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biopet.biopet
Commits
0a07f02f
Commit
0a07f02f
authored
Jun 27, 2015
by
bow
Browse files
Remove 'num_n' in base stats since we already have 'nucleotides.N'
parent
58102415
Changes
1
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Inline
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
View file @
0a07f02f
...
...
@@ -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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