Add source classes for BED and generic Interval types

[clintval]

I need helpers for reading generic interval data, so I added these classes!

BedSource: A source for BED input (similar to IntervalListSource).
IntervalSource: A source for interval data that wraps either BED or Interval List input.

In both classes, you can optionally provide a sequence dictionary that will be used to validate the intervals. I did this because I find myself having a BED and reference FASTA, more often than I have an Interval List and reference FASTA, but I would still like the safety of knowing my intervals are well-formed.

I expect to use these classes like the following, (so even BED data is safe!):

@clp(description="Print intervals from BED or Interval List, validate them all!")
class DoWork(
  @arg(flag='i', doc="The path to the input intervals.") val input: PathToIntervals,
  @arg(flag='r', doc="The path to the reference FASTA.") val reference: PathToFasta,
) extends Tool {
  override def execute(): Unit = {
    val fasta     = ReferenceSequenceFileFactory.getReferenceSequenceFile(reference)
    val intervals = IntervalSource(input, Some(fasta.getSequenceDictionary.fromSam))

    intervals.foreach { interval => println(s"Found interval: $interval") }

    fasta.close()
    intervals.close()
  }
}

This should be OK from a type-alias perspective too, since PathToIntervals is defined as:

/** Represents a path to an intervals file (IntervalList or BED). */
type PathToIntervals = java.nio.file.Path

[tfenne]

Conceptuall on board and thanks for doing this. Might take a while to get to a review though.

[clintval]

No rush! Take what you like from the submission.