen*sizeof(index_t);
_lineSz = 1 << _lineRate;
_sideSz = _lineSz * 1 /* lines per side */;
_sideBwtSz = _sideSz - (sizeof(index_t) * 4);
_sideBwtLen = _sideBwtSz*4;
_numSides = (_bwtSz+(_sideBwtSz)-1)/(_sideBwtSz);
_numLines = _numSides * 1 /* lines per side */;
_ebwtTotLen = _numSides * _sideSz;
_ebwtTotSz = _ebwtTotLen;
assert(repOk());
}
index_t len() const { return _len; }
index_t lenNucs() const { return _len + (_color ? 1 : 0); }
index_t bwtLen() const { return _bwtLen; }
index_t sz() const { return _sz; }
index_t bwtSz() const { return _bwtSz; }
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 sideBwtSz() const { return _sideBwtSz; }
index_t sideBwtLen() const { return _sideBwtLen; }
index_t numSides() const { return _numSides; }
index_t numLines() const { return _numLines; }
index_t ebwtTotLen() const { return _ebwtTotLen; }
index_t 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 = std::numeric_limits<index_t>::max() << _offRate;
_offsLen = (_bwtLen + (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, _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;
}
index_t _len;
index_t _bwtLen;
index_t _sz;
index_t _bwtSz;
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 _sideBwtSz;
index_t _sideBwtLen;
index_t _numSides;
index_t _numLines;
index_t _ebwtTotLen;
index_t _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.
*/
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 EbwtParams<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 EbwtParams<index_t>& ep,
const uint8_t* ebwt,
SideLocus& ltop,
SideLocus& lbot)
{
const index_t sideBwtLen = ep._sideBwtLen;
assert_gt(bot, top);
ltop.initFromRow(top, ep, ebwt);
index_t spread = bot - top;
// Many cache misses on the following lines
if(ltop._charOff + spread < sideBwtLen) {
lbot._charOff = ltop._charOff + spread;
lbot._sideNum = ltop._sideNum;
lbot._sideByteOff = ltop._sideByteOff;
lbot._by = (int)(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(index_t row, const EbwtParams<index_t>& ep, const uint8_t* ebwt) {
const index_t sideSz = ep._sideSz;
// Side length is hard-coded for now; this allows the compiler
// to do clever things to accelerate / and %.
_sideNum = row / ep._sideBwtLen;
assert_lt(_sideNum, ep._numSides);
_charOff = row % ep._sideBwtLen;
_sideByteOff = _sideNum * sideSz;
assert_leq(row, ep._len);
assert_leq(_sideByteOff + sideSz, ep._ebwtTotSz);
// Tons of cache misses on the next line
_by = (int)(_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<index_t>& 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.
*/
index_t toBWRow() const;
#ifndef NDEBUG
/**
* Check that SideLocus is internally consistent and consistent
* with the (provided) EbwtParams.
*/
bool repOk(const EbwtParams<index_t>& ep) const {
ASSERT_ONLY(index_t row = toBWRow());
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;
}
/**
* Return a read-only pointer to the beginning of the top side.
*/
const uint8_t *next_side(const EbwtParams<index_t>& ep, const uint8_t* ebwt) const {
if(_sideByteOff + ep._sideSz < ep._ebwtTotSz) {
return ebwt + _sideByteOff + ep._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 {
if(sizeof(index_t) == 8) {
return _sideNum * (512 - 16 * sizeof(index_t)) + _charOff;
} else {
return _sideNum * (256 - 16 * sizeof(index_t)) + _charOff;
}
}
template <>
inline uint64_t SideLocus<uint64_t>::toBWRow() const {
return _sideNum * (512 - 16 * sizeof(uint64_t)) + _charOff;
}
template <>
inline uint32_t SideLocus<uint32_t>::toBWRow() const {
return _sideNum * (256 - 16 * sizeof(uint32_t)) + _charOff;
}
template <>
inline uint16_t SideLocus<uint16_t>::toBWRow() const {
return _sideNum * (256 - 16 * sizeof(uint16_t)) + _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;
asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
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;
}
// 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().
