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 646f8dead71bd58c639fc6865e4b438c81d54613..15025e3262bbafc7b24d4cf9a84519aa79e23c92 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,