cgatools::mapping::AlleleSequenceAligner Member List

This is the complete list of members for cgatools::mapping::AlleleSequenceAligner, including all inherited members.

allele_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
alleleLength_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
AlleleSequenceAligner(const reference::CrrFile &reference) (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[inline]
begin_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
chr_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
chrSequence_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
endSequencePosition() const	cgatools::mapping::AlleleSequenceAligner	[inline]
getChrSequence() const (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[inline]
length_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
operator[](int i) const	cgatools::mapping::AlleleSequenceAligner	[inline]
reference_ (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[protected]
setInterval(uint16_t chr, size_t begin, size_t length, const std::string *allele)	cgatools::mapping::AlleleSequenceAligner
startSequencePosition() const (defined in cgatools::mapping::AlleleSequenceAligner)	cgatools::mapping::AlleleSequenceAligner	[inline]