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hier_idx.h
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hier_idx.h
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/*
* Copyright 2013, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of Beast. Beast is based on Bowtie 2.
*
* Beast 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.
*
* Beast 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 Beast. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef HIEREBWT_H_
#define HIEREBWT_H_
#include "hier_idx_common.h"
#include "bt2_idx.h"
#include "bt2_io.h"
#include "bt2_util.h"
/**
* Extended Burrows-Wheeler transform data.
* LocalEbwt is a specialized Ebwt index that represents ~64K bps
* and therefore uses two bytes as offsets within 64K bps.
* This class has only two additional member variables to denote the genomic sequenuce it represents:
* (1) the contig index and (2) the offset within the contig.
*
*/
template <typename index_t = uint16_t, typename full_index_t = uint32_t>
class LocalEbwt : public Ebwt<index_t> {
typedef Ebwt<index_t> PARENT_CLASS;
public:
/// Construct an Ebwt from the given input file
LocalEbwt(const string& in,
FILE *in5,
FILE *in6,
char *mmFile5,
char *mmFile6,
full_index_t& tidx,
full_index_t& localOffset,
bool switchEndian,
size_t& bytesRead,
int color,
int needEntireReverse,
bool fw,
int32_t overrideOffRate, // = -1,
int32_t offRatePlus, // = -1,
uint32_t lineRate,
uint32_t offRate,
uint32_t ftabChars,
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<index_t>(in,
color,
needEntireReverse,
fw,
overrideOffRate,
offRatePlus,
useMm,
useShmem,
mmSweep,
loadNames,
loadSASamp,
loadFtab,
loadRstarts,
verbose,
startVerbose,
passMemExc,
sanityCheck,
true)
{
this->_in1Str = in + ".5." + gEbwt_ext;
this->_in2Str = in + ".5." + gEbwt_ext;
readIntoMemory(
in5,
in6,
mmFile5,
mmFile6,
tidx,
localOffset,
switchEndian,
bytesRead,
color,
needEntireReverse,
loadSASamp,
loadFtab,
loadRstarts,
false, //justHeader
lineRate,
offRate,
ftabChars,
mmSweep,
loadNames,
startVerbose);
_tidx = tidx;
_localOffset = localOffset;
// If the offRate has been overridden, reflect that in the
// _eh._offRate field
if(offRatePlus > 0 && this->_overrideOffRate == -1) {
this->_overrideOffRate = this->_eh._offRate + offRatePlus;
}
if(this->_overrideOffRate > this->_eh._offRate) {
this->_eh.setOffRate(this->_overrideOffRate);
assert_eq(this->_overrideOffRate, this->_eh._offRate);
}
assert(this->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>
LocalEbwt(
TStr& s,
full_index_t tidx,
full_index_t local_offset,
index_t local_size,
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,
ostream& out5,
ostream& out6,
int32_t overrideOffRate = -1,
bool verbose = false,
bool passMemExc = false,
bool sanityCheck = false) :
Ebwt<index_t>(packed,
color,
needEntireReverse,
lineRate,
offRate,
ftabChars,
file,
fw,
dcv,
szs,
sztot,
refparams,
seed,
overrideOffRate,
verbose,
passMemExc,
sanityCheck)
{
const EbwtParams<index_t>& eh = this->_eh;
assert(eh.repOk());
uint32_t be = this->toBe();
assert(out5.good());
assert(out6.good());
writeIndex<full_index_t>(out5, tidx, be);
writeIndex<full_index_t>(out5, local_offset, be);
writeU32(out5, eh._len, be); // length of string (and bwt and suffix array)
if(eh._len > 0) {
assert_gt(szs.size(), 0);
assert_gt(sztot, 0);
// Not every fragment represents a distinct sequence - many
// fragments may correspond to a single sequence. Count the
// number of sequences here by counting the number of "first"
// fragments.
