void HashGraph::InsertSequence(const Sequence &seq, uint64 prefix, uint64 mask)
{
if (seq.Size() < kmerLength)
return;
Kmer kmer;
for (int i = 0; i < kmerLength-1; ++i)
kmer.AddRight(seq[i]);
for (int i = kmerLength-1; i < seq.Size(); ++i)
{
kmer.AddRight(seq[i]);
Kmer key = kmer;
Kmer rev_comp = kmer;
rev_comp.ReverseComplement();
if (rev_comp < kmer)
key = rev_comp;
if ((key.Hash() & mask) == prefix)
{
KmerNodeAdapter adp(InsertKmer(kmer), kmer);
if (i >= (int)kmerLength)
{
adp.AddInEdge(3 - seq[i-kmerLength]);
}
if (i+1 < seq.Size())
{
adp.AddOutEdge(seq[i+1]);
}
}
}
}
bool HashGraph::AddEdgesFromSequence(const Sequence &seq)
{
if (seq.Size() < kmerLength)
return false;
bool flag = false;
Kmer kmer;
for (int i = 0; i < kmerLength-1; ++i)
kmer.AddRight(seq[i]);
for (int i = kmerLength-1; i < seq.Size(); ++i)
{
kmer.AddRight(seq[i]);
KmerNodeAdapter adp = GetNodeAdapter(kmer);
if (!adp.IsNull())
{
flag = true;
adp.Increase();
if (i >= (int)kmerLength)
{
adp.AddInEdge(3 - seq[i-kmerLength]);
}
if (i+1 < seq.Size())
{
adp.AddOutEdge(seq[i+1]);
}
}
}
return flag;
}
bool HashGraph::IsValid(const Sequence &seq)
{
Kmer kmer;
for (int i = 0; i < kmerLength-1; ++i)
kmer.AddRight(seq[i]);
for (int i = kmerLength-1; i < seq.Size(); ++i)
{
kmer.AddRight(seq[i]);
if (GetNode(kmer) == NULL)
return false;
}
return true;
}
void HashGraph::AddInternalKmers(const Sequence &seq, int minCount)
{
if (seq.Size() <= kmerLength)
return;
vector<int> v;
int count = 0;
int sum = 0;
Kmer kmer;
for (int i = 0; i < kmerLength-1; ++i)
kmer.AddRight(seq[i]);
for (int i = kmerLength-1; i < seq.Size(); ++i)
{
kmer.AddRight(seq[i]);
KmerNode *node = GetNode(kmer);
if (node != NULL && node->Count() >= (unsigned)minCount)
{
sum += node->Count();
++count;
v.push_back(i);
}
}
if (count > max(seq.Size() - kmerLength*2 + 1, (seq.Size() - kmerLength + 1)/2))
{
Kmer kmer;
for (int i = 0; i < kmerLength-1; ++i)
kmer.AddRight(seq[i]);
for (int i = kmerLength-1; i < seq.Size(); ++i)
{
kmer.AddRight(seq[i]);
if (v.front() <= i && i <= v.back() && GetNode(kmer) == NULL)
{
KmerNodeAdapter adp(InsertKmer(kmer), kmer);
if (i >= (int)kmerLength)
{
adp.AddInEdge(3 - seq[i-kmerLength]);
}
if (i+1 < seq.Size())
{
adp.AddOutEdge(seq[i+1]);
}
}
}
}
}
void AbstractAssembler::ReadBunchOfReads(vector<Read> &reads, int64 expected_num)
{
reads.resize(expected_num);
Sequence seq;
string comment;
int count = 0;
for (int64 i = 0; i < (int64)reads.size(); ++i)
{
if (!read_reader->Read(seq, comment))
{
reads.resize(i);
break;
}
reads[i].Inactivate();
seq.Trim(option.trim);
int from = 0;
int to = 0;
int last = 0;
for (int current = 0; current < seq.Size(); ++current)
{
if (seq[current] == 'N')
{
if (current - last > to - from)
{
from = last;
to = current;
}
last = current + 1;
}
}
if (seq.Size() - last > to - from)
{
from = last;
to = seq.Size();
}
Sequence valid_seq;
seq.GetSubSequence(valid_seq, from, to - from);
seq = valid_seq;
// seq.TrimError();
// seq.ReverseComplement();
// seq.TrimError();
// seq.ReverseComplement();
if (!seq.IsChar())
continue;
++count;
seq.Encode();
reads[i] = seq;
}
printf("reads %d\n", count);
}
int main(int argc, char *argv[])
{
AddParameter("length", &length, INTEGER);
AddParameter("mate", &mate, SIMPLE);
ProcessParameters(argc, argv);
if (argc < 3
|| strcmp(argv[1], "--help") == 0
|| strcmp(argv[1], "-h") == 0)
{
fprintf(stderr, "usage: normReads fa-file norm-fa-file\n");
fprintf(stderr, " [--length l] [--mate]\n");
exit(1);
}
FastAReader reader(argv[1]);
FastAWriter writer(argv[2]);
Sequence seq;
Sequence seq2;
unsigned index = 0;
string comment;
string comment2;
if (mate)
{
while (reader.Read(seq, comment))
{
if (!reader.Read(seq2, comment2))
break;
if (length == 0)
{
writer.Write(seq, comment);
writer.Write(seq2, comment2);
index += 2;
}
else
{
if (seq.Size() >= length && seq2.Size() >= length)
{
seq.Resize(length);
seq2.Resize(length);
writer.Write(seq, comment);
writer.Write(seq2, comment2);
index += 2;
}
}
}
}
else
{
while (reader.Read(seq, comment))
{
if (length == 0)
{
writer.Write(seq, comment);
++index;
}
else
{
if (seq.Size() >= length)
{
seq.Resize(length);
writer.Write(seq, comment);
++index;
}
}
}
}
// fclose(freadFile);
// fclose(ftableFile);
return 0;
}
