cmd

package
v0.16.0 Latest Latest
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This package is not in the latest version of its module.

 Go to latest Published: Apr 16, 2021 License: MIT Imports: 58 Imported by: 2

Documentation

Index

Constants

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const BIG_SLEEP = 100 * time.Millisecond
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const MICRO_SLEEP = time.Millisecond
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const NAP_SLEEP = 10 * time.Millisecond
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const VERSION = "0.16.0"

VERSION of seqkit

Variables

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var IUPACAminoAcids map[byte]bool
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var IUPACBases map[byte]bool
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var RootCmd = &cobra.Command{
	Use:   "seqkit",
	Short: "a cross-platform and ultrafast toolkit for FASTA/Q file manipulation",
	Long: fmt.Sprintf(`SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Version: %s

Author: Wei Shen <shenwei356@gmail.com>

Documents  : http://bioinf.shenwei.me/seqkit
Source code: https://github.com/shenwei356/seqkit
Please cite: https://doi.org/10.1371/journal.pone.0163962

`, VERSION),
}

RootCmd represents the base command when called without any subcommands

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var Threads = runtime.NumCPU()

Threads for bread.NewBufferedReader()

Functions

func Bam2Bundles added in v0.12.1 

func Bam2Bundles(inBam string, outDir string, minBundle int, nrProcBam int, quiet, silent bool)

func BamToolAccStats added in v0.13.0 

func BamToolAccStats(p *BamToolParams)

func BamToolAlnContext added in v0.13.0 

func BamToolAlnContext(p *BamToolParams)

func BamToolDump added in v0.13.0 

func BamToolDump(p *BamToolParams)

func BamToolbox added in v0.13.0 

func BamToolbox(toolYaml string, inFile string, outFile string, quiet bool, silent bool, threads int)

func BashExec added in v0.11.0 

func BashExec(command string)

BashExec executes a command via bash.

func CountReads added in v0.11.0 

func CountReads(bamReader *bam.Reader, bamWriter *bam.Writer, countFile string, field string, rangeMin, rangeMax float64, printPass bool, printPrim bool, printLog bool, printBins int, binMode string, mapQual int, printFreq int, printDump bool, printDelay int, printPdf string, execBefore, execAfter string, includeIds map[string]bool, excludeIds map[string]bool, printQuiet bool)

CountReads counts total, secondary and supplementary reads mapped to each reference.

func Execute 

func Execute()

Execute adds all child commands to the root command sets flags appropriately. This is called by main.main(). It only needs to happen once to the rootCmd.

func FasLinesToSimpleSeq added in v0.13.0 

func FasLinesToSimpleSeq(lines FqLines) (*simpleSeq, error)

FasLinesToSimpleSeq attempts to construct a valid sequence record from a buffer of parsed lines.

func FileExists added in v0.11.0 

func FileExists(fn string) bool

FileExists checks if a file exists by calling os.Stat.

func FileSize added in v0.11.0 

func FileSize(file string) int

FileSize gets size of a file by calling os.Stat.

func FqLinesToSimpleSeq added in v0.13.0 

func FqLinesToSimpleSeq(lines FqLines, qBase int, gaps bool) (*simpleSeq, error)

FqLinesToSimpleSeq attempts to construct a valid fastq record from a buffer of parsed lines.

