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hgfm.h
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/*
* Copyright 2015, Daehwan Kim <[email protected]>
*
* 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 HGFM_H_
#define HGFM_H_
#include "hier_idx_common.h"
#include "gfm.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 LocalGFM : public GFM<index_t> {
typedef GFM<index_t> PARENT_CLASS;
public:
/// Construct an Ebwt from the given input file
LocalGFM(const string& in,
ALTDB<index_t>* altdb,
FILE *in5,
FILE *in6,
char *mmFile5,
char *mmFile6,
full_index_t& tidx,
full_index_t& localOffset,
full_index_t& joinedOffset,
bool switchEndian,
size_t& bytesRead,
size_t& bytesRead2,
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)
bool useHaplotype) : // = false
GFM<index_t>(in,
altdb,
needEntireReverse,
fw,
overrideOffRate,
offRatePlus,
useMm,
useShmem,
mmSweep,
loadNames,
loadSASamp,
loadFtab,
loadRstarts,
true, // load Splice Sites
verbose,
startVerbose,
passMemExc,
sanityCheck,
useHaplotype,
true)
{
this->_in1Str = in + ".5." + gfm_ext;
this->_in2Str = in + ".5." + gfm_ext;
readIntoMemory(
in5,
in6,
mmFile5,
mmFile6,
tidx,
localOffset,
joinedOffset,
switchEndian,
bytesRead,
bytesRead2,
needEntireReverse,
loadSASamp,
loadFtab,
loadRstarts,
false, //justHeader
lineRate,
offRate,
ftabChars,
mmSweep,
loadNames,
startVerbose);
_tidx = tidx;
_localOffset = localOffset;
_joinedOffset = joinedOffset;
// If the offRate has been overridden, reflect that in the
// _eh._offRate field
if(offRatePlus > 0 && this->_overrideOffRate == -1) {
this->_overrideOffRate = this->_gh._offRate + offRatePlus;
}
if(this->_overrideOffRate > this->_gh._offRate) {
this->_gh.setOffRate(this->_overrideOffRate);
assert_eq(this->_overrideOffRate, this->_gh._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>
LocalGFM(
TStr& s,
const EList<full_index_t>& sa,
PathGraph<full_index_t>* pg,
full_index_t tidx,
full_index_t localOffset,
full_index_t joinedOffset,
EList<ALT<full_index_t> >& alts,
index_t local_size,
bool packed,
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) :
GFM<index_t>(packed,
needEntireReverse,
lineRate,
offRate,
ftabChars,
file,
fw,
dcv,
szs,
sztot,
refparams,
seed,
overrideOffRate,
verbose,
passMemExc,
sanityCheck)
{
const GFMParams<index_t>& gh = this->_gh;
assert(gh.repOk());
uint32_t be = this->toBe();
assert(out5.good());
assert(out6.good());
_tidx = tidx;
_localOffset = localOffset;
_joinedOffset = joinedOffset;
writeIndex<full_index_t>(out5, tidx, be);
writeIndex<full_index_t>(out5, localOffset, be);
writeIndex<full_index_t>(out5, joinedOffset, be);
writeIndex<index_t>(out5, gh._len, be); // length of string (and bwt and suffix array)
streampos headerPos = out5.tellp();
writeIndex<index_t>(out5, 0, be); // gbwtLen
writeIndex<index_t>(out5, 0, be); // num of nodes
writeIndex<index_t>(out5, 0, be); // eftabLen
if(gh._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);
}
if(alts.empty()) {
assert(pg == NULL);
buildToDisk(sa, s, out5, out6, headerPos);
} else {
assert(pg != NULL);
// Re-initialize GFM parameters to reflect real number of edges (gbwt string)
this->_gh.init(
this->_gh.len(),
pg->getNumEdges(),
pg->getNumNodes(),
this->_gh.lineRate(),
this->_gh.offRate(),
this->_gh.ftabChars(),
0,
this->_gh.entireReverse());
buildToDisk(*pg, s, out5, out6, headerPos);
}
}
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(
PathGraph<full_index_t>& gbwt,
const TStr& s,
ostream& out1,
ostream& out2,
streampos& headerPos);
template <typename TStr> void buildToDisk(
