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biopet.biopet
Commits
edc5fc7f
Commit
edc5fc7f
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Style fix
parent
d5808c90
Changes
1
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
View file @
edc5fc7f
...
...
@@ -35,7 +35,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
/** Allow reporting of all found (potentially adapter) sequences in the FastQC */
var
sensitiveAdapterSearch
:
Boolean
=
config
(
"sensitiveAdapterSearch"
,
default
=
false
)
var
enableRCtrimming
:
Boolean
=
config
(
"enableRCtrimming"
,
default
=
false
)
var
enableRCtrimming
:
Boolean
=
config
(
"enableRCtrimming"
,
default
=
false
)
/** Class for storing a single FastQC module result */
protected
case
class
FastQCModule
(
name
:
String
,
status
:
String
,
lines
:
Seq
[
String
])
...
...
@@ -189,9 +189,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
val
fromKnownList
:
Set
[
AdapterSequence
]
=
(
adapterSet
++
contaminantSet
)
.
filter
(
x
=>
foundAdapterNames
.
exists
(
_
.
startsWith
(
x
.
name
)))
val
fromKnownListRC
:
Set
[
AdapterSequence
]
=
if
(
enableRCtrimming
)
fromKnownList
.
map
{
val
fromKnownListRC
:
Set
[
AdapterSequence
]
=
if
(
enableRCtrimming
)
fromKnownList
.
map
{
x
=>
AdapterSequence
(
x
.
name
+
"_RC"
,
reverseComplement
(
x
.
seq
))
}
else
Set
.
empty
}
else
Set
.
empty
// list all sequences found by FastQC
val
fastQCFoundSequences
:
Seq
[
AdapterSequence
]
=
if
(
sensitiveAdapterSearch
)
{
...
...
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