func GetSamAcc added in v0.13.0 

func GetSamAcc(r *sam.Record) float64

func GetSamDump added in v0.13.0 

func GetSamDump(field string, r *sam.Record) string

func GetSamEndPos added in v0.13.0 

func GetSamEndPos(r *sam.Record) int

func GetSamHardClipped added in v0.13.0 

func GetSamHardClipped(r *sam.Record) int

func GetSamIsSec added in v0.13.0 

func GetSamIsSec(r *sam.Record) int

func GetSamIsSup added in v0.13.0 

func GetSamIsSup(r *sam.Record) int

func GetSamLeftClip added in v0.13.0 

func GetSamLeftClip(r *sam.Record) int

func GetSamLeftHardClip added in v0.13.0 

func GetSamLeftHardClip(r *sam.Record) int

func GetSamLeftSoftClip added in v0.13.0 

func GetSamLeftSoftClip(r *sam.Record) int

func GetSamLeftSoftClipSeq added in v0.13.0 

func GetSamLeftSoftClipSeq(r *sam.Record) string

func GetSamMapQual added in v0.13.0 

func GetSamMapQual(r *sam.Record) int

func GetSamMapped added in v0.13.0 

func GetSamMapped(r *sam.Record) bool

func GetSamMeanBaseQual added in v0.13.0 

func GetSamMeanBaseQual(r *sam.Record) float64

func GetSamName added in v0.13.0 

func GetSamName(r *sam.Record) string

func GetSamPos added in v0.13.0 

func GetSamPos(r *sam.Record) int

func GetSamReadAln added in v0.13.0 

func GetSamReadAln(r *sam.Record) int

func GetSamReadAlnSeq added in v0.13.0 

func GetSamReadAlnSeq(r *sam.Record) string

func GetSamReadCov added in v0.13.0 

func GetSamReadCov(r *sam.Record) float64

func GetSamReadLen added in v0.13.0 

func GetSamReadLen(r *sam.Record) int

func GetSamReadSeq added in v0.13.0 

func GetSamReadSeq(r *sam.Record) string

func GetSamRef added in v0.13.0 

func GetSamRef(r *sam.Record) string

func GetSamRefAln added in v0.13.0 

func GetSamRefAln(r *sam.Record) int

func GetSamRefCov added in v0.13.0 

func GetSamRefCov(r *sam.Record) float64

func GetSamRefLen added in v0.13.0 

func GetSamRefLen(r *sam.Record) int

func GetSamReverse added in v0.13.0 

func GetSamReverse(r *sam.Record) bool

func GetSamRightClip added in v0.13.0 

func GetSamRightClip(r *sam.Record) int

func GetSamRightHardClip added in v0.13.0 

func GetSamRightHardClip(r *sam.Record) int

func GetSamRightSoftClip added in v0.13.0 

func GetSamRightSoftClip(r *sam.Record) int

func GetSamRightSoftClipSeq added in v0.13.0 

func GetSamRightSoftClipSeq(r *sam.Record) string

func GetSamStrand added in v0.13.0 

func GetSamStrand(r *sam.Record) int

func IsPidAlive added in v0.13.0 

func IsPidAlive(pid int) bool

func LaunchFxWatchers added in v0.13.0 

func LaunchFxWatchers(dirs []string, ctrlChan WatchCtrlChan, re *regexp.Regexp, inFmt, outFmt string, qBase int, allowGaps bool, delta int, timeout string, dropString string, waitPid int, findOnly bool, outw *xopen.Writer)

LaunchFxWatchers launches fastx watcher goroutines on multiple input directories.

func ListTools added in v0.13.0 

func ListTools(p *BamToolParams)

func MaxInts added in v0.11.0 

func MaxInts(s []int) (m int)

MaxInts calculates the maximum of a slice of integers.

func MinInts added in v0.11.0 

func MinInts(s []int) (m int)

MinInts calculates the minimum of a slice of integers.

func NewAnonLinearSeq added in v0.11.0 

func NewAnonLinearSeq(s string) *linear.Seq

NewAnonLinearSeq makes a new anonymous linear.Seq.

func NewBamReader added in v0.11.0 

func NewBamReader(bamFile string, nrProc int) *bam.Reader

NewBamReader creates a new BAM reader from file.

func NewBamReaderChan added in v0.13.0 

func NewBamReaderChan(inFile string, cp int, buff int, threads int) (chan *sam.Record, *bam.Reader)

func NewBamSinkChan added in v0.13.0 

func NewBamSinkChan(cp int) (chan *sam.Record, chan bool)

func NewBamWriterChan added in v0.13.0 

func NewBamWriterChan(inFile string, head *sam.Header, cp int, buff int, threads int) (chan *sam.Record, chan bool)

func NewFxWatcher added in v0.13.0 

func NewFxWatcher(dir string, seqChan chan *simpleSeq, watcherCtrlChanIn, watcherCtrlChanOut WatchCtrlChan, re *regexp.Regexp, inFmt, outFmt string, qBase int, allowGaps bool, minDelta int, dropString string, findOnly bool)

NewFxWatcher streams records from fastx files under a directory.

func NewRawFastaStream added in v0.13.0 

func NewRawFastaStream(name string, inFh *xopen.Reader, inReader *bufio.Reader, seqChan chan *simpleSeq, id string, ctrlChanIn, ctrlChanOut chan SeqStreamCtrl, gaps bool) chan *simpleSeq

NewRawSeqStream initializes a new channel for reading fastq records in a robust way.

func NewRawFastqStream added in v0.13.0 

func NewRawFastqStream(name string, inFh *xopen.Reader, inReader *bufio.Reader, seqChan chan *simpleSeq, qBase int, id string, ctrlChanIn, ctrlChanOut chan SeqStreamCtrl, gaps bool) chan *simpleSeq