const EList<full_index_t>& sa,
const TStr& s,
ostream& out1,
ostream& out2,
streampos& headerPos);
// I/O
void readIntoMemory(
FILE *in5,
FILE *in6,
char *mmFile5,
char *mmFile6,
full_index_t& tidx,
full_index_t& localOffset,
full_index_t& joinedOffset,
bool switchEndian,
size_t& bytesRead,
size_t& bytesRead2,
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->_gh._len > 0) {
PARENT_CLASS::sanityCheckAll(reverse);
}
}
bool empty() const { return this->_gh._len == 0; }
public:
full_index_t _tidx;
full_index_t _localOffset;
full_index_t _joinedOffset;
};
/**
* 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 LocalGFM<index_t, full_index_t>::buildToDisk(
PathGraph<full_index_t>& gbwt,
const TStr& s,
ostream& out5,
ostream& out6,
streampos& headerPos)
{
assert_leq(s.length(), std::numeric_limits<index_t>::max());
const GFMParams<index_t>& gh = this->_gh;
assert(gh.repOk());
assert_lt(s.length(), gh.gbwtLen());
assert_eq(s.length(), gh._len);
assert_gt(gh._lineRate, 3);
index_t gbwtLen = gh._gbwtLen;
streampos out5pos = out5.tellp();
out5.seekp(headerPos);
writeIndex<index_t>(out5, gbwtLen, this->toBe());
writeIndex<index_t>(out5, gh._numNodes, this->toBe());
headerPos = out5.tellp();
out5.seekp(out5pos);
index_t ftabLen = gh._ftabLen;
index_t sideSz = gh._sideSz;
index_t gbwtTotSz = gh._gbwtTotSz;
index_t fchr[] = {0, 0, 0, 0, 0};
EList<index_t> ftab(EBWT_CAT);
EList<index_t> zOffs;
// 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};
// # of occurrences of 1 in M arrays
index_t M_occ = 0, M_occSave = 0;
// Location in F that corresponds to 1 in M
index_t F_loc = 0, F_locSave = 0;
try {
VMSG_NL("Allocating ftab, absorbFtab");
ftab.resize(ftabLen);
ftab.fillZero();
} catch(bad_alloc &e) {
cerr << "Out of memory allocating ftab[] or absorbFtab[] "
<< "in LocalGFM::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> gfmSide(EBWT_CAT);
#else
EList<uint8_t> gfmSide(EBWT_CAT);
#endif
try {
// Used to calculate ftab and eftab, but having gfm costs a lot of memory
this->_gfm.init(new uint8_t[gh._gbwtTotLen], gh._gbwtTotLen, true);
#ifdef SIXTY4_FORMAT
gfmSide.resize(sideSz >> 3);
#else
gfmSide.resize(sideSz);
#endif
} catch(bad_alloc &e) {
cerr << "Out of memory allocating ebwtSide[] in "
<< "LocalGFM::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 = true;
int sideCur = 0;
index_t si = 0; // string offset (chars)
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 LocalGFM loop");
ASSERT_ONLY(uint32_t beforeGbwtOff = (uint32_t)out5.tellp());
while(side < gbwtTotSz) {
// Sanity-check our cursor into the side buffer
assert_geq(sideCur, 0);
assert_lt(sideCur, (int)gh._sideGbwtSz);
assert_eq(0, side % sideSz); // 'side' must be on side boundary
gfmSide[sideCur] = 0; // clear
if(sideCur == 0) {
memset(gfmSide.ptr(), 0, gh._sideGbwtSz);
gfmSide[sideCur] = 0; // clear
}
assert_lt(side + sideCur, gbwtTotSz);
// 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 gbwtChar = 0;
int F = 0, M = 0;
full_index_t pos = 0;
bool count = true;
if(si < gbwtLen) {
gbwt.nextRow(gbwtChar, F, M, pos);
// (that might have triggered sa to calc next suf block)
if(gbwtChar == 'Z') {
// 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
gbwtChar = 0; count = false;
#ifndef NDEBUG
if(zOffs.size() > 0) {
assert_gt(si, zOffs.back());
}
#endif
zOffs.push_back(si); // remember GBWT row that corresponds to the 0th suffix
} else {
gbwtChar = asc2dna[gbwtChar];
assert_lt(gbwtChar, 4);
// Update the fchr
fchr[gbwtChar]++;
}
assert_lt(F, 2);
assert_lt(M, 2);
if(M == 1) {
