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biopet.biopet
Commits
3427e4e1
Commit
3427e4e1
authored
Jan 27, 2016
by
Peter van 't Hof
Browse files
Code improvement
parent
800ad479
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
3427e4e1
...
...
@@ -29,8 +29,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val
wgsExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"wgs"
).
values
.
exists
(
_
.
isDefined
)
val
rnaExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"rna"
).
values
.
exists
(
_
.
isDefined
)
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
filter
(
_
.
_2
.
isDefined
)
.
nonEmpty
.
exists
{
case
((
sample
,
lib
),
value
)
=>
value
.
isDefined
}
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
...
...
@@ -67,8 +66,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Files page, can be used general or at sample level */
def
filesPage
:
ReportPage
=
{
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
filter
(
_
.
_2
.
isDefined
)
.
nonEmpty
.
exists
{
case
((
sample
,
lib
),
value
)
=>
value
.
isDefined
}
ReportPage
(
List
(),
(
if
(
flexiprepExecuted
)
List
(
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"
),
...
...
@@ -82,9 +80,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
filter
(
_
.
_1
.
_1
==
sampleId
)
.
filter
(
_
.
_2
.
isDefined
)
.
nonEmpty
.
exists
{
case
((
sample
,
lib
),
value
)
=>
sample
==
sampleId
&&
value
.
isDefined
}
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
...
...
@@ -103,6 +99,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
flexiprepExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"flexiprep"
).
isDefined
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
),
...
...
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