NewRawSeqStream initializes a new channel for reading fastq records in a robust way.

func NewRawSeqStreamFromFile added in v0.13.0 

func NewRawSeqStreamFromFile(inFastq string, seqChan chan *simpleSeq, qBase int, format string, allowGaps bool) (chan SeqStreamCtrl, chan SeqStreamCtrl)

NewRawSeqStream initializes a new channel for reading fastq records from a file in a robust way.

func NewSAMRecordFromAln added in v0.11.0 

func NewSAMRecordFromAln(name string, ref *sam.Reference, refStart, refEnd, queryStart, queryEnd int, refAln, queryAln string, strand string, mapQ byte, seq string, qual []byte, aux []sam.Aux) (*sam.Record, error)

NewRecordFromAln builds a new SAM record based on the provided local alignment and its reference/query coordinates.

func ParseByteSize added in v0.12.1 

func ParseByteSize(val string) (int64, error)

ParseByteSize parses byte size from string

func PrintTsvLine added in v0.13.0 

func PrintTsvLine(fields []string) string

func RevCompDNA added in v0.11.0 

func RevCompDNA(s string) string

RevCompDNA reverse complements a DNA sequence string.

func ReverseInt added in v0.11.0 

func ReverseInt(d []int) []int

ReverseInt revsrees a slice of integers.

func SamDumper added in v0.13.0 

func SamDumper(fields []string, r *sam.Record) []string

func SubLocationFlanking added in v0.11.0 

func SubLocationFlanking(length, B, E, begin, end int, strictMode bool) (int, int, bool)

SubLocationFlanking returns location of a flanking range (begin:end, relative to amplicon). B/E: 0-based, location of amplicon. begin/end: 1-based, begin: relative location to 5' end of amplicon, end: relative location to 3' end of amplicon. Returned locations are 1-based. 

            F
-----===============-----
 -3-1                        x/y
                    1 3 5    x/y
     F             R
-----=====-----=====-----
=====                        -5:-1
===                          -5:-3
                    =====     1:5
                      ===     3:5
    =================        -1:1
=========================    -5:5
                              x:-y (invalid)

func SubLocationInner added in v0.11.0 

func SubLocationInner(length, B, E, begin, end int, strictMode bool) (int, int, bool)

SubLocationInner returns location of a range (begin:end, relative to amplicon). B/E: 0-based, location of amplicon. begin/end: 1-based, begin: relative location to 5' end of amplicon, end: relative location to 3' end of amplicon. Returned locations are 1-based. 

            F
-----===============-----
     1 3 5                    x/y
              -5-3-1          x/y
     F             R
-----=====-----=====-----     x:y

     ===============          1:-1
     =======                  1:7
       =====                  3:7
          =====               6:10
          =====             -10:-6
             =====           -7:-3
                             -x:y (invalid)

func SumInts added in v0.11.0 

func SumInts(s []int) (r int)

SumInts calculates the sum of a slice of integers.

func ValidateSeq added in v0.11.0 

func ValidateSeq(seq *simpleSeq, gaps bool) error

ValidateSeq validates simpleSeq objects.

Types

type AlignedSeq added in v0.11.0 

type AlignedSeq struct {
	Ref        *Reference
	Query      *Query
	QueryAln   string
	RefAln     string
	RefStart   int
	RefEnd     int
	QueryStart int
	QueryEnd   int
	Score      float64
	Best       bool
	Detector   *SeqDetector
}

AlignedSeq holds alignment results.

func AlignInfo added in v0.11.0 

func AlignInfo(r *Reference, q *Query, f []feat.Pair) *AlignedSeq

AlignInfo constructs an *AlignedSeq structure based on raw alignment results.

func PairwiseAlignSW added in v0.11.0 

func PairwiseAlignSW(r *Reference, q *Query, alnParams *AlnParams) *AlignedSeq

PairwiseAlignSW performs pairwise local alignment of two sequences using the biogo implementation of the Smith-Waterman algorithm.

func (*AlignedSeq) AlnString added in v0.11.0 

func (a *AlignedSeq) AlnString() string

func (*AlignedSeq) Fields added in v0.11.0 

func (a *AlignedSeq) Fields() []string

Fields returns the fields of AlignedSeq in a defined order.

func (*AlignedSeq) String added in v0.11.0 

func (a *AlignedSeq) String() string

String generates string represenattion of a *AlignedSeq.

