mergesv

Type Members

1. case class Args(inputFiles: Map[String, List[File]] = Map(), callerFields: Map[String, Set[String]] = Map(), outputFile: File = null, referenceFasta: File = null, windowsSize: Int = 1000, defaultCi: Int = 75, keepNonVariant: Boolean = false) extends Product with Serializable

   

2. class ArgsParser extends AbstractOptParser[Args]

   

3. case class Init(dict: SAMSequenceDictionary, readers: Map[String, List[VCFFileReader]], headers: Map[String, List[VCFHeader]], samples: Seq[String], writer: VariantContextWriter, referenceReader: IndexedFastaSequenceFile) extends Product with Serializable

   

4. case class Interval(start: Int, end: Int) extends Product with Serializable

   

5. class MultiReader extends Iterator[SvCall] with AutoCloseable

   

6. case class SvCall(contig1: String, pos1: Int, contig2: String, pos2: Int, svType: String, posCi: Interval, endCi: Interval, callers: List[String], orientation1: Boolean = true, orientation2: Boolean = true, existsInSamples: List[String] = Nil, callerFields: Map[String, Map[String, AnyRef]] = Map()) extends Logging with Product with Serializable