assert_neq(F_loc, numeric_limits<index_t>::max());
F_loc = gbwt.nextFLocation();
#ifndef NDEBUG
if(F_loc > 0) {
assert_gt(F_loc, F_locSave);
}
#endif
}
// Suffix array offset boundary? - update offset array
if(M == 1 && (M_occ & gh._offMask) == M_occ) {
assert_lt((M_occ >> gh._offRate), gh._offsLen);
// Write offsets directly to the secondary output
// stream, thereby avoiding keeping them in memory
writeIndex<index_t>(out6, pos, 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, gbwtLen);
inSA = false;
}
#endif
// 'A' used for padding; important that padding be
// counted in the occ[] array
gbwtChar = 0;
F = M = 0;
}
if(count) occ[gbwtChar]++;
if(M) M_occ++;
// Append BWT char to bwt section of current side
if(fw) {
// Forward bucket: fill from least to most
#ifdef SIXTY4_FORMAT
gfmSide[sideCur] |= ((uint64_t)gbwtChar << (bpi << 1));
if(gbwtChar > 0) assert_gt(gfmSide[sideCur], 0);
assert(false);
cerr << "Not implemented" << endl;
exit(1);
#else
pack_2b_in_8b(gbwtChar, gfmSide[sideCur], bpi);
assert_eq((gfmSide[sideCur] >> (bpi*2)) & 3, gbwtChar);
int F_sideCur = (gh._sideGbwtSz + sideCur) >> 1;
int F_bpi = bpi + ((sideCur & 0x1) << 2); // Can be used as M_bpi as well
pack_1b_in_8b(F, gfmSide[F_sideCur], F_bpi);
assert_eq((gfmSide[F_sideCur] >> F_bpi) & 1, F);
int M_sideCur = F_sideCur + (gh._sideGbwtSz >> 2);
pack_1b_in_8b(M, gfmSide[M_sideCur], F_bpi);
assert_eq((gfmSide[M_sideCur] >> F_bpi) & 1, M);
#endif
} else {
// Backward bucket: fill from most to least
#ifdef SIXTY4_FORMAT
gfmSide[sideCur] |= ((uint64_t)gbwtChar << ((31 - bpi) << 1));
if(gbwtChar > 0) assert_gt(gfmSide[sideCur], 0);
// To be implemented ...
assert(false);
cerr << "Not implemented" << endl;
exit(1);
#else
pack_2b_in_8b(gbwtChar, gfmSide[sideCur], 3-bpi);
assert_eq((gfmSide[sideCur] >> ((3-bpi)*2)) & 3, gbwtChar);
// To be implemented ...
assert(false);
cerr << "Not implemented" << endl;
exit(1);
#endif
}
} // end loop over bit-pairs
assert_eq(0, (occ[0] + occ[1] + occ[2] + occ[3] + zOffs.size()) & 3);
#ifdef SIXTY4_FORMAT
assert_eq(0, si & 31);
#else
assert_eq(0, si & 3);
#endif
sideCur++;
if((sideCur << 1) == (int)gh._sideGbwtSz) {
sideCur = 0;
index_t *uside = reinterpret_cast<index_t*>(gfmSide.ptr());
// Write 'A', 'C', 'G' and 'T' tallies
side += sideSz;
assert_leq(side, gh._gbwtTotSz);
uside[(sideSz / sizeof(index_t))-6] = endianizeIndex(F_locSave, this->toBe());
uside[(sideSz / sizeof(index_t))-5] = endianizeIndex(M_occSave, this->toBe());
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());
F_locSave = F_loc;
M_occSave = M_occ;
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 *)gfmSide.ptr(), sideSz);
//
memcpy(((char*)this->_gfm.get()) + side - sideSz, (const char *)gfmSide.ptr(), sideSz);
}
}
VMSG_NL("Exited LocalGFM loop");
// Assert that our loop counter got incremented right to the end
assert_eq(side, gh._gbwtTotSz);
// Assert that we wrote the expected amount to out5
assert_eq(((uint32_t)out5.tellp() - beforeGbwtOff), gh._gbwtTotSz);
// assert that the last thing we did was write a forward bucket
//
// Write zOffs to primary stream
//
assert_gt(zOffs.size(), 0);
writeIndex<index_t>(out5, zOffs.size(), this->toBe());
for(size_t i = 0; i < zOffs.size(); i++) {
writeIndex<index_t>(out5, zOffs[i], this->toBe());
}
//
// Finish building fchr
//
// Exclusive prefix sum on fchr
for(int i = 1; i < 4; i++) {
fchr[i] += fchr[i-1];
}
assert_lt(fchr[3], gbwtLen);
// Shift everybody up by one
for(int i = 4; i >= 1; i--) {
fchr[i] = fchr[i-1];
}
fchr[0] = 0;
// Write fchr to primary file
for(int i = 0; i < 5; i++) {