type AlnDetails added in v0.13.0 

type AlnDetails struct {
	Match         int
	Mismatch      int
	MatchMismatch int
	Insertion     int
	Deletion      int
	Skip          int
	Len           int
	Acc           float64
	WAcc          float64
}

func GetSamAlnDetails added in v0.13.0 

func GetSamAlnDetails(r *sam.Record) *AlnDetails

type AlnParams added in v0.11.0 

type AlnParams struct {
	Match     int
	Mismatch  int
	GapOpen   int
	GapExtend int
}

AlnParams holds the alignment parameters.

type AmpliconFinder added in v0.11.0 

type AmpliconFinder struct {
	Seq []byte
	F   []byte // Forward primer
	R   []byte // R should be reverse complementary sequence of reverse primer

	MaxMismatch int
	FMindex     *fmi.FMIndex
	// contains filtered or unexported fields
}

AmpliconFinder is a struct for locating amplicon via primer(s).

func NewAmpliconFinder added in v0.11.0 

func NewAmpliconFinder(sequence, forwardPrimer, reversePrimerRC []byte, maxMismatch int) (*AmpliconFinder, error)

NewAmpliconFinder returns a AmpliconFinder struct.

func (*AmpliconFinder) Locate added in v0.11.0 

func (finder *AmpliconFinder) Locate() ([]int, error)

Locate returns location of amplicon. Locations are 1-based, nil returns if not found.

func (*AmpliconFinder) LocateRange added in v0.11.0 

func (finder *AmpliconFinder) LocateRange(begin, end int, flanking bool, strictMode bool) ([]int, error)

LocateRange returns location of the range (begin:end, 1-based).

func (*AmpliconFinder) Location added in v0.13.0 

func (finder *AmpliconFinder) Location() ([]int, error)

Location returns location of amplicon. Locations are 1-based, nil returns if not found.

type BamTool added in v0.13.0 

type BamTool struct {
	Name string
	Desc string
	Use  func(params *BamToolParams)
}

type BamToolParams added in v0.13.0 

type BamToolParams struct {
	Yaml    *syaml.Yaml
	InChan  chan *sam.Record
	OutChan chan *sam.Record
	Quiet   bool
	Silent  bool
	Threads int
	Rank    int
	Shed    Toolshed
}

type BedFeature 

type BedFeature struct {
	Chr    string
	Start  int // 1based
	End    int // end included
	Name   *string
	Strand *string
}

BedFeature is the gff BedFeature struct

func ReadBedFeatures 

func ReadBedFeatures(file string) ([]BedFeature, error)

ReadBedFeatures returns gtf BedFeatures of a file

func ReadBedFilteredFeatures 

func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error)

ReadBedFilteredFeatures returns gtf BedFeatures of selected chrs from file

type ColorCycler added in v0.12.1 

type ColorCycler struct {
	Dummy   bool
	Index   int
	Palette []au.Color
}

ColorCycler is a utilty object to cycle between colors and colorize text.

func NewColorCycler added in v0.12.1 

func NewColorCycler(dummy bool) *ColorCycler

NewColorCycler return a new color cycler object.

func PrettyPrintTsv added in v0.12.1 

func PrettyPrintTsv(cols []string, fields [][]string, width int, color bool) (string, *ColorCycler)

PrettyPrintTsv pretty prints and optionally colorizes a "data frame".

func (*ColorCycler) Colorize added in v0.12.1 

func (p *ColorCycler) Colorize(s string) string

Colorize adds the current ANSI color to the text.

func (*ColorCycler) Fancy added in v0.12.1 

func (p *ColorCycler) Fancy(s string, head bool) string

Fancy colorizes text with normal or header styles.

func (*ColorCycler) Header added in v0.12.1 

func (p *ColorCycler) Header(s string) string

Colorize adds the current ANSI color to the text with a header style.

func (*ColorCycler) Next added in v0.12.1 

func (p *ColorCycler) Next()

Next swiches to the next color.

func (*ColorCycler) WrapWriter added in v0.12.1 

func (p *ColorCycler) WrapWriter(fh *os.File) io.Writer

WrapWriter wraps a file into am go-colorable object if necessary.

type Config 

type Config struct {
	Alphabet               *seq.Alphabet
	ChunkSize              int
	BufferSize             int
	Threads                int
	LineWidth              int
	IDRegexp               string
	IDNCBI                 bool
	OutFile                string
	Quiet                  bool
	AlphabetGuessSeqLength int
	ValidateSeqLength      int
}

