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biopet.biopet
Commits
c8a93931
Commit
c8a93931
authored
Feb 10, 2017
by
Peter van 't Hof
Browse files
Add placeholders
parent
5e98e38a
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
c8a93931
...
...
@@ -26,7 +26,6 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import
scala.collection.mutable
import
scala.io.Source
import
slick.driver.H2Driver.api._
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
...
...
@@ -86,8 +85,17 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
/** Function to create summary */
def
run
()
:
Unit
=
{
val
summaryDb
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
val
db
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
//TODO: Add stats
//TODO: Add Files
//TODO: Add executables
db
.
close
()
///////////////// OLD //////////////////
for
(((
name
,
sampleId
,
libraryId
),
summarizables
)
<-
qscript
.
summarizables
;
summarizable
<-
summarizables
)
{
summarizable
.
addToQscriptSummary
(
qscript
,
name
)
}
...
...
@@ -127,7 +135,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
val
map
=
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
settings
,
"files"
->
Map
(
"pipeline"
->
files
),
"executables"
->
executables
.
toMap
)
"executables"
->
executables
)
)
qscript
match
{
...
...
@@ -179,7 +187,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
val
writer
=
new
PrintWriter
(
out
)
writer
.
println
(
ConfigUtils
.
mapToJson
(
combinedMap
).
nospaces
)
writer
.
close
()
summaryDb
.
close
()
///////////////// OLD //////////////////
}
def
prefixSampleLibrary
(
map
:
Map
[
String
,
Any
],
sampleId
:
Option
[
String
],
libraryId
:
Option
[
String
])
:
Map
[
String
,
Any
]
=
{
...
...
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