*/
template <class index_t = uint32_t>
class Ebwt {
public:
#define Ebwt_INITS \
_toBigEndian(currentlyBigEndian()), \
_overrideOffRate(overrideOffRate), \
_verbose(verbose), \
_passMemExc(passMemExc), \
_sanity(sanityCheck), \
fw_(fw), \
_in1(NULL), \
_in2(NULL), \
_zOff(std::numeric_limits<index_t>::max()), \
_zEbwtByteOff(std::numeric_limits<index_t>::max()), \
_zEbwtBpOff(-1), \
_nPat(0), \
_nFrag(0), \
_plen(EBWT_CAT), \
_rstarts(EBWT_CAT), \
_fchr(EBWT_CAT), \
_ftab(EBWT_CAT), \
_eftab(EBWT_CAT), \
_offw(false), \
_offs(EBWT_CAT), \
_offsw(EBWT_CAT), \
_ebwt(EBWT_CAT), \
_useMm(false), \
useShmem_(false), \
_refnames(EBWT_CAT), \
mmFile1_(NULL), \
mmFile2_(NULL), \
_compressed(false), \
_boundaryCheck( 1 )
/// 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)
bool skipLoading = 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;
if(!skipLoading) {
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());
}
// Read conversion table, genome size table, and taxonomy tree
string in3Str = in + ".3." + gEbwt_ext;
if(verbose || startVerbose) cerr << "Opening \"" << in3Str.c_str() << "\"" << endl;
ifstream in3(in3Str.c_str(), ios::binary);
if(!in3.good()) {
cerr << "Could not open index file " << in3Str.c_str() << endl;
}
initial_tax_rank_num();
set<uint64_t> leaves;
size_t num_cids = 0; // number of compressed sequences
_uid_to_tid.clear();
readU32(in3, this->toBe());
uint64_t nref = readIndex<uint64_t>(in3, this->toBe());
if(nref > 0) {
while(!in3.eof()) {
string uid;
uint64_t tid;
while(true) {
char c = '\0';
in3 >> c;
if(c == '\0' || c == '\n') break;
uid.push_back(c);
}
if(uid.find("cid") == 0) {
num_cids++;
}
tid = readIndex<uint64_t>(in3, this->toBe());
_uid_to_tid.expand();
_uid_to_tid.back().first = uid;
_uid_to_tid.back().second = tid;
leaves.insert(tid);
if(nref == _uid_to_tid.size()) break;
}
assert_eq(nref, _uid_to_tid.size());
}
if(num_cids >= 10) {
this->_compressed = true;
}
_tree.clear();
uint64_t ntid = readIndex<uint64_t>(in3, this->toBe());
if(ntid > 0) {
while(!in3.eof()) {
TaxonomyNode node;
uint64_t tid = readIndex<uint64_t>(in3, this->toBe());
node.parent_tid = readIndex<uint64_t>(in3, this->toBe());
node.rank = readIndex<uint16_t>(in3, this->toBe());
node.leaf = (leaves.find(tid) != leaves.end());
_tree[tid] = node;
if(ntid == _tree.size()) break;
}
assert_eq(ntid, _tree.size());
}
_name.clear();
uint64_t nname = readIndex<uint64_t>(in3, this->toBe());
if(nname > 0) {
string name;
while(!in3.eof()) {
uint64_t tid = readIndex<uint64_t>(in3, this->toBe());
in3 >> name;
in3.seekg(1, ios_base::cur);
assert(_name.find(tid) == _name.end());
std::replace(name.begin(), name.end(), '@', ' ');
_name[tid] = name;
if(_name.size() == nname)
break;
}
}
_size.clear();
uint64_t nsize = readIndex<uint64_t>(in3, this->toBe());
if(nsize > 0) {
while(!in3.eof()) {
uint64_t tid = readIndex<uint64_t>(in3, this->toBe());
uint64_t size = readIndex<uint64_t>(in3, this->toBe());
assert(_size.find(tid) == _size.end());
_size[tid] = size;
if(_size.size() == nsize)
break;
}
}
// Calculate average genome size
if(1) { //!this->_offw) { // Skip if there are many sequences (e.g. >64K).
// Now always compute the genome length.
map<uint64_t, uint64_t> tid_count;
map<uint64_t, uint64_t> new_size ;
for (map<uint64_t, uint64_t>::const_iterator size_itr = _size.begin() ; size_itr != _size.end() ; ++size_itr) {
uint64_t c_tid = size_itr->first ;
if (_tree.find(c_tid) == _tree.end() || _tree[c_tid].parent_tid == c_tid) {
continue ;
}
uint64_t add_size = size_itr->second ;
const TaxonomyNode& size_node = _tree[c_tid];
if (!((size_node.rank == RANK_UNKNOWN && size_node.leaf)
|| tax_rank_num[size_node.rank] < tax_rank_num[RANK_SPECIES])
|| size_node.parent_tid == c_tid)
continue ;
c_tid = _tree[c_tid].parent_tid ;
while (true) {
map<uint64_t, TaxonomyNode>::const_iterator tree_itr = _tree.find(c_tid) ;
if(tree_itr == _tree.end())
break;
const TaxonomyNode& node = tree_itr->second;
if(node.rank == RANK_SPECIES || node.rank == RANK_GENUS || node.rank == RANK_FAMILY ||
node.rank == RANK_ORDER || node.rank == RANK_CLASS || node.rank == RANK_PHYLUM) {
new_size[c_tid] += add_size ;
++tid_count[c_tid] ;
}
if(c_tid == tree_itr->second.parent_tid)
break;
c_tid = tree_itr->second.parent_tid;
}
}
for (map<uint64_t, uint64_t>::const_iterator count_itr = tid_count.begin() ; count_itr != tid_count.end() ; ++count_itr) {
_size[count_itr->first] = new_size[count_itr->first] / count_itr->second ;
}
/*for(map<uint64_t, TaxonomyNode>::const_iterator tree_itr = _tree.begin(); tree_itr != _tree.end(); tree_itr++) {
uint64_t tid = tree_itr->first;
const TaxonomyNode& node = tree_itr->second;
if(node.rank == RANK_SPECIES || node.rank == RANK_GENUS || node.rank == RANK_FAMILY ||
node.rank == RANK_ORDER || node.rank == RANK_CLASS || node.rank == RANK_PHYLUM) {
size_t sum = 0, count = 0;
for(map<uint64_t, uint64_t>::const_iterator size_itr = _size.begin(); size_itr != _size.end(); size_itr++) {
uint64_t c_tid = size_itr->first;
map<uint64_t, TaxonomyNode>::const_iterator tree_itr2 = _tree.find(c_tid);
if(tree_itr2 == _tree.end())
continue;
assert(tree_itr2 != _tree.end());
const TaxonomyNode& c_node = tree_itr2->second;
if((c_node.rank == RANK_UNKNOWN && c_node.leaf) ||
tax_rank_num[c_node.rank] < tax_rank_num[RANK_SPECIES]) {
c_tid = c_node.parent_tid;
while(true) {
if(c_tid == tid) {
sum += size_itr->second;
count += 1;
break;
}
tree_itr2 = _tree.find(c_tid);
if(tree_itr2 == _tree.end())
break;
if(c_tid == tree_itr2->second.parent_tid)
break;
c_tid = tree_itr2->second.parent_tid;
}
}
}
if(count > 0) {
_size[tid] = sum / count;
}
}
}*/
}
_paths.buildPaths(_uid_to_tid, _tree);
in3.close();
// Read in the information provided by Li. The SA coordinate that corresponds to the start of genome.
