Index

B

baseQualities() (fastAQ.fastqInfo.FastqParser method)

F

FastaParser (class in fastAQ.fastaInfo) fastAQ (module) fastAQ.commandLineTools (module) fastAQ.commandLineTools.fasta (module) fastAQ.commandLineTools.fastq (module)

fastAQ.fastaInfo (module) fastAQ.fastqInfo (module) fastAQ.sequenceOperations (module) fastAQ.trimming (module) FastqParser (class in fastAQ.fastqInfo)

L

lowQualTrim() (fastAQ.trimming.Trimming method)

M

maskAll() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method) maskSeq() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method)

maskSequence() (fastAQ.sequenceOperations.SequenceManipulation method) mott() (fastAQ.trimming.Trimming method)

R

readFasta() (fastAQ.fastaInfo.FastaParser method) readFastq() (fastAQ.fastqInfo.FastqParser method)

reverseComplement() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method) (fastAQ.sequenceOperations.SequenceManipulation method) reverseComplementAll() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method)

S

seqFromName() (fastAQ.fastaInfo.FastaParser method) seqNames() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method)

sequenceDict() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method) SequenceManipulation (class in fastAQ.sequenceOperations)

T

trimAll() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method) Trimming (class in fastAQ.trimming)

trimSeq() (fastAQ.fastaInfo.FastaParser method) (fastAQ.fastqInfo.FastqParser method) trimSequence() (fastAQ.trimming.Trimming method)