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biopet.biopet
Commits
d207b97f
Commit
d207b97f
authored
9 years ago
by
bow
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Update None pattern match to use catch-all clause
parent
c1ccaa97
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+2
-2
2 additions, 2 deletions
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
with
2 additions
and
2 deletions
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+
2
−
2
View file @
d207b97f
...
...
@@ -48,7 +48,7 @@ class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl.
case
Some
(
n
)
=>
n
->
Map
(
"sequence"
->
seq
,
"count"
->
count
)
// adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
// sequences come from FastQC
case
None
=>
case
_
=>
throw
new
IllegalStateException
(
s
"Adapter '$seq' is clipped but not found by FastQC in 'clipping_$readName'."
)
}
}.
toMap
...
...
@@ -58,7 +58,7 @@ class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl.
Map
.
empty
[
String
,
Map
[
String
,
Any
]]
}
// "adapters" key not found ~ something went wrong in our part
case
None
=>
throw
new
RuntimeException
(
s
"Required key 'adapters' not found in stats entry 'clipping_$readName'."
)
case
_
=>
throw
new
RuntimeException
(
s
"Required key 'adapters' not found in stats entry 'clipping_$readName'."
)
}
initStats
.
updated
(
"adapters"
,
adapterCounts
)
}
...
...
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