/**
* Sanity-check various pieces of the Ebwt
*/
void Ebwt::sanityCheckAll(int reverse) const {
const EbwtParams& eh = this->_eh;
assert(isInMemory());
// Check ftab
for(uint32_t i = 1; i < eh._ftabLen; i++) {
assert_geq(this->ftabHi(i), this->ftabLo(i-1));
assert_geq(this->ftabLo(i), this->ftabHi(i-1));
assert_leq(this->ftabHi(i), eh._bwtLen+1);
}
assert_eq(this->ftabHi(eh._ftabLen-1), eh._bwtLen);
// Check offs
int seenLen = (eh._bwtLen + 31) >> 5;
uint32_t *seen;
try {
seen = new uint32_t[seenLen]; // bitvector marking seen offsets
} catch(bad_alloc& e) {
cerr << "Out of memory allocating seen[] at " << __FILE__ << ":" << __LINE__ << endl;
throw e;
}
memset(seen, 0, 4 * seenLen);
uint32_t offsLen = eh._offsLen;
for(uint32_t i = 0; i < offsLen; i++) {
assert_lt(this->offs()[i], eh._bwtLen);
int w = this->offs()[i] >> 5;
int r = this->offs()[i] & 31;
assert_eq(0, (seen[w] >> r) & 1); // shouldn't have been seen before
seen[w] |= (1 << r);
}
delete[] seen;
// Check nPat
assert_gt(this->_nPat, 0);
// Check plen, flen
for(uint32_t i = 0; i < this->_nPat; i++) {
assert_geq(this->plen()[i], 0);
}
// Check rstarts
if(this->rstarts() != NULL) {
for(uint32_t i = 0; i < this->_nFrag-1; i++) {
assert_gt(this->rstarts()[(i+1)*3], this->rstarts()[i*3]);
if(reverse == REF_READ_REVERSE) {
assert(this->rstarts()[(i*3)+1] >= this->rstarts()[((i+1)*3)+1]);
} else {
assert(this->rstarts()[(i*3)+1] <= this->rstarts()[((i+1)*3)+1]);
}
}
}
// Check ebwt
sanityCheckUpToSide(eh._numSides);
VMSG_NL("Ebwt::sanityCheck passed");
}
/**
* Calculate a vector containing the sizes of all of the patterns in
* all of the given input files, in order. Returns the total size of
* all references combined. Rewinds each istream before returning.
*/
std::pair<size_t, size_t>
fastaRefReadSizes(
EList<FileBuf*>& in,
EList<RefRecord>& recs,
const RefReadInParams& rparms,
BitpairOutFileBuf* bpout,
int& numSeqs)
{
uint32_t unambigTot = 0;
uint32_t bothTot = 0;
RefReadInParams rpcp = rparms;
assert_gt(in.size(), 0);
// For each input istream
for(size_t i = 0; i < in.size(); i++) {
bool first = true;
assert(!in[i]->eof());
// For each pattern in this istream
while(!in[i]->eof()) {
RefRecord rec = fastaRefReadSize(*in[i], rparms, first, bpout);
if((unambigTot + rec.len) < unambigTot) {
cerr << "Error: Reference sequence has more than 2^32-1 characters! Please divide the" << endl
<< "reference into batches or chunks of about 3.6 billion characters or less each" << endl
<< "and index each independently." << endl;
throw 1;
}
// Add the length of this record.
if(rec.first) numSeqs++;
unambigTot += rec.len;
bothTot += rec.len;
bothTot += rec.off;
first = false;
if(rec.len == 0 && rec.off == 0 && !rec.first) continue;
recs.push_back(rec);
}
// Reset the input stream
in[i]->reset();
assert(!in[i]->eof());
#ifndef NDEBUG
// Check that it's really reset
int c = in[i]->get();
assert_eq('>', c);
in[i]->reset();
assert(!in[i]->eof());
#endif
}
assert_geq(bothTot, 0);
assert_geq(unambigTot, 0);
return make_pair(
unambigTot, // total number of unambiguous DNA characters read
bothTot); // total number of DNA characters read, incl. ambiguous ones
}
template <int partition=0> inline ftype pullCapacity(int dim) const {
assert_leq(alpha[dim], -edges[dim]);
assert_geq(alpha[dim], edges[dim]);
// Actually the amount that can be pushed to the other node, so in
// the 1-partition it's
return -edges[dim] + ( (partition == 1) ? 1 : -1) * alpha[dim];
}
inline double TimeTracker::elapsedSeconds() const
{
if(started)
{
clock_t cur_time_diff = paused ? 0 : clock() - start_time;
double r = double(cur_time_diff + offset) / CLOCKS_PER_SEC;
assert_geq(r, 0);
return r;
}
else
{
return 0;
}
}
inline ftype pushCapacity(const node_cptr& src, const node_cptr& dest, int dim, int dir) const {
assert(dest == lattice.neighbor(src, dim, dir));
ftype v;
if(dir == 1) {
v = src->template pushCapacity<partition>(dim);