this->_nPat = 0;
this->_nFrag = 0;
for(size_t i = 0; i < szs.size(); i++) {
if(szs[i].len > 0) this->_nFrag++;
if(szs[i].first && szs[i].len > 0) this->_nPat++;
}
assert_eq(this->_nPat, 1);
assert_geq(this->_nFrag, this->_nPat);
this->_rstarts.reset();
writeIndex(out5, this->_nPat, be);
assert_eq(this->_nPat, 1);
this->_plen.init(new index_t[this->_nPat], this->_nPat);
// For each pattern, set plen
int npat = -1;
for(size_t i = 0; i < szs.size(); i++) {
if(szs[i].first && szs[i].len > 0) {
if(npat >= 0) {
writeIndex(out5, this->plen()[npat], be);
}
npat++;
this->plen()[npat] = (szs[i].len + szs[i].off);
} else {
this->plen()[npat] += (szs[i].len + szs[i].off);
}
}
assert_eq((index_t)npat, this->_nPat-1);
writeIndex(out5, this->plen()[npat], be);
// Write the number of fragments
writeIndex(out5, this->_nFrag, be);
if(refparams.reverse == REF_READ_REVERSE) {
EList<RefRecord> tmp(EBWT_CAT);
reverseRefRecords(szs, tmp, false, verbose);
this->szsToDisk(tmp, out5, refparams.reverse);
} else {
this->szsToDisk(szs, out5, refparams.reverse);
}
VMSG_NL("Constructing suffix-array element generator");
KarkkainenBlockwiseSA<TStr> bsa(s, s.length()+1, dcv, seed, this->_sanity, this->_passMemExc, this->_verbose);
assert(bsa.suffixItrIsReset());
assert_eq(bsa.size(), s.length()+1);
VMSG_NL("Converting suffix-array elements to index image");
buildToDisk(bsa, s, out5, out6);
}
out5.flush(); out6.flush();
if(out5.fail() || out6.fail()) {
cerr << "An error occurred writing the index to disk. Please check if the disk is full." << endl;
throw 1;
}
}
template <typename TStr> void buildToDisk(
InorderBlockwiseSA<TStr>& sa,
const TStr& s,
ostream& out1,
ostream& out2);
// I/O
void readIntoMemory(
FILE *in5,
FILE *in6,
char *mmFile5,
char *mmFile6,
full_index_t& tidx,
full_index_t& localOffset,
bool switchEndian,
size_t bytesRead,
int color,
int needEntireRev,
bool loadSASamp,
bool loadFtab,
bool loadRstarts,
bool justHeader,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
bool mmSweep,
bool loadNames,
bool startVerbose);
/**
* Sanity-check various pieces of the Ebwt
*/
void sanityCheckAll(int reverse) const {
if(this->_eh._len > 0) {
PARENT_CLASS::sanityCheckAll(reverse);
}
}
bool empty() const { return this->_eh._len == 0; }
public:
full_index_t _tidx;
full_index_t _localOffset;
};
/**
* Build an Ebwt from a string 's' and its suffix array 'sa' (which
* might actually be a suffix array *builder* that builds blocks of the
* array on demand). The bulk of the Ebwt, i.e. the ebwt and offs
* arrays, is written directly to disk. This is by design: keeping
* those arrays in memory needlessly increases the footprint of the
* building process. Instead, we prefer to build the Ebwt directly
* "to disk" and then read it back into memory later as necessary.
*
* It is assumed that the header values and join-related values (nPat,
* plen) have already been written to 'out1' before this function
* is called. When this function is finished, it will have
* additionally written ebwt, zOff, fchr, ftab and eftab to the primary
* file and offs to the secondary file.
*
* Assume DNA/RNA/any alphabet with 4 or fewer elements.
* Assume occ array entries are 32 bits each.
*
* @param sa the suffix array to convert to a Ebwt
* @param s the original string
* @param out
*/
template <typename index_t, typename full_index_t>
template <typename TStr>
void LocalEbwt<index_t, full_index_t>::buildToDisk(
InorderBlockwiseSA<TStr>& sa,
const TStr& s,
ostream& out5,
ostream& out6)
{
assert_leq(s.length(), std::numeric_limits<index_t>::max());
const EbwtParams<index_t>& eh = this->_eh;
assert(eh.repOk());
assert_eq(s.length()+1, sa.size());
assert_eq(s.length(), eh._len);
assert_gt(eh._lineRate, 3);
assert(sa.suffixItrIsReset());
index_t len = eh._len;
index_t ftabLen = eh._ftabLen;
index_t sideSz = eh._sideSz;
index_t ebwtTotSz = eh._ebwtTotSz;
index_t fchr[] = {0, 0, 0, 0, 0};
EList<index_t> ftab(EBWT_CAT);
index_t zOff = (index_t)OFF_MASK;
// Save # of occurrences of each character as we walk along the bwt
index_t occ[4] = {0, 0, 0, 0};
index_t occSave[4] = {0, 0, 0, 0};
// Record rows that should "absorb" adjacent rows in the ftab.
