Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
b9173a70
Commit
b9173a70
authored
Apr 21, 2017
by
akaljuvee
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
one log line
parent
3d2cbc8a
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
10 additions
and
3 deletions
+10
-3
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
.../nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
+3
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
...la/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
+1
-2
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+6
-0
No files found.
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala
View file @
b9173a70
...
...
@@ -37,13 +37,15 @@ class VcfStatsForSv(val parent: Configurable) extends ToolCommandFunction with S
var
outputFile
:
File
=
_
override
def
defaultCoreMemory
=
1.0
override
def
defaultResidentFactor
=
2.0
override
def
defaultVmemFactor
=
3.0
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-i"
,
inputFile
)
+
required
(
"-o"
,
outputFile
)
+
repeat
(
"--histBinBoundaries"
,
histogramBinBoundaries
)
def
summaryStats
:
Map
[
String
,
Any
]
=
ConfigUtils
.
yamlTo
Map
(
outputFile
)
def
summaryStats
:
Map
[
String
,
Any
]
=
ConfigUtils
.
fileToConfig
Map
(
outputFile
)
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
.
empty
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala
View file @
b9173a70
...
...
@@ -38,8 +38,7 @@ object VcfStatsForSv extends ToolCommand {
val
stats
:
Map
[
String
,
Any
]
=
getVariantCounts
(
cmdArgs
.
inputFile
,
cmdArgs
.
histBinBoundaries
)
ConfigUtils
.
mapToYamlFile
(
stats
,
cmdArgs
.
outputFile
)
ConfigUtils
.
mapToJsonFile
(
stats
,
cmdArgs
.
outputFile
)
}
/** Parses a vcf-file and counts sv-s by type and size. Sv-s are divided to different size classes, the parameter histogramBinBoundaries gives the boundaries between these classes. */
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
View file @
b9173a70
...
...
@@ -168,6 +168,12 @@ object ConfigUtils extends Logging {
writer
.
close
()
}
def
mapToJsonFile
(
map
:
Map
[
String
,
Any
],
outputFile
:
File
)
=
{
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
anyToJson
(
map
).
toString
())
writer
.
close
()
}
/** Convert json to native scala map/values */
def
jsonToMap
(
json
:
Json
)
:
Map
[
String
,
Any
]
=
{
var
output
:
Map
[
String
,
Any
]
=
Map
()
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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