string in4Str = in + ".4." + gEbwt_ext;
if(verbose || startVerbose) cerr << "Opening \"" << in4Str.c_str() << "\"" << endl;
ifstream in4(in4Str.c_str(), ios::binary);
if(!in4.good()) {
if(verbose || startVerbose) cerr << "Could not open index file " << in4Str.c_str() << endl;
}
else
{
readU32(in4, this->toBe());
_saGenomeBoundary.clear() ;
nsize = readIndex<uint64_t>( in4, this->toBe() ) ;
//cout<<nsize<<" "<<_uid_to_tid.size()<<endl ;
_lastGenomeBoundary = 0 ;
if ( nsize > 0 )
{
uint64_t t ;
for ( t = 0 ; t < nsize ; ++t )
{
uint64_t saCoord = readIndex<uint64_t>( in4, this->toBe() ) ;
uint32_t refIdx = readIndex<uint32_t>( in4, this->toBe() ) ;
/*string uid;
while(true) {
char c = '\0';
in4 >> c;
if(c == '\0' || c == '\n') break;
uid.push_back(c);
}*/
//cout<<saCoord<<" "<<uid<<" "<< uidStrToIdx[ uid ] <<endl ;
_saGenomeBoundary[ saCoord ] = refIdx ;
if ( saCoord > _lastGenomeBoundary )
_lastGenomeBoundary = saCoord ;
}
_boundaryCheckShift = 8 ;
while ( 1 )
{
uint64_t blockSize = ((uint64_t)1)<<_boundaryCheckShift ;
if ( blockSize > _lastGenomeBoundary + 1 )
break ;
uint64_t blockCnt = ( _lastGenomeBoundary + 1 ) / blockSize + 1 ;
if ( blockCnt < 100 * nsize )
{
if ( _boundaryCheckShift > 8 )
--_boundaryCheckShift ;
break ;
}
++_boundaryCheckShift ;
}
//cout<<nsize<<" "<<_lastGenomeBoundary<<" "<<_boundaryCheckShift<<endl ;
_boundaryCheck.resize( ( ( _lastGenomeBoundary + 1 ) >> _boundaryCheckShift ) + 1 ) ;
_boundaryCheck.reset() ;
for ( std::map<uint64_t, uint32_t>::iterator it = _saGenomeBoundary.begin() ; it != _saGenomeBoundary.end() ; ++it )
{
_boundaryCheck.set( (it->first) >> _boundaryCheckShift ) ;
}
}
}
in4.close() ;
}
/// 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(
bool packed,
int color,
int needEntireReverse,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
const string& file, // base filename for EBWT 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) :
Ebwt_INITS,
_eh(
joinedLen(szs),
lineRate,
offRate,
ftabChars,
color,
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>
Ebwt(
TStr& s,
bool packed,
int color,
int needEntireReverse,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
const string& file, // base filename for EBWT files
bool fw,
bool useBlockwise,
index_t bmax,
index_t bmaxSqrtMult,
index_t bmaxDivN,
int dcv,
int nthreads,
EList<FileBuf*>& is,
EList<RefRecord>& szs,
index_t sztot,
const string& conversion_table_fname,
const string& taxonomy_fname,
const string& name_table_fname,
const string& size_table_fname,
const RefReadInParams& refparams,
uint32_t seed,
int32_t overrideOffRate = -1,
bool doSaFile = false,
bool doBwtFile = false,
int kmer_size = 0,
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
initFromVector<TStr>(
s,
is,
szs,
sztot,
refparams,
fout1,
fout2,
saOut,
bwtOut,
kmer_size,
file,
conversion_table_fname,
taxonomy_fname,
name_table_fname,
size_table_fname,
useBlockwise,