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biopet.biopet
Commits
9c2720bf
Commit
9c2720bf
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Fix RGPI config var
parent
8b4d55c2
Changes
1
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Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
9c2720bf
...
...
@@ -89,7 +89,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
RGDT
:
Date
=
_
@Argument
(
doc
=
"Readgroup predicted insert size"
,
shortName
=
"RGPI"
,
required
=
false
)
var
RGPI
:
Int
=
config
(
"RGPI"
)
var
RGPI
:
Option
[
Int
]
=
config
(
"RGPI"
)
var
paired
:
Boolean
=
false
val
flexiprep
=
new
Flexiprep
(
this
)
...
...
@@ -300,7 +300,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if
(
RGCN
!=
null
)
RG
+=
"CN:"
+
RGCN
+
"\\t"
if
(
RGDS
!=
null
)
RG
+=
"DS"
+
RGDS
+
"\\t"
if
(
RGDT
!=
null
)
RG
+=
"DT"
+
RGDT
+
"\\t"
if
(
RGPI
>
0
)
RG
+=
"PI"
+
RGPI
+
"\\t"
if
(
RGPI
.
isDefined
)
RG
+=
"PI"
+
RGPI
.
get
+
"\\t"
return
RG
.
substring
(
0
,
RG
.
lastIndexOf
(
"\\t"
))
}
...
...
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