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
61896d06
Commit
61896d06
authored
Aug 22, 2016
by
Peter van 't Hof
Browse files
Convert igvtools to a java extensions
parent
e5384fc2
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
View file @
61896d06
...
...
@@ -14,16 +14,17 @@
*/
package
nl.lumc.sasc.biopet.extensions.igvtools
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.
{
Biopet
Java
CommandLineFunction
,
Version
}
/**
* General igvtools extension
*
* Created by wyleung on 5-1-15
*/
abstract
class
IGVTools
extends
BiopetCommandLineFunction
with
Version
{
executable
=
config
(
"exe"
,
default
=
"igvtools"
,
namespace
=
"igvtools"
,
freeVar
=
false
)
def
versionCommand
=
executable
+
" version"
abstract
class
IGVTools
extends
BiopetJavaCommandLineFunction
with
Version
{
jarFile
=
config
(
"igvtools_jar"
,
namespace
=
"igvtools"
)
def
versionCommand
=
executable
+
s
" -jar ${jarFile.getAbsolutePath} version"
def
versionRegex
=
"""IGV Version:? ([\w\.]*) .*"""
.
r
override
def
versionExitcode
=
List
(
0
)
}
\ No newline at end of file
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
View file @
61896d06
...
...
@@ -76,25 +76,23 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
}
/** Returns command to execute */
def
cmdLine
=
{
required
(
executable
)
+
required
(
"count"
)
+
optional
(
"--maxZoom"
,
maxZoom
)
+
optional
(
"--windowSize"
,
windowSize
)
+
optional
(
"--extFactor"
,
extFactor
)
+
optional
(
"--preExtFactor"
,
preExtFactor
)
+
optional
(
"--postExtFactor"
,
postExtFactor
)
+
optional
(
"--windowFunctions"
,
windowFunctions
)
+
optional
(
"--strands"
,
strands
)
+
conditional
(
bases
,
"--bases"
)
+
optional
(
"--query"
,
query
)
+
optional
(
"--minMapQuality"
,
minMapQuality
)
+
conditional
(
includeDuplicates
,
"--includeDuplicates"
)
+
conditional
(
pairs
,
"--pairs"
)
+
required
(
input
)
+
required
(
outputArg
)
+
required
(
genomeChromSizes
)
}
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"count"
)
+
optional
(
"--maxZoom"
,
maxZoom
)
+
optional
(
"--windowSize"
,
windowSize
)
+
optional
(
"--extFactor"
,
extFactor
)
+
optional
(
"--preExtFactor"
,
preExtFactor
)
+
optional
(
"--postExtFactor"
,
postExtFactor
)
+
optional
(
"--windowFunctions"
,
windowFunctions
)
+
optional
(
"--strands"
,
strands
)
+
conditional
(
bases
,
"--bases"
)
+
optional
(
"--query"
,
query
)
+
optional
(
"--minMapQuality"
,
minMapQuality
)
+
conditional
(
includeDuplicates
,
"--includeDuplicates"
)
+
conditional
(
pairs
,
"--pairs"
)
+
required
(
input
)
+
required
(
outputArg
)
+
required
(
genomeChromSizes
)
/** This part should never fail, these values are set within this wrapper */
private
def
outputArg
:
String
=
{
...
...
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