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Published: Sep 21, 2016 License: GPL-2.0 Imports: 8 Imported by: 0

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Constants

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const (
	EXIT_SUCCESS = 0
	EXIT_FAILURE = 1
)

Variables

This section is empty.

Functions

func ExitWithMessage

func ExitWithMessage(err error)

func PrintIntrons

func PrintIntrons(i *Intron) string

func ReadBam

func ReadBam(file string, cpus int, qualityFilter int, discardSecondary bool) <-chan *sam.Record

Types

type Intron

type Intron struct {
	Chr    string // chromosome
	Start  int    // [ : inclusive / 0 based
	End    int    // [ : exclusive / 1 based
	Strand bool   // true : + , false: -
	Mate   bool   // true : from a mate read, false : from a first read
	Name   string // Name of the read
	Count  []int  // May store several read counts (if several samples for example), nil by default
}

func Introns

func Introns(read *sam.Record, s Stranded) []*Intron

Returns the introns represented by this read (using CIGAR N operator) If any

type Stranded

type Stranded byte
const (
	NONE     Stranded = iota // Not stranded
	STRANDED                 // Stranded Library +/-
	REVERSE                  // Reverse stranded library -/+
)

func Strand

func Strand(s string) Stranded

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