} else {
v = dest->template pullCapacity<partition>(dim);
}
assert_geq(v, 0);
return v;
}
inline void pushExcess(const node_ptr& src, const node_ptr& dest, const DirDim& dd, ftype amount) {
int direction = dd.direction();
int dim = dd.dimension();
#ifndef NDEBUG
assert(direction == -1 || direction == 1);
assert(dest == lattice.neighbor(src, dim, direction));
assert_equal(src->on(), partition);
assert_equal(dest->on(), partition);
assert_geq(dim, 0);
assert_leq(amount, pushCapacity<partition>(src, dest, dd));
assert_leq(-amount, pushCapacity<partition>(dest, src, dd.reversed()));
assert(direction == 1 || direction == -1);
_debugVerifyNodeReduction(src);
_debugVerifyNodeReduction(dest);
ftype src_pr_excess = src->template excess<partition>();
ftype dest_pr_excess = dest->template excess<partition>();
#endif
src->reduction -= ((partition == 1) ? 1 : -1) * amount;
dest->reduction += ((partition == 1) ? 1 : -1) * amount;
((direction > 0) ? src : dest)
->alpha[dim] += direction * ((partition == 1) ? 1 : -1) * amount;
#ifndef NDEBUG
_debugVerifyNodeReduction(src);
_debugVerifyNodeReduction(dest);
ftype src_af_excess = src->template excess<partition>();
ftype dest_af_excess = dest->template excess<partition>();
assert_equal(src_pr_excess - amount, src_af_excess);
assert_equal(dest_pr_excess + amount, dest_af_excess);
#endif
}
inline ftype pushCapacity(const node_cptr& src, const node_cptr& dest, const DirDim& dd) const {
assert(dest == lattice.neighbor(src, dd));
ftype v;
if(dd.direction() == 1) {
v = src->template pushCapacity<partition>(dd.dimension());
} else {
v = dest->template pullCapacity<partition>(dd.dimension());
}
assert_geq(v, 0);
// cout << "Push capacity from node " << (src - lattice.begin())
// << " to node " << (dest - lattice.begin()) << " is "
// << v << ". " << endl;
return v;
}
static void driver(const string& infile,
vector<string>& infiles,
const string& outfile,
bool reverse = false)
{
vector<FileBuf*> is;
bool bisulfite = false;
RefReadInParams refparams(color, reverse ? reverseType : REF_READ_FORWARD, nsToAs, bisulfite);
assert_gt(infiles.size(), 0);
if(format == CMDLINE) {
// Adapt sequence strings to stringstreams open for input
stringstream *ss = new stringstream();
for(size_t i = 0; i < infiles.size(); i++) {
(*ss) << ">" << i << endl << infiles[i] << endl;
}
FileBuf *fb = new FileBuf(ss);
assert(fb != NULL);
assert(!fb->eof());
assert(fb->get() == '>');
ASSERT_ONLY(fb->reset());
assert(!fb->eof());
is.push_back(fb);
} else {
// Adapt sequence files to ifstreams
for(size_t i = 0; i < infiles.size(); i++) {
FILE *f = fopen(infiles[i].c_str(), "rb");
if (f == NULL) {
cerr << "Error: could not open "<< infiles[i] << endl;
throw 1;
}
FileBuf *fb = new FileBuf(f);
assert(fb != NULL);
assert(!fb->eof());
assert(fb->get() == '>');
ASSERT_ONLY(fb->reset());
assert(!fb->eof());
is.push_back(fb);
}
}
// Vector for the ordered list of "records" comprising the input
// sequences. A record represents a stretch of unambiguous
// characters in one of the input sequences.
vector<RefRecord> szs;
vector<uint32_t> plens;
std::pair<size_t, size_t> sztot;
{
if(verbose) cout << "Reading reference sizes" << endl;
Timer _t(cout, " Time reading reference sizes: ", verbose);
if(!reverse && (writeRef || justRef)) {
// For forward reference, dump it to .3.ebwt and .4.ebwt
// files
string file3 = outfile + ".3." + gEbwt_ext;
string file4 = outfile + ".4." + gEbwt_ext;
// Open output stream for the '.3.ebwt' file which will
// hold the size records.
ofstream fout3(file3.c_str(), ios::binary);
if(!fout3.good()) {
cerr << "Could not open index file for writing: \"" << file3 << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
}
BitpairOutFileBuf bpout(file4.c_str());
// Read in the sizes of all the unambiguous stretches of
// the genome into a vector of RefRecords. The input
// streams are reset once it's done.
