A C++ header library implementing an interval and interval set.
The library implements an Interval class and an IntervalSet class. Intervals provide basic set and arithmetic functions, functions for converting position relative and absolute to the interval and a function to get the subsequence covered by the interval. The subsequence functionpermits any type that implements operator+ between the iterator and the start/stop types.
Intervals have been templated to allow the start and stop types to be any type that behaves like a number. If using a class, then comparator, arithmetic and shift operators must be implemented. The shift operators must return integers.
The IntervalSet has been implemented to provide fast lookup of intervals using interval binning. The get function will
return all intervals in the set that overlap the query.
Overlapping intervals.
Interval<int> A(0, 2);
Interval<int> B(1, 3);
Interval<int> C(2, 4);
A.overlaps(B); // true
A.overlaps(C); // false
B.overlaps(C); // trueCustom position types.
class GenomicPosition {
public:
const std::string chromosome;
const int position;
bool operator<(const GenomicPosition &that) const;
bool operator==(const GenomicPosition &that) const;
GenomicPosition operator+(const GenomicPosition &that) const;
GenomicPosition operator-(const GenomicPosition &that) const;
GenomicPosition operator*(const GenomicPosition &that) const;
GenomicPosition operator/(const GenomicPosition &that) const;
int operator<<(int amount) const;
int operator>>(int amount) const;
}
Interval<GenomicPosition> A{{"chr1", 0}, {"chr1", 100000}};
Interval<GenomicPosition> B{{"chr1", 50000}, {"chr1", 150000}};
A.overlaps(B); // trueThe get_subsequence function.
Interval<int> interval{3, 6};
interval.get_subsequence<std::string>("abcdefghij"); // "def"
interval.get_subsequence<std::vector<int>>({0, 1, 2, 3, 4, 5, 6, 7, 8, 9}); // {3, 4, 5}The interval set.
IntervalSet<int> set;
set.add(Interval<int>{0, 10});
set.add(Interval<int>{2, 12});
set.add(Interval<int>{4, 14});
set.add(Interval<int>{6, 16});
set.add(Interval<int>{8, 18});
set.add(Interval<int>{10, 20});
std::vector<Interval<int>> intervals = set.get(8, 11); // get all intervals
std::vector<Interval<int>> intervals = set.get(14, 18); // get intervals [6, 16), [8, 18), [10, 20)
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