/**
* 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);
}
}
/**
* Report either an unaligned read or a read that exceeded the -m
* ceiling. We output placeholders for most of the fields in this
* case.
*/
void SAMHitSink::reportUnOrMax(PatternSourcePerThread& p,
vector<Hit>* hs,
bool un) // lower bound on number of other hits
{
if(un) HitSink::reportUnaligned(p);
else HitSink::reportMaxed(*hs, p);
ostringstream ss;
bool paired = !p.bufb().empty();
assert(paired || p.bufa().mate == 0);
assert(!paired || p.bufa().mate > 0);
assert(un || hs->size() > 0);
assert(!un || hs == NULL || hs->size() == 0);
size_t hssz = 0;
if(hs != NULL) hssz = hs->size();
if(paired) {
// truncate final 2 chars
for(int i = 0; i < (int)seqan::length(p.bufa().name)-2; i++) {
if(!noQnameTrunc_ && isspace((int)p.bufa().name[i])) break;
ss << p.bufa().name[i];
}
} else {
for(int i = 0; i < (int)seqan::length(p.bufa().name); i++) {
if(!noQnameTrunc_ && isspace((int)p.bufa().name[i])) break;
ss << p.bufa().name[i];
}
}
ss << "\t"
<< (SAM_FLAG_UNMAPPED | (paired ? (SAM_FLAG_PAIRED | SAM_FLAG_FIRST_IN_PAIR | SAM_FLAG_MATE_UNMAPPED) : 0)) << "\t*"
<< "\t0\t0\t*\t*\t0\t0\t"
<< p.bufa().patFw << "\t" << p.bufa().qual << "\tXM:i:"
<< (paired ? (hssz+1)/2 : hssz);
// Add optional fields reporting the primer base and the downstream color,
// which, if they were present, were clipped when the read was read in
if(p.bufa().color && gReportColorPrimer) {
if(p.bufa().primer != '?') {
ss << "\tZP:Z:" << p.bufa().primer;
assert(isprint(p.bufa().primer));
}
if(p.bufa().trimc != '?') {
ss << "\tZp:Z:" << p.bufa().trimc;
assert(isprint(p.bufa().trimc));
}
}
ss << endl;
if(paired) {
// truncate final 2 chars
for(int i = 0; i < (int)seqan::length(p.bufb().name)-2; i++) {
ss << p.bufb().name[i];
}
ss << "\t"
<< (SAM_FLAG_UNMAPPED | (paired ? (SAM_FLAG_PAIRED | SAM_FLAG_SECOND_IN_PAIR | SAM_FLAG_MATE_UNMAPPED) : 0)) << "\t*"
<< "\t0\t0\t*\t*\t0\t0\t"
<< p.bufb().patFw << "\t" << p.bufb().qual << "\tXM:i:"
<< (hssz+1)/2;
// Add optional fields reporting the primer base and the downstream color,
// which, if they were present, were clipped when the read was read in
if(p.bufb().color && gReportColorPrimer) {
if(p.bufb().primer != '?') {
ss << "\tZP:Z:" << p.bufb().primer;
assert(isprint(p.bufb().primer));
}
if(p.bufb().trimc != '?') {
ss << "\tZp:Z:" << p.bufb().trimc;
assert(isprint(p.bufb().trimc));
}
}
ss << endl;
}
lock(0);
out(0).writeString(ss.str());
unlock(0);
}
