case class ReadGroupDictionary(readGroups: Seq[ReadGroup]) extends Product with Serializable
Builds a dictionary containing read groups.
Read groups must have a unique name across all samples in the dictionary. This dictionary provides numerical IDs for each group; these IDs are only consistent when referencing a single dictionary.
- readGroups
A seq of read groups to populate the dictionary.
- Exceptions thrown
IllegalArgumentExceptionThrows an assertion error if there are multiple read groups with the same name.
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def
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def
++(that: ReadGroupDictionary): ReadGroupDictionary
Merges together two read group dictionaries.
Merges together two read group dictionaries.
- that
The read group dictionary to merge with.
- returns
The merged read group dictionary.
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def
==(arg0: Any): Boolean
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def
apply(readGroupId: String): ReadGroup
Returns the read group entry for an associated id.
Returns the read group entry for an associated id.
- readGroupId
The read group to look up.
- returns
Detailed info for a read group.
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def
getIndex(readGroupId: String): Int
Returns the numerical index for a given read group id.
Returns the numerical index for a given read group id.
- readGroupId
The read group to find an index for.
- returns
Returns a numerical index for a read group.
- Note
This index is only guaranteed to have the same value for a given read group id when the index is pulled from the same read group dictionary.
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def
isEmpty: Boolean
- returns
Returns true if this dictionary contains no read groups.
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val
readGroupMap: Map[String, (ReadGroup, Int)]
A representation of this read group dictionary that can be indexed into by read group id.
- val readGroups: Seq[ReadGroup]
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def
size: Int
The number of read groups in the dictionary.
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def
synchronized[T0](arg0: ⇒ T0): T0
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def
toSamples: Seq[Sample]
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Converts this read group dictionary to a set of samples.
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toString(): String
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