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biopet.biopet
Commits
2fbebdfb
Commit
2fbebdfb
authored
Jan 10, 2017
by
Peter van 't Hof
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Merge branch 'fix-xhmm-issues' into 'develop'
fix small issues on XHMM [Biopet-469-related] See merge request !511
parents
50e5cc55
4c2905e2
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3
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12 additions
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10 deletions
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-10
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R
...rc/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R
+1
-1
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
+2
-0
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
...umc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
+9
-9
No files found.
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R
View file @
2fbebdfb
...
...
@@ -31,7 +31,7 @@ CNRoutput <- opt$cnr
windowLength
<-
opt
$
wl
bamFile
<-
args
BAMFiles
<-
strsplit
(
c
(
bamFile
),
" "
)[[
1
]]
BAMFiles
<-
bamFile
bamDataRanges
<-
tryCatch
(
{
getReadCountsFromBAM
(
BAMFiles
,
mode
=
"paired"
,
refSeqName
=
chromosome
,
WL
=
windowLength
,
parallel
=
opt
$
threads
)
...
...
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
View file @
2fbebdfb
...
...
@@ -21,6 +21,8 @@ class XcnvToBed(val root: Configurable) extends ToolCommandFunction {
@Argument
var
sample
:
String
=
_
override
def
defaultCoreMemory
=
4
override
def
cmdLine
=
{
super
.
cmdLine
+
required
(
"-I"
,
inputXcnv
)
+
required
(
"-O"
,
outpuBed
)
+
required
(
"-S"
,
sample
)
}
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
2fbebdfb
...
...
@@ -49,7 +49,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
// the filtered and centered matrix
val
firstMatrix
=
new
XhmmMatrix
(
this
)
firstMatrix
.
inputMatrix
=
merged
.
output
firstMatrix
.
outputMatrix
=
swapExt
(
merged
.
output
,
".depths.data"
,
".filtered_centered.data"
)
firstMatrix
.
outputMatrix
=
swapExt
(
xhmmDir
,
merged
.
output
,
".depths.data"
,
".filtered_centered.data"
)
firstMatrix
.
minTargetSize
=
10
firstMatrix
.
maxTargetSize
=
10000
firstMatrix
.
minMeanTargetRD
=
10
...
...
@@ -57,21 +57,21 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
firstMatrix
.
minMeanSampleRD
=
25
firstMatrix
.
maxMeanSampleRD
=
200
firstMatrix
.
maxSdSampleRD
=
150
firstMatrix
.
outputExcludedSamples
=
Some
(
swapExt
(
merged
.
output
,
".depths.data"
,
".filtered.samples.txt"
))
firstMatrix
.
outputExcludedTargets
=
Some
(
swapExt
(
merged
.
output
,
".depths.data"
,
".filtered.targets.txt"
))
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
)
// pca generation
val
pca
=
new
XhmmPca
(
this
)
pca
.
inputMatrix
=
firstMatrix
.
outputMatrix
pca
.
pcaFile
=
swapExt
(
firstMatrix
.
outputMatrix
,
".filtered_centered.data"
,
".rd_pca.data"
)
pca
.
pcaFile
=
swapExt
(
xhmmDir
,
firstMatrix
.
outputMatrix
,
".filtered_centered.data"
,
".rd_pca.data"
)
add
(
pca
)
// normalization
val
normalize
=
new
XhmmNormalize
(
this
)
normalize
.
inputMatrix
=
firstMatrix
.
outputMatrix
normalize
.
pcaFile
=
pca
.
pcaFile
normalize
.
normalizeOutput
=
swapExt
(
firstMatrix
.
outputMatrix
,
".filtered_centered.data"
,
".normalized.data"
)
normalize
.
normalizeOutput
=
swapExt
(
xhmmDir
,
firstMatrix
.
outputMatrix
,
".filtered_centered.data"
,
".normalized.data"
)
add
(
normalize
)
// normalized & filtered matrix
...
...
@@ -81,9 +81,9 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
secondMatrix
.
centerType
=
"sample"
secondMatrix
.
zScoreData
=
true
secondMatrix
.
maxsdTargetRD
=
30
secondMatrix
.
outputExcludedTargets
=
Some
(
swapExt
(
normalize
.
normalizeOutput
,
".data"
,
".filtered.targets.txt"
))
secondMatrix
.
outputExcludedSamples
=
Some
(
swapExt
(
normalize
.
normalizeOutput
,
".data"
,
".filtered.samples.txt"
))
secondMatrix
.
outputMatrix
=
swapExt
(
normalize
.
normalizeOutput
,
".data"
,
"filtered.data"
)
secondMatrix
.
outputExcludedTargets
=
Some
(
swapExt
(
xhmmDir
,
normalize
.
normalizeOutput
,
".data"
,
".filtered.targets.txt"
))
secondMatrix
.
outputExcludedSamples
=
Some
(
swapExt
(
xhmmDir
,
normalize
.
normalizeOutput
,
".data"
,
".filtered.samples.txt"
))
secondMatrix
.
outputMatrix
=
swapExt
(
xhmmDir
,
normalize
.
normalizeOutput
,
".data"
,
"filtered.data"
)
add
(
secondMatrix
)
// re-synced matrix
...
...
@@ -91,7 +91,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
thirdMatrix
.
inputMatrix
=
merged
.
output
thirdMatrix
.
inputExcludeSamples
=
List
(
firstMatrix
.
outputExcludedSamples
,
secondMatrix
.
outputExcludedSamples
).
flatten
thirdMatrix
.
inputExcludeTargets
=
List
(
firstMatrix
.
outputExcludedTargets
,
secondMatrix
.
outputExcludedTargets
).
flatten
thirdMatrix
.
outputMatrix
=
swapExt
(
merged
.
output
,
".depths.data"
,
".same_filtered.data"
)
thirdMatrix
.
outputMatrix
=
swapExt
(
xhmmDir
,
merged
.
output
,
".depths.data"
,
".same_filtered.data"
)
add
(
thirdMatrix
)
// discovering cnvs
...
...
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