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biopet.biopet
Commits
5da52a7b
Commit
5da52a7b
authored
Mar 07, 2017
by
Peter van 't Hof
Committed by
GitHub
Mar 07, 2017
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Merge pull request #33 from biopet/fix-biopet-592
Remove hard-coded settings in XhmmMatrix.
parents
e863bf38
1f852510
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
...umc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
+0
-7
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
5da52a7b
...
...
@@ -64,13 +64,6 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
val
firstMatrix
=
new
XhmmMatrix
(
this
)
firstMatrix
.
inputMatrix
=
merged
.
output
firstMatrix
.
outputMatrix
=
swapExt
(
xhmmDir
,
merged
.
output
,
".depths.data"
,
".filtered_centered.data"
)
firstMatrix
.
minTargetSize
=
10
firstMatrix
.
maxTargetSize
=
10000
firstMatrix
.
minMeanTargetRD
=
10
firstMatrix
.
maxMeanTargetRD
=
500
firstMatrix
.
minMeanSampleRD
=
25
firstMatrix
.
maxMeanSampleRD
=
200
firstMatrix
.
maxSdSampleRD
=
150
firstMatrix
.
outputExcludedSamples
=
Some
(
swapExt
(
xhmmDir
,
merged
.
output
,
".depths.data"
,
".filtered.samples.txt"
))
firstMatrix
.
outputExcludedTargets
=
Some
(
swapExt
(
xhmmDir
,
merged
.
output
,
".depths.data"
,
".filtered.targets.txt"
))
add
(
firstMatrix
)
...
...
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