fastq

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class DemuxFastqs extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
case class FastqRecord (name: String, bases: String, quals: String, comment: Option[String] = None, readNumber: Option[Int] = None) extends Product with Serializable
Represents a record that can be read from or written to a fastq file.
class FastqSource extends Iterator[FastqRecord] with Closeable
Reads fastq records from any text based source via a reader.
Reads fastq records from any text based source via a reader. Ensures that lines come in the expected groupings of four lines with the correct headers, and that bases and qualities are of the same length. The underlying reader is closed automatically when EOF is reached.
class FastqToBam extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
class FastqWriter extends Closeable with Writer[FastqRecord]
Implements a writer for fastq records.
sealed trait OutputType extends EnumEntry
sealed trait QualityEncoding extends AnyRef
Trait for describing quality score encoding systems.
class QualityEncodingDetector extends AnyRef
Class to detect the quality encoding in use in FASTQ files.
class TrimFastq extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()

object DemuxFastqs
object FastqSource
Provides factory methods for creating a FastqSource from multiple types.
object FastqWriter
Companion object for manufacturing FastqWriter instances.
object OutputType extends FgBioEnum[OutputType]
object QualityEncoding

Packages