writeIndex<index_t>(out5, fchr[i], this->toBe());
}
this->_fchr.init(new index_t[5], 5, true);
memcpy(this->_fchr.get(), fchr, sizeof(index_t) * 5);
// Initialize _zGbwtByteOffs and _zGbwtBpOffs
this->_zOffs = zOffs;
this->postReadInit(gh);
// Build ftab and eftab
EList<pair<index_t, index_t> > tFtab;
tFtab.resizeExact(ftabLen - 1);
for(index_t i = 0; i + 1 < ftabLen; i++) {
index_t q = i;
pair<index_t, index_t> range(0, gh._gbwtLen);
SideLocus<index_t> tloc, bloc;
SideLocus<index_t>::initFromTopBot(range.first, range.second, gh, this->gfm(), tloc, bloc);
index_t j = 0;
for(; j < gh._ftabChars; j++) {
int nt = q & 0x3; q >>= 2;
if(bloc.valid()) {
range = this->mapGLF(tloc, bloc, nt);
} else {
range = this->mapGLF1(range.first, tloc, nt);
}
if(range.first == (index_t)INDEX_MAX || range.first >= range.second) {
break;
}
if(range.first + 1 == range.second) {
tloc.initFromRow(range.first, gh, this->gfm());
bloc.invalidate();
} else {
SideLocus<index_t>::initFromTopBot(range.first, range.second, gh, this->gfm(), tloc, bloc);
}
}
if(range.first >= range.second || j < gh._ftabChars) {
if(i == 0) {
tFtab[i].first = tFtab[i].second = 0;
} else {
tFtab[i].first = tFtab[i].second = tFtab[i-1].second;
}
} else {
tFtab[i].first = range.first;
tFtab[i].second = range.second;
}
#ifndef NDEBUG
if(gbwt.ftab.size() > i) {
assert_eq(tFtab[i].first, gbwt.ftab[i].first);
assert_eq(tFtab[i].second, gbwt.ftab[i].second);
}
#endif
}
// Clear memory
this->_gfm.reset();
this->_fchr.reset();
this->_zOffs.clear();
this->_zGbwtByteOffs.clear();
this->_zGbwtBpOffs.clear();
//
// Finish building ftab and build eftab
//
// Prefix sum on ftable
index_t eftabLen = 0;
for(index_t i = 1; i + 1 < ftabLen; i++) {
if(tFtab[i-1].second != tFtab[i].first) {
eftabLen += 2;
}
}
if(gh._gbwtLen + (eftabLen >> 1) < gh._gbwtLen) {
cerr << "Too many eftab entries: "
<< gh._gbwtLen << " + " << (eftabLen >> 1)
<< " > " << (index_t)INDEX_MAX << endl;
throw 1;
}
EList<index_t> eftab(EBWT_CAT);
try {
eftab.resize(eftabLen);
eftab.fillZero();
} catch(bad_alloc &e) {
cerr << "Out of memory allocating eftab[] "
<< "in LocalGFM::buildToDisk() at " << __FILE__ << ":"
<< __LINE__ << endl;
throw e;
}
index_t eftabCur = 0;
ftab[0] = tFtab[0].first;
ftab[1] = tFtab[0].second;
for(index_t i = 1; i + 1 < ftabLen; i++) {
if(ftab[i] != tFtab[i].first) {
index_t lo = ftab[i];
index_t hi = tFtab[i].first;
assert_lt(eftabCur*2+1, eftabLen);
eftab[eftabCur*2] = lo;
eftab[eftabCur*2+1] = hi;
assert_leq(lo, hi + 4);
ftab[i] = (eftabCur++) ^ (index_t)INDEX_MAX; // insert pointer into eftab
assert_eq(lo, GFM<index_t>::ftabLo(ftab.ptr(), eftab.ptr(), gbwtLen, ftabLen, eftabLen, i));
assert_eq(hi, GFM<index_t>::ftabHi(ftab.ptr(), eftab.ptr(), gbwtLen, ftabLen, eftabLen, i));
}
ftab[i+1] = tFtab[i].second;
}
#ifndef NDEBUG
for(index_t i = 0; i + 1 < ftabLen; i++ ){
assert_eq(tFtab[i].first, GFM<index_t>::ftabHi(ftab.ptr(), eftab.ptr(), gbwtLen, ftabLen, eftabLen, i));
assert_eq(tFtab[i].second, GFM<index_t>::ftabLo(ftab.ptr(), eftab.ptr(), gbwtLen, ftabLen, eftabLen, i+1));
}
#endif
// Write ftab to primary file
for(index_t i = 0; i < ftabLen; i++) {
writeIndex<index_t>(out5, ftab[i], this->toBe());
}
// Write eftab to primary file
out5pos = out5.tellp();
out5.seekp(headerPos);
writeIndex<index_t>(out5, eftabLen, this->toBe());
out5.seekp(out5pos);
for(index_t i = 0; i < eftabLen; i++) {
writeIndex<index_t>(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 LocalGFM::buildToDisk()");
}
/**
* 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 LocalGFM<index_t, full_index_t>::buildToDisk(
