Commit a12e3ec3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix typo bug

parent 0f888fd4
...@@ -207,9 +207,8 @@ object VcfStats extends ToolCommand { ...@@ -207,9 +207,8 @@ object VcfStats extends ToolCommand {
val stats = createStats val stats = createStats
logger.info("Starting on: " + interval) logger.info("Starting on: " + interval)
for ( for (record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd)
record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd) if record.getStart <= interval.getEnd if record.getStart <= interval.getEnd) {
) {
mergeNestedStatsMap(stats.generalStats, checkGeneral(record)) mergeNestedStatsMap(stats.generalStats, checkGeneral(record))
for (sample1 <- samples) yield { for (sample1 <- samples) yield {
val genotype = record.getGenotype(sample1) val genotype = record.getGenotype(sample1)
...@@ -253,7 +252,7 @@ object VcfStats extends ToolCommand { ...@@ -253,7 +252,7 @@ object VcfStats extends ToolCommand {
buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1))) buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
} }
buffer += "qual" -> Map(record.getPhredScaledQual -> 1) buffer += "QUAL" -> Map(record.getPhredScaledQual -> 1)
addToBuffer("general", "Total") addToBuffer("general", "Total")
if (record.isBiallelic) addToBuffer("general", "Biallelic") if (record.isBiallelic) addToBuffer("general", "Biallelic")
......
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