// Given a SMRT sequence and one of its subreads, make the
// reverse complement of the subread in the coordinate of the
// reverse complement sequence of the SMRT sequence.
// Input:
// smrtRead - a SMRT read
// subreadSequence - a subread of smrtRead
// Output:
// subreadSequenceRC - the reverse complement of the subread
// in the coordinate of the reverse
// complement of the SMRT read.
void MakeSubreadRC(SMRTSequence & subreadSequenceRC,
SMRTSequence & subreadSequence,
SMRTSequence & smrtRead)
{
assert(smrtRead.length >= subreadSequence.length);
// Reverse complement sequence of the subread.
subreadSequence.MakeRC(subreadSequenceRC);
// Update start and end positions of subreadSequenceRC in the
// coordinate of reverse compelement sequence of the SMRT read.
subreadSequenceRC.SubreadStart(smrtRead.length - subreadSequence.SubreadEnd());
subreadSequenceRC.SubreadEnd (smrtRead.length - subreadSequence.SubreadStart());
subreadSequenceRC.zmwData = smrtRead.zmwData;
}
void CreateSMRTSequence(SMRTSequence& smrt, Nucleotide* seq, int holeNumber, int start, int end)
{
int size = end - start;
smrt.seq = new Nucleotide[size];
memcpy(smrt.seq, seq, size * sizeof(Nucleotide));
smrt.length = size;
smrt.deleteOnExit = false;
smrt.HoleNumber(holeNumber);
smrt.SubreadStart(start);
smrt.SubreadEnd(end);
std::stringstream ss;
}
// Given a SMRT sequence and a subread interval, make the subread.
// Input:
// smrtRead - a SMRT sequence
// subreadInterval - a subread interval
// params - mapping parameters
// Output:
// subreadSequence - the constructed subread
void MakeSubreadOfInterval(SMRTSequence & subreadSequence,
SMRTSequence & smrtRead,
ReadInterval & subreadInterval,
MappingParameters & params)
{
int start = subreadInterval.start;
int end = subreadInterval.end;
assert(smrtRead.length >= subreadSequence.length);
smrtRead.MakeSubreadAsMasked(subreadSequence, start, end);
if (!params.preserveReadTitle) {
smrtRead.SetSubreadTitle(subreadSequence,
subreadSequence.SubreadStart(),
subreadSequence.SubreadEnd());
}
else {
subreadSequence.CopyTitle(smrtRead.title);
}
subreadSequence.zmwData = smrtRead.zmwData;
}