package
models
Type Members
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trait
Alphabet extends AnyRef
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case class
Attribute(tag: String, tagType: TagType.Value, value: Any) extends Product with Serializable
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case class
Coverage(contigName: String, start: Long, end: Long, count: Double) extends Product with Serializable
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case class
ProgramRecord(id: String, commandLine: Option[String], name: Option[String], version: Option[String], previousID: Option[String]) extends Product with Serializable
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case class
ReadBucket(unpairedPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedFirstPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedSecondPrimaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unpairedSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedFirstSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], pairedSecondSecondaryMappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unmappedReads: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing]) extends Product with Serializable
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case class
RecordGroup(sample: String, recordGroupName: String, sequencingCenter: Option[String] = scala.None, description: Option[String] = scala.None, runDateEpoch: Option[Long] = scala.None, flowOrder: Option[String] = scala.None, keySequence: Option[String] = scala.None, library: Option[String] = scala.None, predictedMedianInsertSize: Option[Int] = scala.None, platform: Option[String] = scala.None, platformUnit: Option[String] = scala.None) extends Product with Serializable
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case class
RecordGroupDictionary(recordGroups: Seq[RecordGroup]) extends Product with Serializable
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case class
ReferenceRegion(referenceName: String, start: Long, end: Long, orientation: Strand = ...) extends Comparable[ReferenceRegion] with Interval with Product with Serializable
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case class
SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], referenceIndex: Option[Int]) extends Serializable with Product
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case class
SingleReadBucket(primaryMapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], secondaryMapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing], unmapped: Iterable[AlignmentRecord] = collection.this.Seq.empty[Nothing]) extends Product with Serializable
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class
SnpTable extends Serializable with Logging
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case class
Symbol(label: Char, complement: Char) extends Product with Serializable
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case class
VCFHeaderWritable(header: VCFHeader) extends Product with Serializable
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