GenomicInterval¶
#include <pbbam/GenomicInterval.h>
-
class
PacBio::BAM::
GenomicInterval
¶ The GenomicInterval class represents a genomic interval (reference name and 0-based coordinates).
Constructors & Related Methods
-
GenomicInterval
()¶ Creates an empty genomic interval.
-
GenomicInterval
(std::string name, Position start, Position stop)¶ Creates a genomic interval on sequence with
name
, using range: [start
,stop
)
-
GenomicInterval
(const std::string &zeroBasedRegionString)¶ Creates a genomic interval, using REGION string.
“<ref>:<start>-<stop>” (“chr8:200-600”)
- Note
- The htslib/samtools REGION string expects start positions to be 1-based. However, throughout pbbam (including the rest of this class), we stick to 0-based start coordinates. Thus, while the syntax matches that of samtools, we are using a 0-based start coordinate here.
-
GenomicInterval
(const GenomicInterval &other)¶
-
GenomicInterval
(GenomicInterval &&other)¶
-
GenomicInterval &
operator=
(const GenomicInterval &other)¶
-
GenomicInterval &
operator=
(GenomicInterval &&other)¶
-
~GenomicInterval
()¶
Comparison Operators
-
bool
operator==
(const GenomicInterval &other) const¶ - Return
- true if same id & underlying interval
-
bool
operator!=
(const GenomicInterval &other) const¶ - Return
- true if either ids or underlying intervals differ
Interval Operations
-
bool
CoveredBy
(const GenomicInterval &other) const¶ - Return
- true if same id and underlying Interval::CoveredBy() other.
-
bool
Covers
(const GenomicInterval &other) const¶ - Return
- true if same id and underlying Interval::Covers() other.
-
bool
Intersects
(const GenomicInterval &other) const¶ - Return
- true if same id and underlying Interval::Intersects() other.
-
bool
IsValid
() const¶ - Return
- true if underlying Interval::IsValid(), and id/endpoints are non-negative.
-
size_t
Length
() const¶ - Return
- length of underlying
Attributes
-
std::string
Name
() const¶ - Return
- interval reference name
-
GenomicInterval &
Name
(const std::string &name)¶ Sets this interval’s reference name.
- Return
- reference to this interval
- Parameters
name
:
-
GenomicInterval &
Interval
(const PacBio::BAM::Interval<Position> &interval)¶ Sets this underlying Interval
- Return
- reference to this interval
- Parameters
interval
:
-
GenomicInterval &
Start
(const Position start)¶ Sets this interval’s start coordinate.
- Return
- reference to this interval
- Parameters
start
:
-
GenomicInterval &
Stop
(const Position stop)¶ Sets this interval’s stop coordinate.
- Return
- reference to this interval
- Parameters
stop
:
-