const EList<full_index_t>& sa,
const TStr& s,
ostream& out5,
ostream& out6,
streampos& headerPos)
{
assert_leq(s.length(), std::numeric_limits<index_t>::max());
const GFMParams<index_t>& gh = this->_gh;
assert(gh.repOk());
assert(gh.linearFM());
assert_lt(s.length(), gh.gbwtLen());
assert_eq(s.length(), gh._len);
assert_gt(gh._lineRate, 3);
index_t len = gh._len;
index_t gbwtLen = gh._gbwtLen;
assert_eq(len + 1, gbwtLen);
streampos out5pos = out5.tellp();
out5.seekp(headerPos);
writeIndex<index_t>(out5, gbwtLen, this->toBe());
writeIndex<index_t>(out5, gh._numNodes, this->toBe());
headerPos = out5.tellp();
out5.seekp(out5pos);
index_t ftabLen = gh._ftabLen;
index_t sideSz = gh._sideSz;
index_t gbwtTotSz = gh._gbwtTotSz;
index_t fchr[] = {0, 0, 0, 0, 0};
EList<index_t> ftab(EBWT_CAT);
EList<index_t> zOffs;
// 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 LocalGFM::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> gfmSide(EBWT_CAT);
#else
EList<uint8_t> gfmSide(EBWT_CAT);
#endif
try {
#ifdef SIXTY4_FORMAT
gfmSide.resize(sideSz >> 3);
#else
gfmSide.resize(sideSz);
#endif
} catch(bad_alloc &e) {
cerr << "Out of memory allocating gfmSide[] in "
<< "LocalGFM::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 = true;
int sideCur = 0;
// Have we skipped the '$' in the last column yet?
ASSERT_ONLY(bool dollarSkipped = false);
index_t si = 0; // string offset (chars)
ASSERT_ONLY(uint32_t lastSufInt = 0);
ASSERT_ONLY(bool inSA = true); // true iff saI still points inside suffix
// array (as opposed to the padding at the
// end)
// Iterate over packed bwt bytes
VMSG_NL("Entering LocalGFM loop");
ASSERT_ONLY(uint32_t beforeGbwtOff = (uint32_t)out5.tellp());
while(side < gbwtTotSz) {
// Sanity-check our cursor into the side buffer
assert_geq(sideCur, 0);
assert_lt(sideCur, (int)gh._sideGbwtSz);
assert_eq(0, side % sideSz); // 'side' must be on side boundary
gfmSide[sideCur] = 0; // clear
assert_lt(side + sideCur, gbwtTotSz);
// Iterate over bit-pairs in the si'th character of the BWT
#ifdef SIXTY4_FORMAT
for(int bpi = 0; bpi < 32; bpi++, si++) {
#else
for(int bpi = 0; bpi < 4; bpi++, si++) {
#endif
int bwtChar;
bool count = true;
if(si <= len) {
// Still in the SA; extract the bwtChar
index_t saElt = (index_t)sa[si];
// (that might have triggered sa to calc next suf block)
if(saElt == 0) {
// Don't add the '$' 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);
zOffs.push_back(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)gh._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 < gh._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 & gh._offMask) == si) {
assert_lt((si >> gh._offRate), gh._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
gfmSide[sideCur] |= ((uint64_t)bwtChar << (bpi << 1));
if(bwtChar > 0) assert_gt(gfmSide[sideCur], 0);
#else
pack_2b_in_8b(bwtChar, gfmSide[sideCur], bpi);
assert_eq((gfmSide[sideCur] >> (bpi*2)) & 3, bwtChar);
#endif
} else {
// Backward bucket: fill from most to least
#ifdef SIXTY4_FORMAT
gfmSide[sideCur] |= ((uint64_t)bwtChar << ((31 - bpi) << 1));
if(bwtChar > 0) assert_gt(gfmSide[sideCur], 0);
#else
pack_2b_in_8b(bwtChar, gfmSide[sideCur], 3-bpi);
assert_eq((gfmSide[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)gh._sideGbwtSz) {
sideCur = 0;
index_t *uside = reinterpret_cast<index_t*>(gfmSide.ptr());
// Write 'A', 'C', 'G' and 'T' tallies
side += sideSz;
assert_leq(side, gh._gbwtTotSz);
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 *)gfmSide.ptr(), sideSz);