// The absorbed rows represent suffixes shorter than the ftabChars
// cutoff.
uint8_t absorbCnt = 0;
EList<uint8_t> absorbFtab(EBWT_CAT);
try {
VMSG_NL("Allocating ftab, absorbFtab");
ftab.resize(ftabLen);
ftab.fillZero();
absorbFtab.resize(ftabLen);
absorbFtab.fillZero();
} catch(bad_alloc &e) {
cerr << "Out of memory allocating ftab[] or absorbFtab[] "
<< "in Ebwt::buildToDisk() at " << __FILE__ << ":"
<< __LINE__ << endl;
throw e;
}
// Allocate the side buffer; holds a single side as its being
// constructed and then written to disk. Reused across all sides.
#ifdef SIXTY4_FORMAT
EList<uint64_t> ebwtSide(EBWT_CAT);
#else
EList<uint8_t> ebwtSide(EBWT_CAT);
#endif
try {
#ifdef SIXTY4_FORMAT
ebwtSide.resize(sideSz >> 3);
#else
ebwtSide.resize(sideSz);
#endif
} catch(bad_alloc &e) {
cerr << "Out of memory allocating ebwtSide[] in "
<< "Ebwt::buildToDisk() at " << __FILE__ << ":"
<< __LINE__ << endl;
throw e;
}
// Points to the base offset within ebwt for the side currently
// being written
index_t side = 0;
// Whether we're assembling a forward or a reverse bucket
bool fw;
int sideCur = 0;
fw = true;
// Have we skipped the '$' in the last column yet?
ASSERT_ONLY(bool dollarSkipped = false);
index_t si = 0; // string offset (chars)
ASSERT_ONLY(uint32_t lastSufInt = 0);
ASSERT_ONLY(bool inSA = true); // true iff saI still points inside suffix
// array (as opposed to the padding at the
// end)
// Iterate over packed bwt bytes
VMSG_NL("Entering Ebwt loop");
ASSERT_ONLY(uint32_t beforeEbwtOff = (uint32_t)out5.tellp());
while(side < ebwtTotSz) {
// Sanity-check our cursor into the side buffer
assert_geq(sideCur, 0);
assert_lt(sideCur, (int)eh._sideBwtSz);
assert_eq(0, side % sideSz); // 'side' must be on side boundary
ebwtSide[sideCur] = 0; // clear
assert_lt(side + sideCur, ebwtTotSz);
// Iterate over bit-pairs in the si'th character of the BWT
#ifdef SIXTY4_FORMAT
for(int bpi = 0; bpi < 32; bpi++, si++) {
#else
for(int bpi = 0; bpi < 4; bpi++, si++) {
#endif
int bwtChar;
bool count = true;
if(si <= len) {
// Still in the SA; extract the bwtChar
index_t saElt = (index_t)sa.nextSuffix();
// (that might have triggered sa to calc next suf block)
if(saElt == 0) {
// Don't add the '$' in the last column to the BWT
// transform; we can't encode a $ (only A C T or G)
// and counting it as, say, an A, will mess up the
// LR mapping
bwtChar = 0; count = false;
ASSERT_ONLY(dollarSkipped = true);
zOff = si; // remember the SA row that
// corresponds to the 0th suffix
} else {
bwtChar = (int)(s[saElt-1]);
assert_lt(bwtChar, 4);
// Update the fchr
fchr[bwtChar]++;
}
// Update ftab
if((len-saElt) >= (index_t)eh._ftabChars) {
// Turn the first ftabChars characters of the
// suffix into an integer index into ftab. The
// leftmost (lowest index) character of the suffix
// goes in the most significant bit pair if the
// integer.
