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biopet.biopet
Commits
4626aad3
Commit
4626aad3
authored
Jul 10, 2017
by
Sander Bollen
Committed by
GitHub
Jul 10, 2017
Browse files
Merge pull request #156 from biopet/fix-BIOPET-741
Fixing grouping in GenotypeGVCFs
parents
050ed7a9
ad759469
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/GenotypeGvcfs.scala
View file @
4626aad3
...
...
@@ -55,7 +55,7 @@ class GenotypeGvcfs(val parent: Configurable) extends QScript with BiopetQScript
job
.
out
=
outputFile
job
.
isIntermediate
=
group
.
nonEmpty
val
subJobs
:
ListBuffer
[
CombineJob
]
=
ListBuffer
()
val
groupedInput
=
makeEqualGroups
(
allInput
)
val
groupedInput
:
List
[
List
[
File
]]
=
makeEqualGroups
(
allInput
)
if
(
groupedInput
.
size
==
1
)
job
.
variant
=
groupedInput
.
head
else
{
for
((
list
,
i
)
<-
groupedInput
.
zipWithIndex
)
{
...
...
@@ -71,7 +71,7 @@ class GenotypeGvcfs(val parent: Configurable) extends QScript with BiopetQScript
val
groupSize
=
if
(
files
.
size
>
(
maxNumberOfFiles
*
maxNumberOfFiles
))
{
files
.
size
/
maxNumberOfFiles
}
else
if
(
files
.
size
<
maxNumberOfFiles
)
files
.
size
else
files
.
size
/
(
files
.
size
/
maxNumberOfFiles
)
else
(
files
.
size
.
toDouble
/
(
files
.
size
.
toDouble
/
maxNumberOfFiles
)
.
ceil
).
ceil
.
toInt
files
.
grouped
(
groupSize
).
toList
}
...
...
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