Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
4ddb5a93
Commit
4ddb5a93
authored
Jul 26, 2016
by
bow
Browse files
Merge branch 'fix-basecounter' into 'develop'
Fix basecounter Fixes #377 and #378 See merge request !440
parents
a16e109d
cdc3eea0
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
View file @
4ddb5a93
...
...
@@ -57,8 +57,13 @@ 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
)
require
(
bamReader
.
hasIndex
,
"Bamfile require an index"
)
val
geneReader
=
GeneAnnotationReader
.
loadRefFlat
(
cmdArgs
.
refFlat
,
bamReader
.
getFileHeader
.
getSequenceDictionary
)
bamReader
.
close
()
logger
.
info
(
"Done reading RefFlat file"
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment