psl

Documentation

Overview

package psl defines the Psl struct containing alignment data as well as functions and methods that operate on the Psl struct

Index

• func Equal(x, y Psl) bool
• func ToString(p *Psl) string
• type Psl
  • func Read(filename string) []Psl
• type PslReader
  • func NewPslReader(filename string) *PslReader

Functions

func Equal

func Equal(x, y Psl) bool

Equal will check two psl structs and compare every single field of data to determine if they are the same.

func ToString

func ToString(p *Psl) string

ToString will print a Psl struct to a human readable string.

Types

type Psl

type Psl struct {
	Match       int
	MisMatch    int
	RepeatMatch int
	Ns          int
	QNumIns     int
	QBaseIns    int
	TNumIns     int
	TBaseIns    int
	Strand      string
	QName       string
	QSize       int
	QStart      int
	QEnd        int
	TName       string
	TSize       int
	TStart      int
	TEnd        int
	BlockCount  int
	BlockSize   []int
	QList       []int
	TList       []int
}

Psl struct declares data fields and types for Psl struct.

func Read

func Read(filename string) []Psl

Read will process a given text file and parse the data fields of each line and return a slice of Psl structs.

type PslReader

type PslReader struct {
	Reader *fileio.ByteReader
	// contains filtered or unexported fields
}

PslReader is a struct that contains a ByteReader with an embedded bufioReader and a 2-D byte slice to reduce memory allocation when reading each line.

func NewPslReader

func NewPslReader(filename string) *PslReader

NewPslReader will open a given text file and return a pointer to a PslReader struct.