atacdemultiplexutils

Oct 2, 2020

Changes in this version

+ func LoadPeaksAndTrimandReturnOrientation(fname Filename, orientationColID int) (nbPeaks int, orientationDict map[uint]string)

Aug 13, 2020

Changes in this version

+ type Reader interface

+ Read func([]byte) (i int, err error)

+ func ReturnFileReader(fname string) (reader Reader)

Aug 4, 2020

Changes in this version

+ func ReturnReaderForSamfile(fname Filename) (*sam.Reader, *os.File)

Jul 21, 2020

Changes in this version

+ var PEAKSCOREDICT map[Peak]float64

Jul 2, 2020

Changes in this version

+ func CheckIfPeakPosIsMutltipleOf3(peakPos []int) (numberOfPeaks int)

type Peak

+ func (peak *Peak) StringToPeakWithPosAndStart(str string, refPosList []int, start int)

Jun 24, 2020

Changes in this version

+ func TryExceCmd(cmd string) error

Jun 18, 2020

Changes in this version

+ func AssertIfFileExists(filename string)

+ func CheckIfFileExists(filename string) bool

+ func CheckIfFolderExists(foldername string) bool

+ func ExceCmdReturnOutput(cmd string) string

Jun 11, 2020

Changes in this version

+ func LoadPeaksDictCustom(fname Filename, sep string, peakPos [3]int) (peakiddict map[string]uint)

Apr 10, 2020

Changes in this version

+ type SymbolType struct

+ SymbolPos []int

+ SymbolStr string

Apr 8, 2020

Changes in this version

+ func MaxIntList(intlist []int) (max int)

Mar 9, 2020

Changes in this version

type Peak

+ func (peak *Peak) StringToPeakWithPos(str string, refPos [3]int)

Mar 4, 2020

Changes in this version

+ func CreatePeakIntervalTreeCustom(peakPos [3]int, sep string)

+ func LoadPeaksCustom(fname Filename, sep string, peakPos [3]int) int

Mar 3, 2020

Changes in this version

+ func LoadPeaksCustomSeparator(fname Filename, sep string) int

+ func LoadRefCustomFileWithSymbol(peaksymbolfile Filename, sep string)

Feb 28, 2020

Changes in this version

+ func LoadPeaksDict(fname Filename) (peakiddict map[string]uint)

type Peak

+ End int

+ Slice [3]string

+ Start int

+ func (peak *Peak) Chr() (chr string)

+ func (peak *Peak) SplitToPeak(split []string)

+ type PeakIntervalTreeObject struct

+ Chrintervaldict map[string]*interval.IntTree

+ Intervalmapping map[uintptr]string

+ Peakiddict *map[string]uint

+ func CreatePeakIntervalTreeObject(peakiddict map[string]uint) (intervalObject PeakIntervalTreeObject)

+ func CreatePeakIntervalTreeObjectFromFile(bedfile Filename) (intervalObject PeakIntervalTreeObject)

Feb 20, 2020

Changes in this version

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

Jan 24, 2020

Changes in this version

type Peak

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

Jan 24, 2020

Changes in this version

+ var PEAKSYMBOLDICT map[Peak]string

+ func LoadRefBedFileWithSymbol(peaksymbolfile Filename)

+ func LoadSymbolFile(peaksymbolfile, peakfile Filename)

+ type Peak [3]string

+ func (peak *Peak) StringToPeak(str string)

+ func (peak *Peak) StringToPeakNoCheck(str string)

Dec 16, 2019

Changes in this version

+ func LoadCellDictsFromBedFileToIndex(fname Filename) map[string]int

+ func LoadPeaksAndTrim(fname Filename) int

Nov 25, 2019

Changes in this version

+ const BUFFERSIZE

+ var CHRINTERVALDICT map[string]*interval.IntTree

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

+ var INTERVALMAPPING map[uintptr]string

+ var PEAKIDDICT map[string]uint

+ func Check(err error)

+ func CloseFile(file closer)

+ func CountNbLines(filename string) int

+ func CreatePeakIntervalTree()

+ func ExceCmd(cmd string)

+ func InitIntervalDictsThreading(threadnb int)

+ func LoadCellDictsToIndex(fname Filename) map[string]int

+ func LoadCellIDDict(fname string) map[string]bool

+ func LoadPeaks(fname Filename)

+ func LoadPeaksSubset(fname Filename, firstPeak, lastPeak int)

+ func ReturnReader(fname string, startingLine int) (*bufio.Scanner, *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 string, separator string, outfname string, ignoreSortingCategory bool, ...)

+ type ArrayFlags []string

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

+ func (i *ArrayFlags) String() string

+ type Filename string

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

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

+ func (i *Filename) String() string

+ type IntInterval struct

+ End int

+ Payload interface{}

+ Start int

+ UID uintptr

+ 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 struct

+ Key string

+ Value int

+ type PairList []Pair

+ 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)