BioKotlin/biokotlin.seqIO

Package-level declarations

Types

FastaIO

class FastaIO(val filename: String, type: SeqType) : SequenceIterator

FastqIO

class FastqIO(val filename: String) : SequenceIterator

FastqIO implements a SequenceIterator for a FASTQ file at path filename

GVCFReader

class GVCFReader(val gvcfFile: String, val referenceFile: String, val sizeOfQueue: Int = 5) : SequenceIterator

This reads a GVCF formatted file. The file is required to only have one sample. The file can only be read one time. Either as an iterator (hasNext(), next()), repeatedly calling read(), or using readAll().

NucSeqIO

class NucSeqIO(filename: String, format: SeqFormat? = null) : Iterable<NucSeqRecord>

ProteinSeqIO

class ProteinSeqIO(filename: String, format: SeqFormat? = null) : Iterable<ProteinSeqRecord>

SeqFormat

enum SeqFormat : Enum<SeqFormat>

SeqType

enum SeqType : Enum<SeqType>

SequenceIterator

interface SequenceIterator : Iterator<SeqRecord>

SequenceWriter

interface SequenceWriter

Functions

main

fun main()

reader

fun reader(filename: String, format: SeqFormat? = null, type: SeqType = SeqType.nucleotide): SequenceIterator

writeFasta

fun writeFasta(input: SequenceIterator, filename: String)

This writes the sequence iterator to the specified filename in Fasta Format

fun writeFasta(input: Collection<SeqRecord>, filename: String)

writeFastq

fun writeFastq(input: Collection<SeqRecord>, filename: String)