atacdemultiplexutils

Documentation

Index

• Constants
• Variables
• func Check(err error)
• func CloseFile(file closer)
• func CountNbLines(filename string) int
• func CreatePeakIntervalTree()
• func ExceCmd(cmd string)
• func InitIntervalDictsThreading(threadnb int)
• func LoadCellDictsFromBedFileToIndex(fname Filename) map[string]int
• func LoadCellDictsToIndex(fname Filename) map[string]int
• func LoadCellIDDict(fname string) map[string]bool
• func LoadPeaks(fname Filename) int
• func LoadPeaksAndTrim(fname Filename) int
• func LoadPeaksSubset(fname Filename, firstPeak, lastPeak int)
• func LoadRefBedFileWithSymbol(peaksymbolfile Filename)
• func LoadSymbolFile(peaksymbolfile, peakfile Filename)
• func ReturnReader(fname string, startingLine int) (*bufio.Scanner, *os.File)
• func ReturnReaderForBamfile(fname string, threadnb int) (*bam.Reader, *os.File)
• func ReturnReaderForBzipfile(fname string, startingLine int) (*bufio.Scanner, *os.File)
• func ReturnReaderForBzipfileOld(fname string, seekPos int) (*bufio.Scanner, *os.File)
• func ReturnReaderForBzipfilePureGo(fname string, startingLine int) (*bufio.Scanner, *os.File)
• func ReturnReaderForGzipfile(fname string, startingLine int) (*bufio.Scanner, *os.File)
• func ReturnWriter(fname string) io.WriteCloser
• func ReturnWriterForBzipfile(fname string) *bzip2.Writer
• func ReturnWriterForGzipFile(fname string) io.WriteCloser
• func SortLogfile(filename Filename, separator string, outfname string, ...)
• type ArrayFlags
  • func (i *ArrayFlags) Set(value string) error
  • func (i *ArrayFlags) String() string
• type Filename
  • func (i *Filename) ReturnReader(startingLine int) (*bufio.Scanner, *os.File)
  • func (i *Filename) Set(filename string) error
  • func (i *Filename) String() string
• type IntInterval
  • func (i IntInterval) ID() uintptr
  • func (i IntInterval) Overlap(b interval.IntRange) bool
  • func (i IntInterval) Range() interval.IntRange
  • func (i IntInterval) String() string
• type Pair
• type PairList
  • func RankByWordCountAndDeleteOldMap(wordFrequencies *map[string]int) PairList
  • func (p PairList) Len() int
  • func (p PairList) Less(i, j int) bool
  • func (p PairList) Swap(i, j int)
• type Peak
  • func (peak *Peak) PeakToString() (peakstr string)
  • func (peak *Peak) StringToPeak(str string)
  • func (peak *Peak) StringToPeakNoCheck(str string)

Constants

const BUFFERSIZE = 1000000

BUFFERSIZE ...

Variables

var CHRINTERVALDICT map[string]*interval.IntTree

CHRINTERVALDICT chr ID <-> interval tree

var CHRINTERVALDICTTHREAD map[int]map[string]*interval.IntTree

CHRINTERVALDICTTHREAD threadNB -> chr ID -> pos

var INTERVALMAPPING map[uintptr]string

INTERVALMAPPING peak ID pos <->pos

var PEAKIDDICT map[string]uint

PEAKIDDICT peak ID<->pos

var PEAKSYMBOLDICT map[Peak]string

PEAKSYMBOLDICT map[peak]symbol

Functions

func Check

func Check(err error)

Check ...

func CloseFile

func CloseFile(file closer)

CloseFile close file checking error

func CountNbLines

func CountNbLines(filename string) int

CountNbLines count nb lines in a file

func CreatePeakIntervalTree

func CreatePeakIntervalTree()

CreatePeakIntervalTree ...

func ExceCmd

func ExceCmd(cmd string)

ExceCmd ...

func InitIntervalDictsThreading

func InitIntervalDictsThreading(threadnb int)

InitIntervalDictsThreading Init interval dict threading map by copying the interval map for each trheads

func LoadCellDictsFromBedFileToIndex

func LoadCellDictsFromBedFileToIndex(fname Filename) map[string]int

LoadCellDictsFromBedFileToIndex create cell ID <-> index dict using a single cell bed file storing unique CELL ID Ex: chr1 15555 15522 CELLID1 chr1 25555 25522 CELLID1 chr1 35555 35522 CELLID1 chr1 15555 15522 CELLID2 chr1 25555 25522 CELLID2

will give map(CELLID1:0, CELLID2:1)

func LoadCellDictsToIndex

func LoadCellDictsToIndex(fname Filename) map[string]int

LoadCellDictsToIndex create cell ID index dict

func LoadCellIDDict

func LoadCellIDDict(fname string) map[string]bool

LoadCellIDDict create cell ID bool dict

func LoadPeaks

func LoadPeaks(fname Filename) int

LoadPeaks load peak file and return peak peak id -> dict

func LoadPeaksAndTrim

func LoadPeaksAndTrim(fname Filename) int

LoadPeaksAndTrim load peak file and return peak peak id trimmed for "chr" -> dict

func LoadPeaksSubset

func LoadPeaksSubset(fname Filename, firstPeak, lastPeak int)

