//-----------------------------------------------------------------------------------------------------------
AlignmentIterator ImplAlignmentVector::begin() const
{
return AlignmentIterator( new ImplAlignmentVector_Iterator( mPairs, mRowFrom, mRowFrom, mRowTo ));
}
AlignmentIterator ImplAlignmentVector::end() const
{
return AlignmentIterator( new ImplAlignmentVector_Iterator(mPairs, NO_POS, mRowFrom, mRowTo));
}
inline
AlignmentIterator Reference :: getAlignments ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignments ( ( uint32_t ) categories ) ); }
inline
AlignmentIterator Reference :: getFilteredAlignmentSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getFilteredAlignmentSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); }
inline
AlignmentIterator Reference :: getAlignmentSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentSlice ( start, length, ( uint32_t ) categories ) ); }
inline
AlignmentIterator Reference :: getAlignmentSlice ( int64_t start, uint64_t length ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentSlice ( start, length ) ); }
inline
AlignmentIterator ReadCollection :: getAlignmentRange ( uint64_t first, uint64_t count, Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentRange ( first, count, ( uint32_t ) categories ) ); }
