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
a25cc635
Commit
a25cc635
authored
Feb 15, 2017
by
Peter van 't Hof
Browse files
Adding possibility to change metrics on preprocess bam
parent
9869bfcd
Changes
2
Hide whitespace changes
Inline
Side-by-side
carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
a25cc635
...
...
@@ -61,6 +61,8 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
override
def
preProcessBam
=
Some
(
createFile
(
"filter.bam"
))
override
def
metricsPreprogressBam
=
false
val
controls
:
List
[
String
]
=
config
(
"control"
,
default
=
Nil
)
override
def
summarySettings
=
super
.
summarySettings
++
Map
(
"controls"
->
controls
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
a25cc635
...
...
@@ -90,6 +90,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
sample
=>
def
metricsPreprogressBam
=
true
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
lib
=>
...
...
@@ -263,7 +265,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
if
(
mergeStrategy
!=
MergeStrategy
.
None
&&
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
nonEmpty
)
{
val
bamMetrics
=
new
BamMetrics
(
qscript
)
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
inputBam
=
preProcessBam
.
get
bamMetrics
.
inputBam
=
if
(
metricsPreprogressBam
)
preProcessBam
.
get
else
bamFile
.
get
bamMetrics
.
outputDir
=
new
File
(
sampleDir
,
"metrics"
)
add
(
bamMetrics
)
...
...
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