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biopet.biopet
Commits
4013b925
Commit
4013b925
authored
Jun 17, 2015
by
Peter van 't Hof
Browse files
style changes
parent
7e1ef164
Changes
2
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public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
4013b925
...
...
@@ -16,15 +16,15 @@ object BammetricsReport extends ReportBuilder {
def
indexPage
=
ReportPage
(
Map
(),
List
(),
Map
())
def
bamMetricsPage
(
summary
:
Summary
,
sampleId
:
Option
[
String
],
libId
:
Option
[
String
])
=
{
def
bamMetricsPage
(
summary
:
Summary
,
sampleId
:
Option
[
String
],
libId
:
Option
[
String
])
=
{
val
targets
=
(
summary
.
getLibraryValue
(
sampleId
,
libId
,
"bammetrics"
,
"settings"
,
"amplicon_name"
),
summary
.
getLibraryValue
(
sampleId
,
libId
,
"bammetrics"
,
"settings"
,
"roi_name"
)
)
match
{
case
(
Some
(
amplicon
:
String
),
Some
(
roi
:
List
[
_
]))
=>
amplicon
::
roi
.
map
(
_
.
toString
)
case
(
_
,
Some
(
roi
:
List
[
_
]))
=>
roi
.
map
(
_
.
toString
)
case
_
=>
Nil
}
)
match
{
case
(
Some
(
amplicon
:
String
),
Some
(
roi
:
List
[
_
]))
=>
amplicon
::
roi
.
map
(
_
.
toString
)
case
(
_
,
Some
(
roi
:
List
[
_
]))
=>
roi
.
map
(
_
.
toString
)
case
_
=>
Nil
}
ReportPage
(
(
if
(
targets
.
isEmpty
)
Map
()
else
Map
(
"Targets"
->
ReportPage
(
...
...
@@ -40,7 +40,6 @@ object BammetricsReport extends ReportBuilder {
)
}
def
alignmentSummaryPlot
(
outputDir
:
File
,
prefix
:
String
,
summary
:
Summary
,
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
View file @
4013b925
...
...
@@ -12,7 +12,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
)
}
def
libraryPage
(
sampleId
:
String
,
libraryId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
def
libraryPage
(
sampleId
:
String
,
libraryId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
def
libririesSections
:
List
[(
String
,
ReportSection
)]
=
{
List
(
...
...
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