From 2ecea20471ca31703284f4239ac43fd09674ec8c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 23 Aug 2015 13:13:04 +0200
Subject: [PATCH] Added validation
---
.../sasc/biopet/utils/intervals/BedRecord.scala | 16 ++++++++++++++++
.../biopet/utils/intervals/BedRecordList.scala | 12 +++++++++++-
2 files changed, 27 insertions(+), 1 deletion(-)
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
index 4c50cc857..c395d0bc5 100644
--- 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
@@ -60,6 +60,22 @@ case class BedRecord(chr: String,
.flatten
.mkString("\t")
}
+
+ def validate = {
+ 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 _ =>
+ }
+ blockCount match {
+ case Some(count) => {
+ require(count == blockSizes.length, "Number of sizes is not the same as blockCount")
+ require(count == blockStarts.length, "Number of starts is not the same as blockCount")
+ }
+ case _ =>
+ }
+ this
+ }
}
object BedRecord {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index 906f90df1..783f32481 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
@@ -70,7 +70,17 @@ object BedRecordList {
}
def fromFile(bedFile: File) = {
- fromList(Source.fromFile(bedFile).getLines().map(BedRecord.fromLine(_)))
+ var lineCount = 0L
+ fromList(Source.fromFile(bedFile).getLines().map(line => {
+ lineCount += 1
+ try {
+ BedRecord.fromLine(line).validate
+ } catch {
+ case e: Exception =>
+ Logging.logger.error(s"Parsing line number $lineCount failed on file: ${bedFile.getAbsolutePath}")
+ throw e
+ }
+ }))
}
def combineOverlap(list: BedRecordList): BedRecordList = {
--
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