Type Members

1.  sealed trait Allele extends AnyRef

   Represents an allele in a VCF or Variant.

   Represents an allele in a VCF or Variant. The only requirement of the trait is that implementing classes override toString to provide the correct string representation of the allele.

2.  case class AlleleSet(ref: SimpleAllele, alts: IndexedSeq[Allele]) extends Iterable[Allele] with Product with Serializable

   Simple class to encapsulate a set of alleles where one allele represents the allele that is present in the reference genome, and the remainder represent alternative alleles.

   Simple class to encapsulate a set of alleles where one allele represents the allele that is present in the reference genome, and the remainder represent alternative alleles.

   ref

   the reference allele

   alts

   the ordered list of alternate alleles

3.  class ArrayAttr[A] extends IndexedSeq[A]

   Class that is used to store multi-valued attributes from a VCF (e.g.

   Class that is used to store multi-valued attributes from a VCF (e.g. AD=10,20) and correctly handle missing values.

   It is possible for one or all values in the collection to be missing. If accessed directly, e.g. by index or by iteration, missing values will return one of the following based on the type of the attribute:

   • Variant.Missing for Strings
   • Variant.MissingInt for Ints
   • Variant.MissingFloat for Floating point numbers

   If you need to deal with the possibility of missing values it is strongly recommended that you use the isMissing() and/or isDefined() methods or use the get() which returns an option type.

   A

   the type of values stored in the collection

4.  final case class Genotype(alleles: AlleleSet, sample: String, calls: IndexedSeq[Allele], phased: Boolean = false, attrs: Map[String, Any] = Variant.EmptyGtAttrs) extends Product with Serializable

   A genotype for a variant.

   A genotype for a variant.

   alleles

   the set of alleles for the variant

   sample

   the name of the sample for which this is a genotype

   calls

   the called alleles for the sample

   phased

   whether or not the calls are phased

5.  final case class Variant(chrom: String, pos: Int, id: Option[String] = None, alleles: AlleleSet, qual: Option[Double] = None, filters: Set[String] = Variant.EmptyFilters, attrs: ListMap[String, Any] = Variant.EmptyInfo, genotypes: Map[String, Genotype] = Variant.EmptyGenotypes) extends Product with Serializable

   Represents a variant from a VCF or similar source.

   Represents a variant from a VCF or similar source.

   Attributes from the INFO field are available via the apply(), get(), and getOrElse() methods. Attribute that are defined but missing in the VCF (e.g. DP=.) are not stored. All multi-valued attributes are stored as instances of ArrayAttr which is a custom subclass of IndexedSeq which provides methods to help in dealing with missing values in cases where a subset of values are missing (e.g. AD=10,.,20).

   chrom

   the chromosome on which a variant resides.

   pos

   the start position of the variant

   id

   the optional ID (e.g. rs number) of the variant

   alleles

   the set of alleles recorded for the variant

   qual

   the optional phred-scaled quality score of the variant

   filters

   the set of filters applied to the variant. An empty set indicates the variant has not had filtration applied. A single value of "PASS" is applied if the variant passes filters, and one or more non-PASS strings if the variant fails filters.

   attrs

   a map of attributes that come from the INFO field of a VCF

   genotypes

   a map of sample name -> genotype for the variant

6.  case class VcfContigHeader(index: Int, name: String, length: Option[Int] = None, assembly: Option[String] = None) extends VcfHeaderEntry with Product with Serializable

   A contig line/entry in the VCF header.

   A contig line/entry in the VCF header.

   index

   the index of the contig in the list of contigs

   name

   the name of the contig

   length

   the length of the contig in bases, optional

   assembly

   the optional name of the assembly from which the contig is drawn

7.  sealed trait VcfCount extends AnyRef

   Trait used to represent how many instances of an attribute are to be expected in a VCFs INFO or genotype fields.

8.  sealed trait VcfFieldType extends EnumEntry

   Trait for the set of acceptable atomic types that can appear in VCF's INFO and genotype fields.

9.  case class VcfFilterHeader(id: String, description: String) extends VcfHeaderEntry with Product with Serializable

   An entry describing a filter used in either the FILTER field or samples' FT field.

   An entry describing a filter used in either the FILTER field or samples' FT field.

   id

   the name of the filter as it will appear in the FILTER or FT fields

   description

   a human readable description of the filter

10.  case class VcfFormatHeader(id: String, count: VcfCount, kind: VcfFieldType, description: String) extends VcfHeaderEntry with Product with Serializable

    An entry in the VCF header describing a FORMAT field whose values appear in each genotype.

    An entry in the VCF header describing a FORMAT field whose values appear in each genotype.

    id

    the ID of the fields (i.e. the string that appears in the FORMAT field)

    count

    the expected count of values per sample

    kind

    the atomic type of each value

    description

    a human readable description of the field

11.  case class VcfGeneralHeader(headerType: String, id: String, data: Map[String, String] = Map.empty) extends VcfHeaderEntry with Product with Serializable

    Catch all for header line types we don't care enough to have specific implementations of.

12.  case class VcfHeader(contigs: IndexedSeq[VcfContigHeader], infos: Seq[VcfInfoHeader], formats: Seq[VcfFormatHeader], filters: Seq[VcfFilterHeader], others: Seq[VcfGeneralHeader], samples: IndexedSeq[String]) extends Product with Serializable

    The header of a VCF file.

    The header of a VCF file.

    contigs

    the ordered list of contig entries in the VCF header (may be empty)

    infos

    the list of INFO entries in the header

    formats

    the list of FORMAT entries in the header

    filters

    the list of FILTER entries in the header

    others

    the list of all other header entries

    samples

    the ordered list of samples that appear in the VCF

13.  sealed trait VcfHeaderEntry extends AnyRef

    Trait representing an entry/line in a VCF header.

14.  case class VcfInfoHeader(id: String, count: VcfCount, kind: VcfFieldType, description: String, source: Option[String] = None, version: Option[String] = None) extends VcfHeaderEntry with Product with Serializable

    An entry in the VCF header describing an INFO field.

    An entry in the VCF header describing an INFO field.

    id

    the ID of the INFO field, i.e. the value that precedes the = in the INFO field

    count

    the expected count of values for the field

    kind

    the atomic type of values for the field

    description

    a description of the field, intended for people not for parsing

    source

    an optional source describing where the field came from

    version

    an optional version for the INFO field

15.  class VcfSource extends FgBioDef.View[Variant] with Closeable

    Provides a reader over a source of VCF-like data that could be a VCF file or a BCF file.

    Provides a reader over a source of VCF-like data that could be a VCF file or a BCF file. Has facilities for iterating over the entire stream of variants as well as querying by genomic location if an index is present.

16.  class VcfWriter extends commons.io.Writer[Variant]

    Writes Variants to a file or other storage mechanism.