uint32_t sufInt = 0;
for(int i = 0; i < eh._ftabChars; i++) {
sufInt <<= 2;
assert_lt((index_t)i, len-saElt);
sufInt |= (unsigned char)(s[saElt+i]);
}
// Assert that this prefix-of-suffix is greater
// than or equal to the last one (true b/c the
// suffix array is sorted)
#ifndef NDEBUG
if(lastSufInt > 0) assert_geq(sufInt, lastSufInt);
lastSufInt = sufInt;
#endif
// Update ftab
assert_lt(sufInt+1, ftabLen);
ftab[sufInt+1]++;
if(absorbCnt > 0) {
// Absorb all short suffixes since the last
// transition into this transition
absorbFtab[sufInt] = absorbCnt;
absorbCnt = 0;
}
} else {
// Otherwise if suffix is fewer than ftabChars
// characters long, then add it to the 'absorbCnt';
// it will be absorbed into the next transition
assert_lt(absorbCnt, 255);
absorbCnt++;
}
// Suffix array offset boundary? - update offset array
if((si & eh._offMask) == si) {
assert_lt((si >> eh._offRate), eh._offsLen);
// Write offsets directly to the secondary output
// stream, thereby avoiding keeping them in memory
writeIndex(out6, saElt, this->toBe());
}
} else {
// Strayed off the end of the SA, now we're just
// padding out a bucket
#ifndef NDEBUG
if(inSA) {
// Assert that we wrote all the characters in the
// string before now
assert_eq(si, len+1);
inSA = false;
}
#endif
// 'A' used for padding; important that padding be
// counted in the occ[] array
bwtChar = 0;
}
if(count) occ[bwtChar]++;
// Append BWT char to bwt section of current side
if(fw) {
// Forward bucket: fill from least to most
#ifdef SIXTY4_FORMAT
ebwtSide[sideCur] |= ((uint64_t)bwtChar << (bpi << 1));
if(bwtChar > 0) assert_gt(ebwtSide[sideCur], 0);
#else
pack_2b_in_8b(bwtChar, ebwtSide[sideCur], bpi);
assert_eq((ebwtSide[sideCur] >> (bpi*2)) & 3, bwtChar);
#endif
} else {
// Backward bucket: fill from most to least
#ifdef SIXTY4_FORMAT
ebwtSide[sideCur] |= ((uint64_t)bwtChar << ((31 - bpi) << 1));
if(bwtChar > 0) assert_gt(ebwtSide[sideCur], 0);
#else
pack_2b_in_8b(bwtChar, ebwtSide[sideCur], 3-bpi);
assert_eq((ebwtSide[sideCur] >> ((3-bpi)*2)) & 3, bwtChar);
#endif
}
} // end loop over bit-pairs
assert_eq(dollarSkipped ? 3 : 0, (occ[0] + occ[1] + occ[2] + occ[3]) & 3);
#ifdef SIXTY4_FORMAT
assert_eq(0, si & 31);
#else
assert_eq(0, si & 3);
#endif
sideCur++;
if(sideCur == (int)eh._sideBwtSz) {
sideCur = 0;
index_t *uside = reinterpret_cast<index_t*>(ebwtSide.ptr());
// Write 'A', 'C', 'G' and 'T' tallies
side += sideSz;
assert_leq(side, eh._ebwtTotSz);
uside[(sideSz / sizeof(index_t))-4] = endianizeIndex(occSave[0], this->toBe());
uside[(sideSz / sizeof(index_t))-3] = endianizeIndex(occSave[1], this->toBe());
uside[(sideSz / sizeof(index_t))-2] = endianizeIndex(occSave[2], this->toBe());
uside[(sideSz / sizeof(index_t))-1] = endianizeIndex(occSave[3], this->toBe());
occSave[0] = occ[0];
occSave[1] = occ[1];
occSave[2] = occ[2];
occSave[3] = occ[3];
// Write backward side to primary file
out5.write((const char *)ebwtSide.ptr(), sideSz);
}
}
VMSG_NL("Exited Ebwt loop");
assert_neq(zOff, (index_t)OFF_MASK);
if(absorbCnt > 0) {
// Absorb any trailing, as-yet-unabsorbed short suffixes into
// the last element of ftab
absorbFtab[ftabLen-1] = absorbCnt;
}
// Assert that our loop counter got incremented right to the end
assert_eq(side, eh._ebwtTotSz);
// Assert that we wrote the expected amount to out1
assert_eq(((uint32_t)out5.tellp() - beforeEbwtOff), eh._ebwtTotSz);
// assert that the last thing we did was write a forward bucket
//
// Write zOff to primary stream
//
writeIndex(out5, zOff, this->toBe());
//
// Finish building fchr
//
// Exclusive prefix sum on fchr
