ReadEnds(
::libmaus2::bambam::BamAlignment const & p,
::libmaus2::bambam::BamAlignment const & q,
header_type const & header,
bool const copyAlignment = false,
uint64_t const rtagId = 0
)
{
reset();
fillFragPair(p,q,header,*this,rtagId);
if ( copyAlignment )
{
this->p = p.sclone();
this->q = q.sclone();
}
}
ReadEnds(
::libmaus::bambam::BamAlignment const & p,
::libmaus::bambam::BamAlignment const & q,
::libmaus::bambam::BamHeader const & header,
::libmaus::bambam::ReadEnds & RE,
bool const copyAlignment = false
)
{
reset();
fillFragPair(p,q,header,RE);
if ( copyAlignment )
{
this->p = p.sclone();
this->q = q.sclone();
}
}
ReadEnds(
uint8_t const * pD,
uint64_t const pblocksize,
uint8_t const * qD,
uint64_t const qblocksize,
header_type const & header,
bool const copyAlignment = false,
uint64_t const rtagId = 0
)
{
reset();
fillFragPair(pD,pblocksize,qD,qblocksize,header,*this,rtagId);
if ( copyAlignment )
{
BamAlignment::shared_ptr_type palgn(new libmaus2::bambam::BamAlignment);
palgn->copyFrom(pD,pblocksize);
BamAlignment::shared_ptr_type qalgn(new libmaus2::bambam::BamAlignment);
qalgn->copyFrom(qD,qblocksize);
this->p = palgn;
this->q = qalgn;
}
}