From 42334159cc70787b147a54d8f6bed77d3959c9e5 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sat, 27 Jun 2015 20:55:04 +0200
Subject: [PATCH] Update 'num_qual_gte' to 'num_qual' array
---
.../scala/nl/lumc/sasc/biopet/tools/SeqStat.scala | 15 ++++-----------
1 file changed, 4 insertions(+), 11 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
index 89fed08e6..baaa52589 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
@@ -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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