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biopet.biopet
Commits
2f23e353
Commit
2f23e353
authored
Jul 22, 2016
by
Peter van 't Hof
Browse files
Added check for outputDir
parent
a16e109d
Changes
1
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Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
View file @
2f23e353
...
...
@@ -57,7 +57,11 @@ object BaseCounter extends ToolCommand {
//Sets picard logging level
htsjdk
.
samtools
.
util
.
Log
.
setGlobalLogLevel
(
htsjdk
.
samtools
.
util
.
Log
.
LogLevel
.
valueOf
(
logger
.
getLevel
.
toString
))
require
(
cmdArgs
.
outputDir
.
exists
(),
s
"Output dir does not exist: ${cmdArgs.outputDir}"
)
require
(
cmdArgs
.
outputDir
.
isDirectory
,
s
"Output dir is not a dir: ${cmdArgs.outputDir}"
)
logger
.
info
(
"Start reading RefFlat file"
)
val
bamReader
=
SamReaderFactory
.
makeDefault
().
open
(
cmdArgs
.
bamFile
)
val
geneReader
=
GeneAnnotationReader
.
loadRefFlat
(
cmdArgs
.
refFlat
,
bamReader
.
getFileHeader
.
getSequenceDictionary
)
bamReader
.
close
()
...
...
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