Commit 41a9e407 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change to IndexedSeq

parent a99720fa
......@@ -13,8 +13,8 @@ case class BedRecord(chr: String,
thickEnd: Option[Int] = None,
rgbColor: Option[(Int, Int, Int)] = None,
blockCount: Option[Int] = None,
blockSizes: Array[Int] = Array(),
blockStarts: Array[Int] = Array(),
blockSizes: IndexedSeq[Int] = IndexedSeq(),
blockStarts: IndexedSeq[Int] = IndexedSeq(),
protected[intervals] val _originals: List[BedRecord] = Nil) {
def originals(nested: Boolean = true): List[BedRecord] = {
......@@ -70,7 +70,7 @@ case class BedRecord(chr: String,
}
override def toString = {
def arrayToOption[T](array: Array[T]): Option[Array[T]] = {
def arrayToOption[T](array: IndexedSeq[T]): Option[IndexedSeq[T]] = {
if (array.isEmpty) None
else Some(array)
}
......@@ -84,7 +84,7 @@ case class BedRecord(chr: String,
}
def validate = {
require(start <= end, "Start is greater then end")
require(start < end, "Start is greater then end")
(thickStart, thickEnd) match {
case (Some(s), Some(e)) => require(s <= e, "Thick start is greater then end")
case _ =>
......@@ -119,8 +119,8 @@ object BedRecord {
values.lift(7) map (_.toInt),
values.lift(8).map(_.split(",", 3).map(_.toInt)).map(x => (x.headOption.getOrElse(0), x.lift(1).getOrElse(0), x.lift(2).getOrElse(0))),
values.lift(9).map(_.toInt),
values.lift(10).map(_.split(",").map(_.toInt)).getOrElse(Array()),
values.lift(11).map(_.split(",").map(_.toInt)).getOrElse(Array())
values.lift(10).map(_.split(",").map(_.toInt).toIndexedSeq).getOrElse(IndexedSeq()),
values.lift(11).map(_.split(",").map(_.toInt).toIndexedSeq).getOrElse(IndexedSeq())
)
}
}
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