Commit 0a07f02f authored by bow's avatar bow
Browse files

Remove 'num_n' in base stats since we already have 'nucleotides.N'

parent 58102415
...@@ -296,11 +296,8 @@ object SeqStat extends ToolCommand { ...@@ -296,11 +296,8 @@ object SeqStat extends ToolCommand {
val commandArgs: Args = parseArgs(args) val commandArgs: Args = parseArgs(args)
logger.info("Start seqstat") logger.info("Start seqstat")
seqStat(new FastqReader(commandArgs.fastq))
val reader = new FastqReader(commandArgs.fastq)
summarize() summarize()
logger.debug(nucs)
logger.info("Seqstat done") logger.info("Seqstat done")
val report: Map[String, Any] = Map( val report: Map[String, Any] = Map(
...@@ -313,7 +310,6 @@ object SeqStat extends ToolCommand { ...@@ -313,7 +310,6 @@ object SeqStat extends ToolCommand {
), ),
("stats", Map( ("stats", Map(
("bases", Map( ("bases", Map(
("num_n", nucleotideHistoMap.getOrElse('N', 0)),
("num_total", nucleotideHistoMap.values.sum), ("num_total", nucleotideHistoMap.values.sum),
("num_qual_gte", baseQualHistoMap.toMap), ("num_qual_gte", baseQualHistoMap.toMap),
("nucleotides", nucleotideHistoMap.toMap) ("nucleotides", nucleotideHistoMap.toMap)
......
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