/**
* Report a maxed-out read.
*/
void VerboseHitSink::reportMaxed(
vector<Hit>& hs,
size_t threadId,
PatternSourcePerThread& p)
{
HitSink::reportMaxed(hs, threadId, p);
if(sampleMax_) {
RandomSource rand;
rand.init(p.bufa().seed);
assert_gt(hs.size(), 0);
bool paired = hs.front().mate > 0;
size_t num = 1;
if(paired) {
num = 0;
int bestStratum = 999;
for(size_t i = 0; i < hs.size()-1; i += 2) {
int strat = min(hs[i].stratum, hs[i+1].stratum);
if(strat < bestStratum) {
bestStratum = strat;
num = 1;
} else if(strat == bestStratum) {
num++;
}
}
assert_leq(num, hs.size());
uint32_t r = rand.nextU32() % num;
num = 0;
for(size_t i = 0; i < hs.size()-1; i += 2) {
int strat = min(hs[i].stratum, hs[i+1].stratum);
if(strat == bestStratum) {
if(num == r) {
hs[i].oms = hs[i+1].oms = (uint32_t)(hs.size()/2);
reportHits(NULL, &hs, i, i+2, threadId, 0, 0, true, p.rdid());
break;
}
num++;
}
}
assert_eq(num, r);
} else {
for(size_t i = 1; i < hs.size(); i++) {
assert_geq(hs[i].stratum, hs[i-1].stratum);
if(hs[i].stratum == hs[i-1].stratum) num++;
else break;
}
assert_leq(num, hs.size());
uint32_t r = rand.nextU32() % num;
Hit& h = hs[r];
h.oms = (uint32_t)hs.size();
reportHits(&h, NULL, 0, 1, threadId, 0, 0, true, p.rdid());
}
}
}
/**
* Report maxed-out read; if sampleMax_ is set, then report 1 alignment
* at random.
*/
void SAMHitSink::reportMaxed(vector<Hit>& hs, PatternSourcePerThread& p) {
if(sampleMax_) {
HitSink::reportMaxed(hs, p);
RandomSource rand;
rand.init(p.bufa().seed);
assert_gt(hs.size(), 0);
bool paired = hs.front().mate > 0;
size_t num = 1;
if(paired) {
num = 0;
int bestStratum = 999;
for(size_t i = 0; i < hs.size()-1; i += 2) {
int strat = min(hs[i].stratum, hs[i+1].stratum);
if(strat < bestStratum) {
bestStratum = strat;
num = 1;
} else if(strat == bestStratum) {
num++;
}
}
assert_leq(num, hs.size());
uint32_t r = rand.nextU32() % num;
num = 0;
for(size_t i = 0; i < hs.size()-1; i += 2) {
int strat = min(hs[i].stratum, hs[i+1].stratum);
if(strat == bestStratum) {
if(num == r) {
reportSamHits(hs, i, i+2, 0, hs.size()/2+1);
break;
}
num++;
}
}
assert_eq(num, r);
} else {
for(size_t i = 1; i < hs.size(); i++) {
assert_geq(hs[i].stratum, hs[i-1].stratum);
if(hs[i].stratum == hs[i-1].stratum) num++;
else break;
}
assert_leq(num, hs.size());
uint32_t r = rand.nextU32() % num;
reportSamHit(hs[r], /*MAPQ*/0, /*XM:I*/hs.size()+1);
}
} else {
reportUnOrMax(p, &hs, false);
}
}
/**
* Called by startThread when a new search thread is initialized. Actually do alignment.
*/
void work() {
Read r;
HitSet hitset;
AlignResult res;
RandomSource rnd;
int64_t ltotHits = 0, lalReads = 0, lunalReads = 0, lmaxReads = 0;
int64_t ltotSeedHits = 0, lmaxSeedHits = 0;
int64_t lunsampled = 0;
int64_t skipped = 0;
while(rs_->next(r)) {
assert(r.repOk());
if(skipped < readskip) {
skipped++;
continue;
}
rnd.init(randseed ^ r.rand.nextU32());
// If sampleRate < 1.0f, apply sampling odds to this read;
// if it isn't chosen, skip it.
if(sampleRate < 1.0f && rnd.nextDouble() >= sampleRate) {
// Not chosen
lunsampled++;
continue;
}
r.color = /*r.hitset.color =*/ color;
// If the number of unskipped reads exceeds the readmax
// ceiling, break out of the loop. Note that there's a
// minor race condition here.
if(nreads.value() + 1 > readmax) {
if(verbose) {
cout << "Stopping because readmax " << readmax
<< " was exceeded" << endl;
}
break;
}
// Trim as requested by the user. Could do something more
// sophisticated here.
r.trim3(trim3);
r.trim5(trim5);
//r.initHitset();
hitset.reset();
nreads++;
// The read must be at least as long as the mer length that
// was used when building the index.
if(r.seq.length() < (size_t)ap.iSeedLen) {
if(!quiet) {
cerr << "Warning: Skipping read " << r.name
<< " because length " << r.seq.length()
<< " was less than indexable seed length "
<< ap.iSeedLen << endl;
}
os_->printUnalignedRead(r, r.seq, r.qual, FILTER_TOO_SHORT_FOR_INDEX);
continue;
}
// The read must be at least as long as the mer length that
// was used when building the index.
size_t clen = r.seq.length();
if(ap.minLen != -1 && clen < (size_t)ap.adjMinLen) {
if(!quiet) {
cerr << "Warning: Skipping read " << r.name
<< " because length " << clen
<< " was such that alignment length would be less "
<< "than --minlen: " << ap.minLen << endl;
}
os_->printUnalignedRead(r, r.seq, r.qual, FILTER_TOO_SHORT_FOR_MINLEN_PARAMS);
continue;
}
// The read is trimmed and has passed all filters. Next we
// align it.
if(verbose) cout << " aligning read: " << r << endl;
if(!ind_->empty()) {
res.clear(); // clear the alignment results structure
//assert(iformat == INPUT_CHAININ || r.hitset.maxedStratum == -1);
ind_->query(r, *refs_, rmap_, amap_, hitset, *os_, res, ap, true, rnd, tid_);
// Update per-thread counters
if(res.hits > 0) {
lalReads++;
ltotHits += res.hits;
} else if(res.maxed) lmaxReads++;
else lunalReads++;
ltotSeedHits += res.seedHits;
lmaxSeedHits = max<int64_t>(lmaxSeedHits, res.seedHits);
if(res.bail) {
// The aligner signaled that we should bail at this
// point.
throw 1;
}
} else {
// If the index is empty, there can't possibly be any
// hits. TODO: this seems like something that should
// cause an error early on.
hitset.reportUpTo(r, *os_, ap.khits, *refs_, rmap_, false, amap_);
}
if((nreads.value()+1) % updateEvery == 0) {
// Fold per-thread counters into global counters
unalReads += lunalReads;
alReads += lalReads;
maxReads += lmaxReads;
maxSeedHits.max(lmaxSeedHits);
totSeedHits += ltotSeedHits;
totAls += ltotHits;
totUnsampled += lunsampled;
lunalReads = 0;
lalReads = 0;
lmaxReads = 0;
ltotSeedHits = 0;
ltotHits = 0;
lunsampled = 0;
}
}
// Update global counters in synchronized fashion
unalReads += lunalReads;
alReads += lalReads;
maxReads += lmaxReads;
maxSeedHits.max(lmaxSeedHits);
totSeedHits += ltotSeedHits;
totAls += ltotHits;
totUnsampled += lunsampled;
}
