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biopet.biopet
Commits
3b0bbaf7
Commit
3b0bbaf7
authored
Nov 17, 2014
by
Peter van 't Hof
Browse files
Added collect consensus
parent
d7e3156a
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
3b0bbaf7
...
...
@@ -47,6 +47,11 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val
catVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
variants
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
variants
).
toList
,
outputDir
+
"fastas/variant.snps_only.fasta"
)
add
(
catVariantsSnps
)
val
catConsensus
=
Cat
(
this
,
refVariants
.
consensus
::
samplesOutput
.
map
(
_
.
_2
.
output
.
consensus
).
toList
,
outputDir
+
"fastas/consensus.fasta"
)
add
(
catConsensus
)
val
catConsensusSnps
=
Cat
(
this
,
refVariantSnps
.
consensus
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
consensus
).
toList
,
outputDir
+
"fastas/consensus.snps_only.fasta"
)
add
(
catConsensusSnps
)
val
catConsensusVariants
=
Cat
(
this
,
refVariants
.
consensusVariants
::
samplesOutput
.
map
(
_
.
_2
.
output
.
consensusVariants
).
toList
,
outputDir
+
"fastas/consensus.variant.fasta"
)
add
(
catConsensusVariants
)
val
catConsensusVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
consensusVariants
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
consensusVariants
).
toList
,
outputDir
+
"fastas/consensus.variant.snps_only.fasta"
)
...
...
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