for(int i = 1; i < 4; i++) {
fchr[i] += fchr[i-1];
}
assert_eq(fchr[3], len);
// Shift everybody up by one
for(int i = 4; i >= 1; i--) {
fchr[i] = fchr[i-1];
}
fchr[0] = 0;
if(this->_verbose) {
for(int i = 0; i < 5; i++)
cout << "fchr[" << "ACGT$"[i] << "]: " << fchr[i] << endl;
}
// Write fchr to primary file
for(int i = 0; i < 5; i++) {
writeIndex(out5, fchr[i], this->toBe());
}
//
// Finish building ftab and build eftab
//
// Prefix sum on ftable
index_t eftabLen = 0;
assert_eq(0, absorbFtab[0]);
for(index_t i = 1; i < ftabLen; i++) {
if(absorbFtab[i] > 0) eftabLen += 2;
}
assert_leq(eftabLen, (index_t)eh._ftabChars*2);
eftabLen = eh._ftabChars*2;
EList<index_t> eftab(EBWT_CAT);
try {
eftab.resize(eftabLen);
eftab.fillZero();
} catch(bad_alloc &e) {
cerr << "Out of memory allocating eftab[] "
<< "in Ebwt::buildToDisk() at " << __FILE__ << ":"
<< __LINE__ << endl;
throw e;
}
index_t eftabCur = 0;
for(index_t i = 1; i < ftabLen; i++) {
index_t lo = ftab[i] + Ebwt<index_t>::ftabHi(ftab.ptr(), eftab.ptr(), len, ftabLen, eftabLen, i-1);
if(absorbFtab[i] > 0) {
// Skip a number of short pattern indicated by absorbFtab[i]
index_t hi = lo + absorbFtab[i];
assert_lt(eftabCur*2+1, eftabLen);
eftab[eftabCur*2] = lo;
eftab[eftabCur*2+1] = hi;
ftab[i] = (eftabCur++) ^ (index_t)OFF_MASK; // insert pointer into eftab
assert_eq(lo, Ebwt<index_t>::ftabLo(ftab.ptr(), eftab.ptr(), len, ftabLen, eftabLen, i));
assert_eq(hi, Ebwt<index_t>::ftabHi(ftab.ptr(), eftab.ptr(), len, ftabLen, eftabLen, i));
} else {
ftab[i] = lo;
}
}
assert_eq(Ebwt<index_t>::ftabHi(ftab.ptr(), eftab.ptr(), len, ftabLen, eftabLen, ftabLen-1), len+1);
// Write ftab to primary file
for(index_t i = 0; i < ftabLen; i++) {
writeIndex(out5, ftab[i], this->toBe());
}
// Write eftab to primary file
for(index_t i = 0; i < eftabLen; i++) {
writeIndex(out5, eftab[i], this->toBe());
}
// Note: if you'd like to sanity-check the Ebwt, you'll have to
// read it back into memory first!
assert(!this->isInMemory());
VMSG_NL("Exiting Ebwt::buildToDisk()");
}
/**
* Read an Ebwt from file with given filename.
*/
template <typename index_t, typename full_index_t>
void LocalEbwt<index_t, full_index_t>::readIntoMemory(
FILE *in5,
FILE *in6,
char *mmFile5,
char *mmFile6,
full_index_t& tidx,
full_index_t& localOffset,
bool switchEndian,
size_t bytesRead,
int color,
int entireRev,
bool loadSASamp,
bool loadFtab,
bool loadRstarts,
bool justHeader,
int32_t lineRate,
int32_t offRate,
int32_t ftabChars,
bool mmSweep,
bool loadNames,
bool startVerbose)
{
#ifdef BOWTIE_MM
char *mmFile[] = { mmFile5, mmFile6 };
#endif
// Reads header entries one by one from primary stream
tidx = readIndex<full_index_t>(in5, switchEndian); bytesRead += sizeof(full_index_t);
localOffset = readIndex<full_index_t>(in5, switchEndian); bytesRead += sizeof(full_index_t);
uint32_t len = readU32(in5, switchEndian); bytesRead += 4;
// Create a new EbwtParams from the entries read from primary stream
this->_eh.init(len, lineRate, offRate, ftabChars, color, entireRev);
if(len <= 0) {
return;
}
// Set up overridden suffix-array-sample parameters
uint32_t offsLen = this->_eh._offsLen;
uint32_t offRateDiff = 0;
uint32_t offsLenSampled = offsLen;
if(this->_overrideOffRate > offRate) {
offRateDiff = this->_overrideOffRate - offRate;
}
if(offRateDiff > 0) {
offsLenSampled >>= offRateDiff;
if((offsLen & ~((index_t)OFF_MASK << offRateDiff)) != 0) {
offsLenSampled++;
}
}
// Can't override the offrate or isarate and use memory-mapped
// files; ultimately, all processes need to copy the sparser sample
// into their own memory spaces.
