sort

Documentation

Overview

Package sort holds structs and functions for sorting genomic data types

Index

• func GirafExternalMergeSort(girafFile string, nodeIdSortOrder []uint32, linesPerChunk int, outFile string)
• func GoExternalMergeSort[E any](data <-chan E, recordsPerTmpFile int, tmpDir string, less func(a, b E) bool) <-chan E
• type MergeSort
• type MergeSortSingle

Functions

func GirafExternalMergeSort

func GirafExternalMergeSort(girafFile string, nodeIdSortOrder []uint32, linesPerChunk int, outFile string)

Sorts giraf by startposition and startnode given the node order defined in nodeIdSortOrder This was intended to be paired with a list of sorted nodes such as simpleGraph.GetSortOrder() so that the file result would be a topologically sorted giraf file, however this can be used with any given node sort order.

func GoExternalMergeSort

func GoExternalMergeSort[E any](data <-chan E, recordsPerTmpFile int, tmpDir string, less func(a, b E) bool) <-chan E

GoExternalMergeSort inputs generic data records from a channel and a function to compare multiple data records and outputs a channel of sorted data records. This function sorts externally via merge sort and therefore is appropriate for very large amounts of data.

Types

type MergeSort

type MergeSort interface {
	Len() int
	Swap(i, j int)
	Less(i, j int) bool
	Push(x interface{})
	Pop() interface{}
	Write(file string) // Write entire slice to file
}

Interface for generic merge sort of file types.

type MergeSortSingle

type MergeSortSingle interface {
	WriteToFileHandle(io.Writer)            // Write receiver to input file
	NextRealRecord(*fileio.EasyReader) bool // Must skip any comment lines, cannot return nil
	Copy() interface{}                      // Copies value in receiver pointer to the to interface
}