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biopet.biopet
Commits
af8a8b8d
Commit
af8a8b8d
authored
Feb 02, 2017
by
akaljuvee
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parent
154f1717
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8 deletions
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-8
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+13
-8
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
af8a8b8d
...
...
@@ -93,14 +93,19 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
logger
.
info
(
"Running pre commands"
)
for
(
function
<-
functions
)
function
match
{
case
f
:
BiopetCommandLineFunction
=>
f
.
preProcessExecutable
()
f
.
beforeGraph
()
f
.
internalBeforeGraph
()
f
.
commandLine
case
f
:
WriteSummary
=>
f
.
init
()
case
_
=>
var
count
=
0
for
(
function
<-
functions
)
{
function
match
{
case
f
:
BiopetCommandLineFunction
=>
f
.
preProcessExecutable
()
f
.
beforeGraph
()
f
.
internalBeforeGraph
()
f
.
commandLine
case
f
:
WriteSummary
=>
f
.
init
()
case
_
=>
}
count
+=
1
if
(
count
%
500
==
0
)
logger
.
info
(
s
"Preprocessing done for ${count} jobs"
)
}
val
logDir
=
new
File
(
outputDir
,
".log"
+
File
.
separator
+
qSettings
.
runName
.
toLowerCase
)
...
...
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