if(this->_useMm && (offRateDiff)) {
cerr << "Error: Can't use memory-mapped files when the offrate is overridden" << endl;
throw 1;
}
// Read nPat from primary stream
this->_nPat = readIndex<index_t>(in5, switchEndian);
assert_eq(this->_nPat, 1);
bytesRead += sizeof(index_t);
this->_plen.reset();
// Read plen from primary stream
if(this->_useMm) {
#ifdef BOWTIE_MM
this->_plen.init((index_t*)(mmFile[0] + bytesRead), this->_nPat, false);
bytesRead += this->_nPat*sizeof(index_t);
fseek(in5, this->_nPat*sizeof(index_t), SEEK_CUR);
#endif
} else {
try {
if(this->_verbose || startVerbose) {
cerr << "Reading plen (" << this->_nPat << "): ";
logTime(cerr);
}
this->_plen.init(new index_t[this->_nPat], this->_nPat, true);
if(switchEndian) {
for(index_t i = 0; i < this->_nPat; i++) {
this->plen()[i] = readIndex<index_t>(in5, switchEndian);
}
} else {
size_t r = MM_READ(in5, (void*)(this->plen()), this->_nPat*sizeof(index_t));
if(r != (size_t)(this->_nPat*sizeof(index_t))) {
cerr << "Error reading _plen[] array: " << r << ", " << this->_nPat*sizeof(index_t) << endl;
throw 1;
}
}
} catch(bad_alloc& e) {
cerr << "Out of memory allocating plen[] in Ebwt::read()"
<< " at " << __FILE__ << ":" << __LINE__ << endl;
throw e;
}
}
bool shmemLeader;
// TODO: I'm not consistent on what "header" means. Here I'm using
// "header" to mean everything that would exist in memory if we
// started to build the Ebwt but stopped short of the build*() step
// (i.e. everything up to and including join()).
if(justHeader) return;
this->_nFrag = readIndex<index_t>(in5, switchEndian);
bytesRead += sizeof(index_t);
if(this->_verbose || startVerbose) {
cerr << "Reading rstarts (" << this->_nFrag*3 << "): ";
logTime(cerr);
}
assert_geq(this->_nFrag, this->_nPat);
this->_rstarts.reset();
if(loadRstarts) {
if(this->_useMm) {
#ifdef BOWTIE_MM
this->_rstarts.init((index_t*)(mmFile[0] + bytesRead), this->_nFrag*3, false);
bytesRead += this->_nFrag*sizeof(index_t)*3;
fseek(in5, this->_nFrag*sizeof(index_t)*3, SEEK_CUR);
#endif
} else {
this->_rstarts.init(new index_t[this->_nFrag*3], this->_nFrag*3, true);
if(switchEndian) {
for(index_t i = 0; i < this->_nFrag*3; i += 3) {
// fragment starting position in joined reference
// string, text id, and fragment offset within text
this->rstarts()[i] = readIndex<index_t>(in5, switchEndian);
this->rstarts()[i+1] = readIndex<index_t>(in5, switchEndian);
this->rstarts()[i+2] = readIndex<index_t>(in5, switchEndian);
}
} else {
size_t r = MM_READ(in5, (void *)this->rstarts(), this->_nFrag*sizeof(index_t)*3);
if(r != (size_t)(this->_nFrag*sizeof(index_t)*3)) {
cerr << "Error reading _rstarts[] array: " << r << ", " << (this->_nFrag*sizeof(index_t)*3) << endl;
throw 1;
}
}
}
} else {
// Skip em
assert(this->rstarts() == NULL);
bytesRead += this->_nFrag*sizeof(index_t)*3;
fseek(in5, this->_nFrag*sizeof(index_t)*3, SEEK_CUR);
}
this->_ebwt.reset();
if(this->_useMm) {
#ifdef BOWTIE_MM
this->_ebwt.init((uint8_t*)(mmFile[0] + bytesRead), this->_eh._ebwtTotLen, false);
bytesRead += this->_eh._ebwtTotLen;
fseek(in5, this->_eh._ebwtTotLen, SEEK_CUR);
#endif
} else {
// Allocate ebwt (big allocation)
if(this->_verbose || startVerbose) {
cerr << "Reading ebwt (" << this->_eh._ebwtTotLen << "): ";
logTime(cerr);
}
bool shmemLeader = true;
