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biopet.biopet
Commits
9f156daf
Commit
9f156daf
authored
May 11, 2016
by
Peter van 't Hof
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Added bedtools sorted flag as default
parent
bffd796d
Changes
2
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-0
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+2
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+3
-0
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
9f156daf
...
...
@@ -41,6 +41,8 @@ class BamMetrics(val root: Configurable) extends QScript
@Input
(
doc
=
"Bam File"
,
shortName
=
"BAM"
,
required
=
true
)
var
inputBam
:
File
=
_
override
def
defaults
=
Map
(
"bedtoolscoverage"
->
Map
(
"sorted"
->
true
))
/** return location of summary file */
def
summaryFile
=
(
sampleId
,
libId
)
match
{
case
(
Some
(
s
),
Some
(
l
))
=>
new
File
(
outputDir
,
s
+
"-"
+
l
+
".BamMetrics.summary.json"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
View file @
9f156daf
...
...
@@ -41,6 +41,8 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
@Argument
(
doc
=
"diffStrand"
,
required
=
false
)
var
diffStrand
:
Boolean
=
false
var
sorted
:
Boolean
=
config
(
"sorted"
,
default
=
false
,
freeVar
=
false
)
override
def
defaultCoreMemory
=
4.0
/** Returns command to execute */
...
...
@@ -50,6 +52,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
conditional
(
depth
,
"-d"
)
+
conditional
(
sameStrand
,
"-s"
)
+
conditional
(
diffStrand
,
"-S"
)
+
conditional
(
sorted
,
"-sorted"
)
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
...
...
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