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biopet.biopet
Commits
feeafebb
Commit
feeafebb
authored
Aug 20, 2014
by
Peter van 't Hof
Browse files
Fix bug on single end library's
parent
20871e07
Changes
1
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
View file @
feeafebb
...
...
@@ -147,7 +147,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
val
s
=
for
((
key
,
value
)
<-
chunks
)
yield
value
.
seqstatR1after
.
getSummary
Option
(
Seqstat
.
mergeSummarys
(
s
.
toList
))
}
val
R2_proc
:
Option
[
Json
]
=
if
(!
flexiprep
.
paired
&&
flexiprep
.
skipClip
&&
flexiprep
.
skipTrim
)
None
val
R2_proc
:
Option
[
Json
]
=
if
(!
flexiprep
.
paired
||
(
flexiprep
.
skipClip
&&
flexiprep
.
skipTrim
)
)
None
else
if
(
chunks
.
size
==
1
)
Option
(
chunks
.
head
.
_2
.
seqstatR2after
.
getSummary
)
else
{
val
s
=
for
((
key
,
value
)
<-
chunks
)
yield
value
.
seqstatR2after
.
getSummary
...
...
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