writeU<int32_t>(fout3, 1, bigEndian); // endianness sentinel
if(color) {
refparams.color = false;
// Make sure the .3.ebwt and .4.ebwt files contain
// nucleotides; not colors
TIndexOff numSeqs = 0;
fastaRefReadSizes(is, szs, plens, refparams, &bpout, numSeqs);
refparams.color = true;
writeU<TIndexOffU>(fout3, (TIndexOffU)szs.size(), bigEndian); // write # records
for(size_t i = 0; i < szs.size(); i++) {
szs[i].write(fout3, bigEndian);
}
szs.clear();
plens.clear();
// Now read in the colorspace size records; these are
// the ones that were indexed
TIndexOff numSeqs2 = 0;
sztot = fastaRefReadSizes(is, szs, plens, refparams, NULL, numSeqs2);
assert_geq(numSeqs, numSeqs2);
} else {
TIndexOff numSeqs = 0;
sztot = fastaRefReadSizes(is, szs, plens, refparams, &bpout, numSeqs);
writeU<TIndexOffU>(fout3, (TIndexOffU)szs.size(), bigEndian); // write # records
for(size_t i = 0; i < szs.size(); i++) szs[i].write(fout3, bigEndian);
}
if(sztot.first == 0) {
cerr << "Error: No unambiguous stretches of characters in the input. Aborting..." << endl;
throw 1;
}
assert_gt(sztot.first, 0);
assert_gt(sztot.second, 0);
bpout.close();
fout3.close();
#ifndef NDEBUG
if(sanityCheck) {
BitPairReference bpr(
outfile, // ebwt basename
color, // expect color?
true, // sanity check?
&infiles,// files to check against
NULL, // sequences to check against
format == CMDLINE, // whether infiles contains strings
true, // load sequence?
false, // use memory-mapped files
false, // use shared memory
false, // sweep through memory-mapped memory
false, // be talkative
false); // be talkative
}
#endif
} else {
// Read in the sizes of all the unambiguous stretches of the
// genome into a vector of RefRecords
TIndexOff numSeqs = 0;
sztot = fastaRefReadSizes(is, szs, plens, refparams, NULL, numSeqs);
#ifndef NDEBUG
if(refparams.color) {
refparams.color = false;
vector<RefRecord> szs2;
vector<uint32_t> plens2;
TIndexOff numSeqs2 = 0;
fastaRefReadSizes(is, szs2, plens2, refparams, NULL, numSeqs2);
assert_leq(numSeqs, numSeqs2);
// One less color than base
refparams.color = true;
}
#endif
}
}
if(justRef) return;
assert_gt(sztot.first, 0);
assert_gt(sztot.second, 0);
assert_gt(szs.size(), 0);
// Construct Ebwt from input strings and parameters
Ebwt<TStr> ebwt(refparams.color ? 1 : 0,
lineRate,
linesPerSide,
offRate, // suffix-array sampling rate
-1, // ISA sampling rate
ftabChars, // number of chars in initial arrow-pair calc
nthreads,
outfile, // basename for .?.ebwt files
!reverse, // fw
!entireSA, // useBlockwise
bmax, // block size for blockwise SA builder
bmaxMultSqrt, // block size as multiplier of sqrt(len)
bmaxDivN, // block size as divisor of len
noDc? 0 : dcv,// difference-cover period
is, // list of input streams
szs, // list of reference sizes
plens, // list of not-all-gap reference sequence lengths
(TIndexOffU)sztot.first, // total size of all unambiguous ref chars
refparams, // reference read-in parameters
seed, // pseudo-random number generator seed
-1, // override offRate
-1, // override isaRate
verbose, // be talkative
autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically
sanityCheck); // verify results and internal consistency
// Note that the Ebwt is *not* resident in memory at this time. To
// load it into memory, call ebwt.loadIntoMemory()
if(verbose) {
// Print Ebwt's vital stats
ebwt.eh().print(cout);
}
if(sanityCheck) {
// Try restoring the original string (if there were
// multiple texts, what we'll get back is the joined,
// padded string, not a list)
ebwt.loadIntoMemory(
refparams.color ? 1 : 0,
-1,
false,
false);
TStr s2; ebwt.restore(s2);
ebwt.evictFromMemory();
{
TStr joinedss = Ebwt<TStr>::join(
is, // list of input streams
szs, // list of reference sizes
(TIndexOffU)sztot.first, // total size of all unambiguous ref chars
refparams, // reference read-in parameters
seed); // pseudo-random number generator seed
if(refparams.reverse == REF_READ_REVERSE) {
reverseInPlace(joinedss);
}
assert_eq(length(joinedss), length(s2));
assert_eq(joinedss, s2);
}
if(verbose) {
if(length(s2) < 1000) {
cout << "Passed restore check: " << s2 << endl;
} else {
cout << "Passed restore check: (" << length(s2) << " chars)" << endl;
}
}
}
}