From 0a07f02ff6609cabdf6bf5918c9be3672099a40a Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sat, 27 Jun 2015 20:33:57 +0200
Subject: [PATCH] Remove 'num_n' in base stats since we already have
'nucleotides.N'
---
.../src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala | 6 +-----
1 file changed, 1 insertion(+), 5 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 5c16999e4..89fed08e6 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
@@ -296,11 +296,8 @@ object SeqStat extends ToolCommand {
val commandArgs: Args = parseArgs(args)
logger.info("Start seqstat")
-
- val reader = new FastqReader(commandArgs.fastq)
+ seqStat(new FastqReader(commandArgs.fastq))
summarize()
-
- logger.debug(nucs)
logger.info("Seqstat done")
val report: Map[String, Any] = Map(
@@ -313,7 +310,6 @@ object SeqStat extends ToolCommand {
),
("stats", Map(
("bases", Map(
- ("num_n", nucleotideHistoMap.getOrElse('N', 0)),
("num_total", nucleotideHistoMap.values.sum),
("num_qual_gte", baseQualHistoMap.toMap),
("nucleotides", nucleotideHistoMap.toMap)
--
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