From 1c09d9c2a575dfa59edb13b519f01e07fd8d8c72 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 20 Aug 2015 11:07:44 +0200
Subject: [PATCH] Added a bedRecord with a parser
---
.../biopet/utils/intervals/BedRecord.scala | 46 +++++++++++++++++++
1 file changed, 46 insertions(+)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
new file mode 100644
index 000000000..441c0652d
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
@@ -0,0 +1,46 @@
+package nl.lumc.sasc.biopet.utils.intervals
+
+/**
+ * Created by pjvanthof on 20/08/15.
+ */
+case class BedRecord(chr: String,
+ start: Int,
+ end: Int,
+ name: Option[String] = None,
+ score: Option[Double] = None,
+ strand: Boolean = true,
+ thickStart: Option[Int] = None,
+ thickEnd: Option[Int] = None,
+ rgbColor: Option[(Int, Int, Int)] = None,
+ blockCount: Option[Int] = None,
+ blockSizes: Array[Int] = Array(),
+ blockStarts: Array[Int] = Array()) {
+ override def toString = {
+ s"$chr\t$start\t$end"
+ }
+}
+
+object BedRecord {
+ def fromLine(line: String): BedRecord = {
+ val values = line.split("\t")
+ require(values.length >= 3)
+ BedRecord(
+ values(0),
+ values(1).toInt,
+ values(2).toInt,
+ values.lift(3),
+ values.lift(4).map(_.toInt),
+ values.lift(5) match {
+ case Some("-") => false
+ case Some("+") => true
+ case _ => throw new IllegalStateException("")
+ },
+ values.lift(6).map(_.toInt),
+ values.lift(7)map(_.toInt),
+ values.lift(8).map(_.split(",", 3).map(_.toInt)).map(x => (x(0),x(1),x(2))),
+ values.lift(9).map(_.toInt),
+ values.lift(10).map(_.split(",").map(_.toInt)).getOrElse(Array()),
+ values.lift(11).map(_.split(",").map(_.toInt)).getOrElse(Array())
+ )
+ }
+}
\ No newline at end of file
--
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