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biopet.biopet
Commits
78159ed9
Commit
78159ed9
authored
Apr 09, 2017
by
Peter van 't Hof
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trying to fix weird error in testing
parent
261ebe2a
Changes
2
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2 changed files
with
7 additions
and
4 deletions
+7
-4
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/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+5
-4
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
78159ed9
...
...
@@ -154,6 +154,7 @@ class BamMetrics(val parent: Configurable) extends QScript
val
biStrict
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.sam"
),
minOverlap
=
config
(
"strict_intersect_overlap"
,
default
=
1.0
))
biStrict
.
jobOutputFile
=
new
File
(
targetDir
,
".biStrict.Bedtools.out"
)
val
biopetFlagstatStrict
=
BiopetFlagstat
(
this
,
biStrict
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatStrict
,
targetName
+
"_flagstats_strict"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biStrict
,
biopetFlagstatStrict
)))
...
...
@@ -161,6 +162,7 @@ class BamMetrics(val parent: Configurable) extends QScript
val
biLoose
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.loose.sam"
),
minOverlap
=
config
(
"loose_intersect_overlap"
,
default
=
0.01
))
biLoose
.
jobOutputFile
=
new
File
(
targetDir
,
".biLoose.Bedtools.out"
)
val
biopetFlagstatLoose
=
BiopetFlagstat
(
this
,
biLoose
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_flagstats_loose"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biLoose
,
biopetFlagstatLoose
)))
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
View file @
78159ed9
...
...
@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class
BedtoolsIntersect
(
val
parent
:
Configurable
)
extends
Bedtools
{
@Input
(
doc
=
"Input file (bed/gff/vcf/bam)"
)
var
input
:
File
=
null
var
input
:
File
=
_
@Input
(
doc
=
"Intersect file (bed/gff/vcf)"
)
var
intersectFile
:
File
=
null
var
intersectFile
:
File
=
_
@Output
(
doc
=
"output File"
)
var
output
:
File
=
null
var
output
:
File
=
_
@Argument
(
doc
=
"Min overlap"
,
required
=
false
)
var
minOverlap
:
Option
[
Double
]
=
config
(
"minoverlap"
)
...
...
@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"intersect"
)
+
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"intersect"
)
+
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
optional
(
"-f"
,
minOverlap
)
+
...
...
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