if(this->useShmem_) {
uint8_t *tmp = NULL;
shmemLeader = ALLOC_SHARED_U8(
(this->_in1Str + "[ebwt]"), this->_eh._ebwtTotLen, &tmp,
"ebwt[]", (this->_verbose || startVerbose));
assert(tmp != NULL);
this->_ebwt.init(tmp, this->_eh._ebwtTotLen, false);
if(this->_verbose || startVerbose) {
cerr << " shared-mem " << (shmemLeader ? "leader" : "follower") << endl;
}
} else {
try {
this->_ebwt.init(new uint8_t[this->_eh._ebwtTotLen], this->_eh._ebwtTotLen, true);
} catch(bad_alloc& e) {
cerr << "Out of memory allocating the ebwt[] array for the Bowtie index. Please try" << endl
<< "again on a computer with more memory." << endl;
throw 1;
}
}
if(shmemLeader) {
// Read ebwt from primary stream
uint64_t bytesLeft = this->_eh._ebwtTotLen;
char *pebwt = (char*)this->ebwt();
while (bytesLeft>0){
size_t r = MM_READ(in5, (void *)pebwt, bytesLeft);
if(MM_IS_IO_ERR(in5, r, bytesLeft)) {
cerr << "Error reading _ebwt[] array: " << r << ", "
<< bytesLeft << endl;
throw 1;
}
pebwt += r;
bytesLeft -= r;
}
if(switchEndian) {
uint8_t *side = this->ebwt();
for(size_t i = 0; i < this->_eh._numSides; i++) {
index_t *cums = reinterpret_cast<index_t*>(side + this->_eh._sideSz - sizeof(index_t)*2);
cums[0] = endianSwapIndex(cums[0]);
cums[1] = endianSwapIndex(cums[1]);
side += this->_eh._sideSz;
}
}
#ifdef BOWTIE_SHARED_MEM
if(useShmem_) NOTIFY_SHARED(this->ebwt(), this->_eh._ebwtTotLen);
#endif
} else {
// Seek past the data and wait until master is finished
fseek(in5, this->_eh._ebwtTotLen, SEEK_CUR);
#ifdef BOWTIE_SHARED_MEM
if(useShmem_) WAIT_SHARED(this->ebwt(), this->_eh._ebwtTotLen);
#endif
}
}
// Read zOff from primary stream
this->_zOff = readIndex<index_t>(in5, switchEndian);
bytesRead += sizeof(index_t);
assert_lt(this->_zOff, len);
try {
// Read fchr from primary stream
if(this->_verbose || startVerbose) cerr << "Reading fchr (5)" << endl;
this->_fchr.reset();
if(this->_useMm) {
#ifdef BOWTIE_MM
this->_fchr.init((index_t*)(mmFile[0] + bytesRead), 5, false);
bytesRead += 5*sizeof(index_t);
fseek(in5, 5*sizeof(index_t), SEEK_CUR);
#endif
} else {
this->_fchr.init(new index_t[5], 5, true);
for(index_t i = 0; i < 5; i++) {
this->fchr()[i] = readIndex<index_t>(in5, switchEndian);
assert_leq(this->fchr()[i], len);
assert(i <= 0 || this->fchr()[i] >= this->fchr()[i-1]);
}
}
assert_gt(this->fchr()[4], this->fchr()[0]);
// Read ftab from primary stream
if(this->_verbose || startVerbose) {
if(loadFtab) {
cerr << "Reading ftab (" << this->_eh._ftabLen << "): ";
logTime(cerr);
} else {
cerr << "Skipping ftab (" << this->_eh._ftabLen << "): ";
}
}
this->_ftab.reset();
if(loadFtab) {
if(this->_useMm) {
#ifdef BOWTIE_MM
this->_ftab.init((index_t*)(mmFile[0] + bytesRead), this->_eh._ftabLen, false);
bytesRead += this->_eh._ftabLen*sizeof(index_t);
fseek(in5, this->_eh._ftabLen*sizeof(index_t), SEEK_CUR);
#endif
} else {
this->_ftab.init(new index_t[this->_eh._ftabLen], this->_eh._ftabLen, true);
if(switchEndian) {
for(uint32_t i = 0; i < this->_eh._ftabLen; i++)
this->ftab()[i] = readIndex<index_t>(in5, switchEndian);
} else {
size_t r = MM_READ(in5, (void *)this->ftab(), this->_eh._ftabLen*sizeof(index_t));
if(r != (size_t)(this->_eh._ftabLen*sizeof(index_t))) {
cerr << "Error reading _ftab[] array: " << r << ", " << (this->_eh._ftabLen*sizeof(index_t)) << endl;
