chainfile

type Alignment struct {
	RefOffset   int64 `db:"ref_offset"`   // Offset of the aligned block in the reference chromosome from the start of the chain.
	QueryOffset int64 `db:"query_offset"` // Offset of the aligned block in the query chromosome from the start of the chain.
	Size        int64 `db:"size"`         // Size of the aligned block in bases.
}

type Chain struct {
	Score       int64              // Alignment score.
	RefName     types.Chromosome   // Reference chromosome name.
	RefSize     int64              // Size of the reference chromosome.
	RefStrand   string             // Strand in the reference genome ('+' or '-').
	RefStart    int64              // Start position in the reference genome.
	RefEnd      int64              // End position in the reference genome.
	QueryName   types.Chromosome   // Query chromosome name.
	QuerySize   int64              // Size of the query chromosome.
	QueryStrand string             // Strand in the query genome ('+' or '-').
	QueryStart  int64              // Start position in the query genome.
	QueryEnd    int64              // End position in the query genome.
	ID_         int64              // Unique identifier for the chain.
	Alignments  augmentedtree.Tree // Interval tree of alignments.
}

type ChainFile struct {
	// ChainsByChromosome maps a chromosome name to an interval tree of chains.
	ChainsByChromosome map[types.Chromosome]augmentedtree.Tree
	// ChainByID maps a chain ID to a chain.
	ChainByID map[int64]*Chain
}

type Interval struct {
	Start int64
	End   int64
}