From da93f0caf3cf3a7031bfec3c7ed15e606dd7782e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Mar 2015 14:01:12 +0100
Subject: [PATCH] Fix format and typo's
---
.../sasc/biopet/tools/VEPNormalizer.scala | 19 +++++++++----------
1 file changed, 9 insertions(+), 10 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
index 646f8dead..15025e326 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
@@ -188,28 +188,27 @@ object VEPNormalizer extends ToolCommand {
* @return An array with the new records
*/
def explodeTranscripts(record: VariantContext, csqInfos: Array[String], removeCsq: Boolean): Array[VariantContext] = {
- val arti = parseCsq(record)
-
- for (transcript <- arti) yield {
+ for (transcript <- parseCsq(record)) yield {
(for (
fieldId <- 0 until csqInfos.size if transcript.isDefinedAt(fieldId);
- value = transcript(fieldId).trim if value.nonEmpty
+ value = transcript(fieldId) if value.nonEmpty
) yield csqInfos(fieldId) -> value)
.filterNot(_._2.isEmpty)
- .foldLeft(createBuilder(record, removeCsq))((builder, artibute) => builder.attribute(artibute._1, artibute._2))
+ .foldLeft(createBuilder(record, removeCsq))((builder, attribute) => builder.attribute(attribute._1, attribute._2))
.make()
}
}
def standardTranscripts(record: VariantContext, csqInfos: Array[String], removeCsq: Boolean): VariantContext = {
- val arti = parseCsq(record)
+ val attribs = parseCsq(record)
(for (fieldId <- 0 until csqInfos.size) yield csqInfos(fieldId) -> {
for (
- transcript <- arti if transcript.isDefinedAt(fieldId);
- value = transcript(fieldId).trim if value.nonEmpty
+ transcript <- attribs if transcript.isDefinedAt(fieldId);
+ value = transcript(fieldId) if value.nonEmpty
) yield value
- }).filter(_._2.nonEmpty)
+ })
+ .filter(_._2.nonEmpty)
.foldLeft(createBuilder(record, removeCsq))((builder, attribute) => builder.attribute(attribute._1, attribute._2))
.make()
}
@@ -223,7 +222,7 @@ object VEPNormalizer extends ToolCommand {
record.getAttributeAsString("CSQ", "unknown").
stripPrefix("[").
stripSuffix("]").
- split(",").map(_.split("""\|"""))
+ split(",").map(_.split("""\|""").map(_.trim))
}
case class Args(inputVCF: File = null,
--
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