Index

Modules: readfx, readfx/oligoutils, readfx/seqtypes, readfx/sequtils, readfx/writer.

API symbols

`$`:

• readfx: proc `$`(rec: FQRecord): string
• readfx: proc `$`(rec: FQRecordPtr): string

avgQuality:

• sequtils: proc avgQuality(record: FQRecord; offset: int = 33): float
• sequtils: proc avgQuality(quality: string; offset: int = 33): float

Bufio:

• readfx: tuple Bufio

close:

• readfx: proc close[T](f: var Bufio[T]): int
• writer: proc close(w: var FastxWriter)

composition:

• sequtils: proc composition(record: FQRecord): SeqComp

DefaultBufferSize:

• writer: const DefaultBufferSize

DefaultCompressionLevel:

• writer: const DefaultCompressionLevel

DefaultFastaWidth:

• writer: const DefaultFastaWidth

eof:

• readfx: proc eof[T](f: Bufio[T]): bool

fafmt:

• readfx: proc fafmt(rec: FQRecord; width: int = 60): string

FastxDestination:

• writer: object FastxDestination

FastxDestinationKind:

• writer: enum FastxDestinationKind

FastxFormat:

• writer: enum FastxFormat

FastxWriter:

• writer: object FastxWriter

fastxWriter:

• writer: proc fastxWriter(format: FastxFormat; compression: bool = false; destination: FastxDestination = stdoutDestination(); bufferSize: int = DefaultBufferSize; compressionLevel: int = DefaultCompressionLevel; compressionThreads: int = 1; fastaWidth: int = DefaultFastaWidth): FastxWriter

fileDestination:

• writer: proc fileDestination(path: string): FastxDestination

filtPolyX:

• sequtils: proc filtPolyX(read: FQRecord; minLen: int = 10; trackStats: bool = false): FQRecord

findOligoMatches:

• oligoutils: proc findOligoMatches(sequence, primer: string; threshold: float; max_mismatches = 0; min_matches = 6): seq[int]

findPrimerMatches:

• oligoutils: proc findPrimerMatches(sequence, primer: string; threshold: float; max_mismatches = 0; min_matches = 6): seq[seq[int]]

flush:

• writer: proc flush(w: var FastxWriter)

Forward:

• seqtypes: Strand.Forward

FQPair:

• seqtypes: object FQPair

FQPairPtr:

• seqtypes: object FQPairPtr

FQRecord:

• seqtypes: object FQRecord

FQRecordPtr:

• seqtypes: object FQRecordPtr

fxdFile:

• writer: FastxDestinationKind.fxdFile

fxdStdout:

• writer: FastxDestinationKind.fxdStdout

fxfFasta:

• writer: FastxFormat.fxfFasta

fxfFastq:

• writer: FastxFormat.fxfFastq

gcContent:

• sequtils: proc gcContent(record: FQRecord): float
• sequtils: proc gcContent(sequence: string): float

GzFile:

• readfx: type GzFile

index:

• readfx: proc index[S, T](a: var seq[Interval[S, T]]): int

Interval:

• readfx: tuple Interval

kseq_init:

• readfx: proc kseq_init(fp: gzFile): ptr kseq_t

kseq_read:

• readfx: proc kseq_read(seq: ptr kseq_t): int

kseq_rewind:

• readfx: proc kseq_rewind(seq: ptr kseq_t)

maskLowQuality:

• sequtils: proc maskLowQuality(record: var FQRecord; minQual: int; offset: int = 33; maskChar: char = 'N')

matchIUPAC:

• oligoutils: proc matchIUPAC(primerBase, referenceBase: char): bool

open:

• readfx: proc open[T](f: var Bufio[T]; fn: string; mode: FileMode = fmRead; sz: int = 0x00010000): int

overlap:

• readfx: iterator overlap[S, T](a: seq[Interval[S, T]]; st: S; en: S): Interval[S, T]

qualCharToInt:

• sequtils: proc qualCharToInt(c: char; offset: int = 33): int

qualIntToChar:

• sequtils: proc qualIntToChar(q: int; offset: int = 33): char

qualityTrim:

• sequtils: proc qualityTrim(record: var FQRecord; minQual: int; offset: int = 33)

read:

• readfx: proc read[T](f: var Bufio[T]; buf: var string; sz: int; offset: int = 0): int

readByte:

• readfx: proc readByte[T](f: var Bufio[T]): int

readFastx:

• readfx: proc readFastx[T](f: var Bufio[T]; r: var FQRecord): bool

readFQ:

• readfx: iterator readFQ(path: string): FQRecord

readFQInterleavedPairPtr:

• readfx: iterator readFQInterleavedPairPtr(path: string; checkNames: bool = false): FQPairPtr

readFQPair:

• readfx: iterator readFQPair(path1: string; path2: string; checkNames: bool = false): FQPair

readFQPairPtr:

• readfx: iterator readFQPairPtr(path1: string; path2: string; checkNames: bool = false): FQPairPtr

readFQPtr:

• readfx: iterator readFQPtr(path: string): FQRecordPtr

readLine:

• readfx: proc readLine[T](f: var Bufio[T]; buf: var string): bool

readUntil:

• readfx: proc readUntil[T](f: var Bufio[T]; buf: var string; dret: var char; delim: int = -1; offset: int = 0): int

revCompl:

• sequtils: proc revCompl(record: var FQRecord)
• sequtils: proc revCompl(record: FQRecord): FQRecord
• sequtils: proc revCompl(sequence: string): string

Reverse:

• seqtypes: Strand.Reverse

SeqComp:

• seqtypes: object SeqComp

sort:

• readfx: proc sort[S, T](a: var seq[Interval[S, T]])

stdoutDestination:

• writer: proc stdoutDestination(): FastxDestination

Strand:

• seqtypes: enum Strand

subSequence:

• sequtils: proc subSequence(record: FQRecord; start: int; length: int = -1): FQRecord

trimEnd:

• sequtils: proc trimEnd(record: FQRecord; bases: int): FQRecord

trimQuality:

• sequtils: proc trimQuality(quality: string; minQual: int; offset: int = 33): string

trimStart:

• sequtils: proc trimStart(record: FQRecord; bases: int): FQRecord

Unknown:

• seqtypes: Strand.Unknown

writeRecord:

• writer: proc writeRecord(w: var FastxWriter; record: FQRecord)
• writer: proc writeRecord(w: var FastxWriter; name: string; sequence: string; quality: string = ""; comment: string = "")

xopen:

• readfx: proc xopen[T](fn: string; mode: FileMode = fmRead; sz: int = 0x00010000): Bufio[T]