bool OperationList::waitFor(bool interruptible)
{
bool rval = true;
if(mLocking)
{
mLock.lock();
}
// copy operations to wait for
OpList opList = mOperations;
if(mLocking)
{
mLock.unlock();
}
// wait for operations
OpList::iterator end = opList.end();
for(OpList::iterator i = opList.begin(); i != end; ++i)
{
rval = (*i)->waitFor(interruptible);
// break out if interruptible and interrupted
if(interruptible && !rval)
{
break;
}
}
return rval;
}
void Scaffold::merge(const Scaffold& lhs,
const Scaffold& rhs,
Scaffold& merged,
bool introns_overwrite_matches)
{
OpList ops;
assert (merged.ref_id() == 0);
assert (lhs.ref_id() == rhs.ref_id());
ops.insert(ops.end(), lhs._augmented_ops.begin(), lhs._augmented_ops.end());
ops.insert(ops.end(), rhs._augmented_ops.begin(), rhs._augmented_ops.end());
sort(ops.begin(), ops.end(), AugmentedCuffOp::g_left_lt);
AugmentedCuffOp::merge_ops(ops, merged._augmented_ops, introns_overwrite_matches);
assert (ops.empty() || !(merged._augmented_ops.empty()));
merged._ref_id = lhs.ref_id();
merged._mates_in_scaff.insert(merged._mates_in_scaff.end(),
lhs._mates_in_scaff.begin(),
lhs._mates_in_scaff.end());
merged._mates_in_scaff.insert(merged._mates_in_scaff.end(),
rhs._mates_in_scaff.begin(),
rhs._mates_in_scaff.end());
sort(merged._mates_in_scaff.begin(),
merged._mates_in_scaff.end());
vector<const MateHit*>::iterator new_end = unique(merged._mates_in_scaff.begin(),
merged._mates_in_scaff.end());
merged._mates_in_scaff.erase(new_end, merged._mates_in_scaff.end());
int r_check = merged.left();
for (size_t i = 0; i < merged._augmented_ops.size(); ++i)
r_check += merged._augmented_ops[i].genomic_length;
assert(r_check == merged.right());
if (lhs.strand() != CUFF_STRAND_UNKNOWN)
merged._strand = lhs.strand();
if (rhs.strand() != CUFF_STRAND_UNKNOWN)
merged._strand = rhs.strand();
merged._has_intron = has_intron(merged);
assert(merged._strand != CUFF_STRAND_UNKNOWN || !merged.has_intron() );
assert(!merged.is_ref());
if (library_type == "transfrags")
{
double avg_fpkm = lhs.fpkm() + rhs.fpkm();
avg_fpkm /= 2;
merged.fpkm(avg_fpkm);
}
}
void Scaffold::merge(const vector<Scaffold>& s,
Scaffold& merged,
bool introns_overwrite_matches)
{
OpList ops;
CuffStrand strand = CUFF_STRAND_UNKNOWN;
for (size_t i = 0; i < s.size(); ++i)
{
ops.insert(ops.end(), s[i]._augmented_ops.begin(), s[i]._augmented_ops.end());
merged._mates_in_scaff.insert(merged._mates_in_scaff.end(),
s[i]._mates_in_scaff.begin(),
s[i]._mates_in_scaff.end());
if (s[i].strand() != CUFF_STRAND_UNKNOWN)
{
//assert (strand == CUFF_STRAND_UNKNOWN || strand == s[i].strand());
strand = s[i].strand();
}
}
sort(merged._mates_in_scaff.begin(),merged._mates_in_scaff.end());
vector<const MateHit*>::iterator new_end = unique(merged._mates_in_scaff.begin(),
merged._mates_in_scaff.end());
merged._mates_in_scaff.erase(new_end, merged._mates_in_scaff.end());
sort(ops.begin(), ops.end(), AugmentedCuffOp::g_left_lt);
//merged._contigs.push_back(CuffAlign(ops.front().g_left(), vector<CuffOp>()));
if (ops.empty())
return;
AugmentedCuffOp::merge_ops(ops, merged._augmented_ops, introns_overwrite_matches);
//assert (ops.empty() || !(merged._augmented_ops.empty()));
#ifdef DEBUG
if (merged._augmented_ops.empty() ||
merged._augmented_ops.front().opcode != CUFF_MATCH ||
merged._augmented_ops.back().opcode != CUFF_MATCH)
{
AugmentedCuffOp::merge_ops(ops, merged._augmented_ops, introns_overwrite_matches);
}
#endif
merged._ref_id = s.front().ref_id();
merged._strand = strand;
int r_check = merged.left();
for (size_t i = 0; i < merged._augmented_ops.size(); ++i)
r_check += merged._augmented_ops[i].genomic_length;
#ifdef DEBUG
if (r_check != merged.right())
{
AugmentedCuffOp::merge_ops(ops, merged._augmented_ops, introns_overwrite_matches);
}
#endif
assert (r_check == merged.right());
merged._has_intron = has_intron(merged);
assert(merged._strand != CUFF_STRAND_UNKNOWN || !merged.has_strand_support());
if (library_type == "transfrags")
{
double avg_fpkm = 0.0;
BOOST_FOREACH (const Scaffold& sc, s)
{
avg_fpkm += sc.fpkm();
}
avg_fpkm /= s.size();
merged.fpkm(avg_fpkm);
}