Config is the global falgs

type FqLine added in v0.13.0 

type FqLine struct {
	Line     string
	FqlState FqlState
}

type FqLines added in v0.13.0 

type FqLines []FqLine

type FqlState added in v0.13.0 

type FqlState struct {
	Header  bool
	Seq     bool
	Plus    bool
	Qual    bool
	Partial bool
	Invalid bool
}

type FxWatcher added in v0.13.0 

type FxWatcher struct {
	Base string
	Pool *WatchedFxPool
}

type Locus added in v0.12.1 

type Locus struct {
	Chrom     string
	Start     int
	End       int
	Order     int
	NrRecords int
	Size      int
}

type Queries added in v0.11.0 

type Queries []*Query

Queries is a slice of pointers to Query.

type Query added in v0.11.0 

type Query struct {
	Name      string
	Seq       string
	Strand    string
	NullScore float64
}

Query holds information about a query sequence.

type Range added in v0.11.0 

type Range struct {
	Start float64
	End   float64
}

Range defines a half-open slice over a sequence [Start, End).

func (Range) Len added in v0.11.0 

func (r Range) Len() float64

Range returns the length of a range.

type Ranges added in v0.11.0 

type Ranges []Range

Ranges is a slice of ranges.

type ReadCounts added in v0.11.0 

type ReadCounts []*RefCounts

ReadCounts holds read counts for all references.

func NewReadCounts added in v0.11.0 

func NewReadCounts(refs []*sam.Reference) ReadCounts

NewReadCounts initializes a new read count slice.

func (ReadCounts) Sorted added in v0.11.0 

func (c ReadCounts) Sorted() ReadCounts

Sorted created a sorted copy of a read counts slice.

type RecordLoopBuffer added in v0.7.0 

type RecordLoopBuffer struct {
	Size, Capacity int
	Current        *RecordNode
}

RecordLoopBuffer is a loop buffer for FASTA/Q records

func NewRecordLoopBuffer added in v0.7.0 

func NewRecordLoopBuffer(capacity int) (*RecordLoopBuffer, error)

NewRecordLoopBuffer creats new RecordLoopBuffer object with certern capacity

func (*RecordLoopBuffer) Add added in v0.7.0 

func (buf *RecordLoopBuffer) Add(value *fastx.Record)

Add add new RecordNode

func (*RecordLoopBuffer) Backward added in v0.7.0 

func (buf *RecordLoopBuffer) Backward(n int)

Backward moves the current pointer backward N nodes

func (*RecordLoopBuffer) Next added in v0.7.0 

func (buf *RecordLoopBuffer) Next() *RecordNode

Next returns next node

func (*RecordLoopBuffer) Prev added in v0.7.0 

func (buf *RecordLoopBuffer) Prev() *RecordNode

Prev returns previous node

type RecordNode added in v0.7.0 

type RecordNode struct {
	Value *fastx.Record
	// contains filtered or unexported fields
}

RecordNode is the node for double-linked loop list

func (RecordNode) String added in v0.7.0 

func (node RecordNode) String() string

type RefCounts added in v0.11.0 

type RefCounts struct {
	Ref      *sam.Reference
	Count    float64
	SecCount float64
	SupCount float64
}

RefCounts is a structure holding read count information for a given reference.

type RefWithFaidx added in v0.13.0 

type RefWithFaidx struct {
	Fasta   string
	IdxFile string

	Cache bool
	// contains filtered or unexported fields
}

func NewRefWitdFaidx added in v0.13.0 

func NewRefWitdFaidx(file string, cache bool, quiet bool) *RefWithFaidx

func (*RefWithFaidx) IdxSubSeq added in v0.13.0 

func (idx *RefWithFaidx) IdxSubSeq(chrom string, start, end int) (string, error)

type Reference added in v0.11.0 

type Reference struct {
	Name   string
	Seq    string
	Ranges Ranges
}

Reference holds information about a reference sequence along with the target ranges.

type Scorer added in v0.11.0 

type Scorer interface {
	Score() int
}

Scorer is an interface for getting alignment score.

type SeqColorizer added in v0.12.1 

type SeqColorizer struct {
	NucPalette    map[byte]au.Color
	ProtPalette   map[byte]au.Color
	QualPalette   map[byte]au.Color
	QualBgPalette map[byte]au.Color
	Alphabet      string
}

SeqColorizer is a sequence colorizer object.

func NewSeqColorizer added in v0.12.1 

func NewSeqColorizer(alphabet string) *SeqColorizer

NewSeqColorizer return a new sequence colorizer object.

