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
99dd330b
Commit
99dd330b
authored
Apr 30, 2015
by
Peter van 't Hof
Browse files
Change bed files in summary
parent
9085dba2
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
99dd330b
...
...
@@ -48,10 +48,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
}
/** returns files to store in summary */
def
summaryFiles
=
Map
(
"input_bam"
->
inputBam
)
def
summaryFiles
=
Map
(
"input_bam"
->
inputBam
)
++
ampliconBedFile
.
map
(
"amplicon"
->
_
).
toMap
++
ampliconBedFile
.
map
(
x
=>
"roi_"
+
x
.
getName
.
stripSuffix
(
".bed"
)
->
x
).
toMap
/** return settings */
def
summarySettings
=
Map
(
"ampliconBedFile"
->
ampliconBedFile
,
"roiBedFiles"
->
roiBedFiles
)
def
summarySettings
=
Map
(
"amplicon_name"
->
ampliconBedFile
.
collect
{
case
x
=>
x
.
getName
.
stripSuffix
(
".bed"
)
},
"roi_name"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)))
/** executed before script */
def
init
()
{
...
...
@@ -130,7 +133,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val
biStrict
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.bam"
),
minOverlap
=
config
(
"strictintersectoverlap"
,
default
=
1.0
))
minOverlap
=
config
(
"strict
_
intersect
_
overlap"
,
default
=
1.0
))
biStrict
.
isIntermediate
=
true
add
(
biStrict
)
add
(
SamtoolsFlagstat
(
this
,
biStrict
.
output
,
targetDir
))
...
...
@@ -140,7 +143,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val
biLoose
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.loose.bam"
),
minOverlap
=
config
(
"looseintersectoverlap"
,
default
=
0.01
))
minOverlap
=
config
(
"loose
_
intersect
_
overlap"
,
default
=
0.01
))
biLoose
.
isIntermediate
=
true
add
(
biLoose
)
add
(
SamtoolsFlagstat
(
this
,
biLoose
.
output
,
targetDir
))
...
...
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