Commit 42334159 authored by bow's avatar bow
Browse files

Update 'num_qual_gte' to 'num_qual' array

parent 0a07f02f
......@@ -263,18 +263,11 @@ object SeqStat extends ToolCommand {
for (pos <- 0 until quals.length) {
val key: Int = pos - phredEncoding.id
if (key > 0) {
// count till the max of baseHistogram.length
for (histokey <- 0 until key + 1) {
baseHistogram(histokey) += quals(pos)
}
if (key >= 0) {
baseHistogram(key) += quals(pos)
}
}
for (pos <- 0 until baseHistogram.length) {
baseQualHistoMap += (pos -> baseHistogram(pos))
}
for (pos <- 0 until readStats.qual.length) {
val key: Int = pos - phredEncoding.id
if (key > 0) {
......@@ -311,7 +304,7 @@ object SeqStat extends ToolCommand {
("stats", Map(
("bases", Map(
("num_total", nucleotideHistoMap.values.sum),
("num_qual_gte", baseQualHistoMap.toMap),
("num_qual", baseHistogram.toList),
("nucleotides", nucleotideHistoMap.toMap)
)),
("reads", Map(
......@@ -325,6 +318,6 @@ object SeqStat extends ToolCommand {
))
)
println(ConfigUtils.mapToJson(report).spaces2)
println(ConfigUtils.mapToJson(report))
}
}
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