Commit 4dd30a28 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix 'n' bug for seqstat

parent 5d854a9f
......@@ -278,7 +278,7 @@ object Seqstat extends ToolCommand {
}
for (pos <- 0 until readStats.qual.length) {
var key: Int = pos - phredEncoding.id
val key: Int = pos - phredEncoding.id
if (key > 0) {
// count till the max of baseHistogram.length
for (histokey <- 0 until key + 1) {
......@@ -319,7 +319,7 @@ object Seqstat extends ToolCommand {
),
("stats", Map(
("bases", Map(
("num_n", nucleotideHistoMap('N')),
("num_n", nucleotideHistoMap.getOrElse('N', 0)),
("num_total", nucleotideHistoMap.values.sum),
("num_qual_gte", baseQualHistoMap.toMap),
("nucleotides", nucleotideHistoMap.toMap)
......@@ -335,9 +335,6 @@ object Seqstat extends ToolCommand {
))
)
val jsonReport: Json = {
ConfigUtils.mapToJson(report)
}
println(jsonReport.spaces2)
println(ConfigUtils.mapToJson(report).spaces2)
}
}
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