Go Language LiftOver (GLO) provides genomic coordinate conversion capabilities in the manner of UCSC's LiftOver tool. It allows for genomic coordinates to be mapped between two reference genome assemblies by utilizing Chain Files to determine the mapping between assemblies.

Installation

GLO does not have any external dependencies beyond Go core packages. To install a copy locally, you can use go get, e.g.

go get github.com/blachlylab/GLO

Use

To use the package, you must first import it into your Go program.

import "github.com/blachlylab/GLO"

The liftover capabilities can then easily by utilized by first initializing the LiftOver struct that tracks the Chain File mappings between assemlbies, then passing the struct requests as needed, e.g.

// Initialize new struct instance
liftover := new(LiftOver)
liftover.Init()

// Load the hg19-to-hg38 chain file
liftover.LoadChainFile("hg19", "hg38", "hg19ToHg38.over.chain")

// Generate a ChainInterval struct that is used to pass in the request. The
// response will also be returned as a set of zero or more ChainIntervals.

target := ChainInterval{Contig: "chrX", Strt: 115149220, End: 115149335}
response := liftover.Lift("hg19", "hg38", &target)}

// The response variable will now contain zero or more ChainIntervals,
// depending on if the specified interval had no equivalent in the 
// target genome, had a unique overlap in the target genome, or was split
// between multiple regions in the target genome.
// Each ChainInterval object will have three relevant attributes:
// .Contig 		The chromosome/contig of the interval (string)
// .Start		The start of the genomic coordinate range (int64)
// .End			The end of the genomic coordinate range (int64)