GenomicCoordinates

Overview

GenomicCoordinates is a Julia package designed to handle genomic coordinates efficiently. It allows to:

• convert chromosome names to Int for higher performace during comparison and sorting operations
• define genomic intervals
• effeciently find overlaps in two vectors of genomic intervals.

Usage

using GenomicCoordinates

# convert chromosome names to Int
chr2int("chrX")

# define intervals
i1 = GenomicInterval(1,   0, 200)
i2 = GenomicInterval(1, 201, 400)
i3 = GenomicInterval(1, 401, 600)

gene1 = GenomicInterval(1,  50,  70)
gene2 = GenomicInterval(1, 150, 200)
gene3 = GenomicInterval(1, 350, 400)

# find overlapping intervals
GenomicCoordinates.find_intersections([i1, i2, i3], [gene1, gene2])
# [ [1,2], [3], [] ]