fasta

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sealed trait AssemblyReportColumn extends EnumEntry
Trait that entries in AssemblyReportColumn will extend.
class CollectAlternateContigNames extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
class HardMaskFasta extends FgBioTool with LazyLogging
Tool to take in a FASTA file and convert soft-masked (i.e.
Tool to take in a FASTA file and convert soft-masked (i.e. lower-case) sequence to hard-masked sequence (i.e. Ns), for tools that cannot correctly interpret soft-masking.

Annotations
@ClpAnnotation()
class ReferenceSequenceIterator extends Iterator[ReferenceSequence]
Simple Iterator that wraps a ReferenceSequence and provides a standard Iterator over all the reference sequences in order.
case class SequenceDictionary(infos: IndexedSeq[SequenceMetadata]) extends Iterable[SequenceMetadata] with Product with Serializable
Contains an ordered collection of sequences.
case class SequenceMetadata extends Product with Serializable
Stores information about a single Sequence (ex.
Stores information about a single Sequence (ex. chromosome, contig)
sealed trait SequenceRole extends EnumEntry
Trait that entries in SequenceRole will extend.
sealed trait Topology extends EnumEntry
The base trait for all topologies.
class UpdateFastaContigNames extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()

object AssemblyReportColumn extends FgBioEnum[AssemblyReportColumn]
Enum to represent columns in a NCBI assembly report.
object Converters
Contains useful converters to and from HTSJDK objects.
object ReferenceSequenceIterator
object SequenceDictionary extends Serializable
object SequenceMetadata extends Serializable
object SequenceRole extends FgBioEnum[SequenceRole]
Enum to represent the various types of sequence-roles in NCBI assembly report.
object Topology extends FgBioEnum[Topology]
An enumeration representing the various reference sequence topologies.

Packages