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biopet.biopet
Commits
bff12a5f
Commit
bff12a5f
authored
Dec 06, 2016
by
Peter van 't Hof
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Move config report
parent
9dc9ee63
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2
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2 changed files
with
6 additions
and
4 deletions
+6
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+4
-2
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
.../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
+2
-2
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
bff12a5f
...
...
@@ -104,8 +104,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case
_
=>
}
val
logDir
=
new
File
(
outputDir
,
".log"
+
File
.
separator
+
BiopetQCommandLine
.
timestamp
)
if
(
outputDir
.
getParentFile
.
canWrite
||
(
outputDir
.
exists
&&
outputDir
.
canWrite
))
globalConfig
.
writeReport
(
qSettings
.
runName
,
new
File
(
outputDir
,
".log/"
+
qSettings
.
runName
))
globalConfig
.
writeReport
(
new
File
(
logDir
,
"config"
))
else
Logging
.
addError
(
"Parent of output dir: '"
+
outputDir
.
getParent
+
"' is not writeable, output directory cannot be created"
)
logger
.
info
(
"Checking input files"
)
...
...
@@ -126,7 +128,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if
(!
skipWriteDependencies
)
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
outputDir
,
".log"
+
File
.
separator
+
BiopetQCommandLine
.
timestamp
+
File
.
separator
+
"graph"
))
new
File
(
logDir
,
"graph"
))
Logging
.
checkErrors
()
logger
.
info
(
"Script complete without errors"
)
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
View file @
bff12a5f
...
...
@@ -189,7 +189,7 @@ class Config(protected var _map: Map[String, Any],
}
else
ConfigValue
(
requestedIndex
,
null
,
null
,
freeVar
)
}
def
writeReport
(
id
:
String
,
directory
:
File
)
:
Unit
=
{
def
writeReport
(
directory
:
File
)
:
Unit
=
{
directory
.
mkdirs
()
def
convertIndexValuesToMap
(
input
:
List
[(
ConfigValueIndex
,
Any
)],
forceFreeVar
:
Option
[
Boolean
]
=
None
)
:
Map
[
String
,
Any
]
=
{
...
...
@@ -205,7 +205,7 @@ class Config(protected var _map: Map[String, Any],
}
def
writeMapToJsonFile
(
map
:
Map
[
String
,
Any
],
name
:
String
)
:
Unit
=
{
val
file
=
new
File
(
directory
,
id
+
"."
+
name
+
".json"
)
val
file
=
new
File
(
directory
,
name
+
".json"
)
val
writer
=
new
PrintWriter
(
file
)
writer
.
write
(
ConfigUtils
.
mapToJson
(
map
).
spaces2
)
writer
.
close
()
...
...
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