Commit da93f0ca authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix format and typo's

parent 9a2c81d5
......@@ -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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