/**
* 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);
}
}
