Index

Modules: abi2fq, abichromatogram, abif, abimerge, abimetadata.

API symbols

A:

• abichromatogram: Channel.A

ABIFTrace:

• abif: type ABIFTrace

abifVersion:

• abif: proc abifVersion(): string

C:

• abichromatogram: Channel.C

canDisplayTag:

• abimetadata: proc canDisplayTag(tagName: string; entry: DirectoryEntry): bool

Channel:

• abichromatogram: enum Channel

close:

• abif: proc close(trace: ABIFTrace)

Config:

• abi2fq: object Config
• abimerge: object Config
• abimetadata: object Config

DirectoryEntry:

• abif: object DirectoryEntry

displaySingleTag:

• abimetadata: proc displaySingleTag(trace: ABIFTrace; tagName: string; debug: bool)

ElementType:

• abif: enum ElementType

etBool:

• abif: ElementType.etBool

etByte:

• abif: ElementType.etByte

etChar:

• abif: ElementType.etChar

etCString:

• abif: ElementType.etCString

etDate:

• abif: ElementType.etDate

etDouble:

• abif: ElementType.etDouble

etFloat:

• abif: ElementType.etFloat

etLong:

• abif: ElementType.etLong

etPoint:

• abif: ElementType.etPoint

etPString:

• abif: ElementType.etPString

etRational:

• abif: ElementType.etRational

etRect:

• abif: ElementType.etRect

etShort:

• abif: ElementType.etShort

etTag:

• abif: ElementType.etTag

etThumb:

• abif: ElementType.etThumb

etTime:

• abif: ElementType.etTime

etVPoint:

• abif: ElementType.etVPoint

etVRect:

• abif: ElementType.etVRect

etWord:

• abif: ElementType.etWord

exportFasta:

• abif: proc exportFasta(trace: ABIFTrace; outFile: string = "")

exportFastq:

• abif: proc exportFastq(trace: ABIFTrace; outFile: string = "")

formatTagValue:

• abimetadata: proc formatTagValue(tagName: string; entry: DirectoryEntry; trace: ABIFTrace): string

G:

• abichromatogram: Channel.G

getData:

• abif: proc getData(trace: ABIFTrace; tag: string): string

getFullTagValue:

• abimetadata: proc getFullTagValue(tagName: string; entry: DirectoryEntry; trace: ABIFTrace): string

getQualityValues:

• abif: proc getQualityValues(trace: ABIFTrace): seq[int]

getSampleName:

• abif: proc getSampleName(trace: ABIFTrace): string

getSequence:

• abif: proc getSequence(trace: ABIFTrace): string

getTagNames:

• abif: proc getTagNames(trace: ABIFTrace): seq[string]

isHumanReadableType:

• abimetadata: proc isHumanReadableType(tagType: ElementType): bool

listMetadata:

• abimetadata: proc listMetadata(trace: ABIFTrace; debug: bool; limit: int = 0)

main:

• abi2fq: proc main()
• abimetadata: proc main()

makeMatrix:

• abimerge: proc makeMatrix[T](rows, cols: int; initValue: T): seq[seq[T]]

matchIUPAC:

• abimerge: proc matchIUPAC(a, b: char): bool

mergeSequences:

• abimerge: proc mergeSequences(forwardSeq: string; forwardQual: seq[int]; reverseSeq: string; reverseQual: seq[int]; config: Config): tuple[seq: string, qual: seq[int]]

modifyTag:

• abimetadata: proc modifyTag(trace: ABIFTrace; tagName: string; newValue: string; outputFile: string): bool

newABIFTrace:

• abif: proc newABIFTrace(filename: string; trimming: bool = false): ABIFTrace

parseCommandLine:

• abi2fq: proc parseCommandLine(): Config
• abimetadata: proc parseCommandLine(): Config

printHelp:

• abi2fq: proc printHelp()
• abimetadata: proc printHelp()

revcompl:

• abimerge: proc revcompl(s: string): string

reverseString:

• abimerge: proc reverseString(str: string): string

simpleSmithWaterman:

• abimerge: proc simpleSmithWaterman(alpha, beta: string; weights: swWeights): swAlignment

splitAmbiguousBases:

• abi2fq: proc splitAmbiguousBases(sequence: string): tuple[seq1: string, seq2: string]

swAlignment:

• abimerge: object swAlignment

swDefaults:

• abimerge: let swDefaults

swWeights:

• abimerge: object swWeights

T:

• abichromatogram: Channel.T

TraceData:

• abichromatogram: object TraceData

TraceDataPoint:

• abichromatogram: object TraceDataPoint

translateIUPAC:

• abimerge: proc translateIUPAC(c: char): char

trimSequence:

• abi2fq: proc trimSequence(sequence: string; qualities: seq[int]; windowSize: int; threshold: int): tuple[seq: string, qual: seq[int]]

verifyTagUpdate:

• abimetadata: proc verifyTagUpdate(inputFile, outputFile, tagName: string): bool

verifyTagUpdateBasic:

• abimetadata: proc verifyTagUpdateBasic(inputFile, outputFile, tagName: string; newValue: string; offset: int): bool

writeFastq:

• abi2fq: proc writeFastq(sequence: string; qualities: seq[int]; name: string; outFile: string = ""; fasta: bool = false; splitSeq1: string = ""; splitSeq2: string = "")