LoadPeaksSubset load peak file but using only a subset of peaks and return peak peak id -> dict

func LoadRefBedFileWithSymbol

func LoadRefBedFileWithSymbol(peaksymbolfile Filename)

LoadRefBedFileWithSymbol peaksymbolfile, peakfile Filename

func LoadSymbolFile

func LoadSymbolFile(peaksymbolfile, peakfile Filename)

LoadSymbolFile peaksymbolfile, peakfile Filename

func ReturnReader

func ReturnReader(fname string, startingLine int) (*bufio.Scanner, *os.File)

ReturnReader ...

func ReturnReaderForBamfile

func ReturnReaderForBamfile(fname string, threadnb int) (*bam.Reader, *os.File)

ReturnReaderForBamfile ...

func ReturnReaderForBzipfile

func ReturnReaderForBzipfile(fname string, startingLine int) (*bufio.Scanner, *os.File)

ReturnReaderForBzipfile ...

func ReturnReaderForBzipfileOld

func ReturnReaderForBzipfileOld(fname string, seekPos int) (*bufio.Scanner, *os.File)

ReturnReaderForBzipfileOld ...

func ReturnReaderForBzipfilePureGo

func ReturnReaderForBzipfilePureGo(fname string, startingLine int) (*bufio.Scanner, *os.File)

ReturnReaderForBzipfilePureGo ...

func ReturnReaderForGzipfile

func ReturnReaderForGzipfile(fname string, startingLine int) (*bufio.Scanner, *os.File)

ReturnReaderForGzipfile ...

func ReturnWriter

func ReturnWriter(fname string) io.WriteCloser

ReturnWriter ...

func ReturnWriterForBzipfile

func ReturnWriterForBzipfile(fname string) *bzip2.Writer

ReturnWriterForBzipfile ...

func ReturnWriterForGzipFile

func ReturnWriterForGzipFile(fname string) io.WriteCloser

ReturnWriterForGzipFile ...

func SortLogfile

func SortLogfile(filename Filename, separator string, outfname string,
	ignoreSortingCategory bool, ignoreError bool)

SortLogfile sort a file according to key value input:

filename string,
separator string,
outfname string,
ignoreSortingCategory bool,
ignoreError bool

Types

type ArrayFlags

type ArrayFlags []string

ArrayFlags ...

func (*ArrayFlags) Set

func (i *ArrayFlags) Set(value string) error

Set ...

func (*ArrayFlags) String

func (i *ArrayFlags) String() string

String ...

type Filename

type Filename string

Filename type used to check if files exists

func (*Filename) ReturnReader

func (i *Filename) ReturnReader(startingLine int) (*bufio.Scanner, *os.File)

ReturnReader Return reader for file

func (*Filename) Set

func (i *Filename) Set(filename string) error

Set ...

func (*Filename) String

func (i *Filename) String() string

type IntInterval

type IntInterval struct {
	Start, End int
	UID        uintptr
	Payload    interface{}
}

IntInterval Integer-specific intervals

func (IntInterval) ID

func (i IntInterval) ID() uintptr

ID Return the ID of Interval

func (IntInterval) Overlap

func (i IntInterval) Overlap(b interval.IntRange) bool

Overlap rule for two Interval

func (IntInterval) Range

func (i IntInterval) Range() interval.IntRange

Range Return the range of Interval

func (IntInterval) String

func (i IntInterval) String() string

String Return the string re[ of Interval

type Pair

type Pair struct {
	Key   string
	Value int
}

Pair ...

type PairList

type PairList []Pair

PairList ...

func RankByWordCountAndDeleteOldMap

func RankByWordCountAndDeleteOldMap(wordFrequencies *map[string]int) PairList

RankByWordCountAndDeleteOldMap ...

func (PairList) Len

func (p PairList) Len() int

Len

func (PairList) Less

func (p PairList) Less(i, j int) bool

func (PairList) Swap

func (p PairList) Swap(i, j int)

type Peak

type Peak [3]string

Peak Descriptor of a peak as string slice

func (*Peak) PeakToString

func (peak *Peak) PeakToString() (peakstr string)

PeakToString Convert Peak to string

func (*Peak) StringToPeak

func (peak *Peak) StringToPeak(str string)

StringToPeak Convert Peak string to peak

func (*Peak) StringToPeakNoCheck

func (peak *Peak) StringToPeakNoCheck(str string)

StringToPeakNoCheck Convert Peak string to peak