throw 1;
}
}
}
// Read etab from primary stream
if(this->_verbose || startVerbose) {
if(loadFtab) {
cerr << "Reading eftab (" << this->_eh._eftabLen << "): ";
logTime(cerr);
} else {
cerr << "Skipping eftab (" << this->_eh._eftabLen << "): ";
}
}
this->_eftab.reset();
if(this->_useMm) {
#ifdef BOWTIE_MM
this->_eftab.init((index_t*)(mmFile[0] + bytesRead), this->_eh._eftabLen, false);
bytesRead += this->_eh._eftabLen*sizeof(index_t);
fseek(in5, this->_eh._eftabLen*sizeof(index_t), SEEK_CUR);
#endif
} else {
this->_eftab.init(new index_t[this->_eh._eftabLen], this->_eh._eftabLen, true);
if(switchEndian) {
for(uint32_t i = 0; i < this->_eh._eftabLen; i++)
this->eftab()[i] = readIndex<index_t>(in5, switchEndian);
} else {
size_t r = MM_READ(in5, (void *)this->eftab(), this->_eh._eftabLen*sizeof(index_t));
if(r != (size_t)(this->_eh._eftabLen*sizeof(index_t))) {
cerr << "Error reading _eftab[] array: " << r << ", " << (this->_eh._eftabLen*sizeof(index_t)) << endl;
throw 1;
}
}
}
for(uint32_t i = 0; i < this->_eh._eftabLen; i++) {
if(i > 0 && this->eftab()[i] > 0) {
assert_geq(this->eftab()[i], this->eftab()[i-1]);
} else if(i > 0 && this->eftab()[i-1] == 0) {
assert_eq(0, this->eftab()[i]);
}
}
} else {
assert(this->ftab() == NULL);
assert(this->eftab() == NULL);
// Skip ftab
bytesRead += this->_eh._ftabLen*sizeof(index_t);
fseek(in5, this->_eh._ftabLen*sizeof(index_t), SEEK_CUR);
// Skip eftab
bytesRead += this->_eh._eftabLen*sizeof(index_t);
fseek(in5, this->_eh._eftabLen*sizeof(index_t), SEEK_CUR);
}
} catch(bad_alloc& e) {
cerr << "Out of memory allocating fchr[], ftab[] or eftab[] arrays for the Bowtie index." << endl
<< "Please try again on a computer with more memory." << endl;
throw 1;
}
this->_offs.reset();
if(loadSASamp) {
bytesRead = 4; // reset for secondary index file (already read 1-sentinel)
shmemLeader = true;
if(this->_verbose || startVerbose) {
cerr << "Reading offs (" << offsLenSampled << " " << std::setw(2) << sizeof(index_t)*8 << "-bit words): ";
logTime(cerr);
}
if(!this->_useMm) {
if(!this->useShmem_) {
// Allocate offs_
try {
this->_offs.init(new index_t[offsLenSampled], offsLenSampled, true);
} catch(bad_alloc& e) {
cerr << "Out of memory allocating the offs[] array for the Bowtie index." << endl
<< "Please try again on a computer with more memory." << endl;
throw 1;
}
} else {
index_t *tmp = NULL;
shmemLeader = ALLOC_SHARED_U32(
(this->_in2Str + "[offs]"), offsLenSampled*2, &tmp,
"offs", (this->_verbose || startVerbose));
this->_offs.init((index_t*)tmp, offsLenSampled, false);
}
}
if(this->_overrideOffRate < 32) {
if(shmemLeader) {
// Allocate offs (big allocation)
if(switchEndian || offRateDiff > 0) {
assert(!this->_useMm);
const uint32_t blockMaxSz = (2 * 1024 * 1024); // 2 MB block size
const uint32_t blockMaxSzUIndex = (blockMaxSz / sizeof(index_t)); // # UIndexs per block
char *buf;
try {
buf = new char[blockMaxSz];
} catch(std::bad_alloc& e) {
cerr << "Error: Out of memory allocating part of _offs array: '" << e.what() << "'" << endl;
throw e;
}
for(index_t i = 0; i < offsLen; i += blockMaxSzUIndex) {
index_t block = min<index_t>((index_t)blockMaxSzUIndex, (index_t)(offsLen - i));
size_t r = MM_READ(in6, (void *)buf, block * sizeof(index_t));