func (*SeqColorizer) Color added in v0.12.1 

func (p *SeqColorizer) Color(seq []byte) []byte

ColorAmino adds ANSI colors to DNA/RNA or protein sequences.

func (*SeqColorizer) ColorAmino added in v0.12.1 

func (p *SeqColorizer) ColorAmino(seq []byte) []byte

ColorAmino adds ANSI colors to protein sequences.

func (*SeqColorizer) ColorNucleic added in v0.12.1 

func (p *SeqColorizer) ColorNucleic(seq []byte) []byte

ColorNucleic adds ANSI colors to DNA/RNA sequences.

func (*SeqColorizer) ColorNucleicWithQuals added in v0.12.1 

func (p *SeqColorizer) ColorNucleicWithQuals(seq []byte, quals []byte) []byte

ColorNucleic adds ANSI colors to DNA/RNA, use quality palette as background.

func (*SeqColorizer) ColorQuals added in v0.12.1 

func (p *SeqColorizer) ColorQuals(quals []byte) []byte

ColorAmino adds grayscale colors to DNA/RNA or protein sequences.

func (*SeqColorizer) ColorWithQuals added in v0.12.1 

func (p *SeqColorizer) ColorWithQuals(seq []byte, quals []byte) []byte

ColorAmino adds ANSI colors to DNA/RNA or protein sequences, use quality palette as background.

func (*SeqColorizer) WrapWriter added in v0.12.1 

func (p *SeqColorizer) WrapWriter(fh *os.File) io.Writer

WrapWriter wraps a file into am go-colorable object if necessary.

type SeqDetector added in v0.11.0 

type SeqDetector struct {
	Queries   Queries
	SearchAll bool
	Stranded  bool
	NullMode  string
	Cutoff    float64
	AlnParams *AlnParams
}

SeqDetector holds paramters for sequence detection.

func NewSeqDetector added in v0.11.0 

func NewSeqDetector(searchAll bool, stranded bool, nullMode string, cutoff float64, alnParams *AlnParams) *SeqDetector

NewSeqDetector initilizes a SeqDetector object.

func (*SeqDetector) AddAnonQueries added in v0.11.0 

func (d *SeqDetector) AddAnonQueries(qrs []string)

AddAnonQueries adds anonymous queries from a list of comma separated strings.

func (*SeqDetector) Detect added in v0.11.0 

func (d *SeqDetector) Detect(r *Reference, rec bool) []*AlignedSeq

Detect performs an optinally recursive alignments of the queries of a given reference sequence.

func (*SeqDetector) LoadQueries added in v0.11.0 

func (d *SeqDetector) LoadQueries(fx string)

LoadQueries loads queries from a fasta file and calculates null scores for each.

type SeqStreamCtrl added in v0.13.0 

type SeqStreamCtrl int
const (
	StreamTry SeqStreamCtrl = iota
	StreamQuit
	StreamEOF
	StreamExited
)

type Toolshed added in v0.13.0 

type Toolshed map[string]BamTool

func NewToolshed added in v0.13.0 

func NewToolshed() Toolshed

func (Toolshed) String added in v0.13.0 

func (s Toolshed) String() string

type TopBuffer added in v0.11.0 

type TopBuffer []topEntry

TopBuffer is a slice of topEntries.

type WatchCtrl added in v0.13.0 

type WatchCtrl int

type WatchCtrlChan added in v0.13.0 

type WatchCtrlChan chan WatchCtrl

type WatchedFx added in v0.13.0 

type WatchedFx struct {
	Name        string
	LastSize    int64
	LastTry     time.Time
	BytesRead   int64
	IsDir       bool
	SeqChan     chan *simpleSeq
	CtrlChanIn  chan SeqStreamCtrl
	CtrlChanOut chan SeqStreamCtrl
}

type WatchedFxPool added in v0.13.0 

type WatchedFxPool struct {
	Map *sync.Map
}

func (*WatchedFxPool) Delete added in v0.13.0 

func (m *WatchedFxPool) Delete(k string)

func (*WatchedFxPool) Get added in v0.13.0 

func (m *WatchedFxPool) Get(k string) *WatchedFx

func (*WatchedFxPool) Insert added in v0.13.0 

func (m *WatchedFxPool) Insert(k string, v *WatchedFx)

func (*WatchedFxPool) IsEmpty added in v0.13.0 

func (m *WatchedFxPool) IsEmpty() bool

func (*WatchedFxPool) Range added in v0.13.0 

func (m *WatchedFxPool) Range(f func(key, value interface{}) bool)

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