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biopet.biopet
Commits
2b9a6487
Commit
2b9a6487
authored
Jun 22, 2015
by
Peter van 't Hof
Browse files
All regions on 1 page now
parent
6e820b47
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
2b9a6487
...
...
@@ -57,8 +57,11 @@ object ShivaReport extends MultisampleReportBuilder {
var
regionPages
:
Map
[
String
,
ReportPage
]
=
Map
()
def
createPage
(
name
:
String
,
amplicon
:
Boolean
=
false
)
:
ReportPage
=
{
//TODO: get target content
ReportPage
(
Map
(),
List
(
"Coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp"
)),
Map
(
"target"
->
name
))
ReportPage
(
Map
(),
List
(
"Coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp"
)),
Map
(
"target"
->
name
)
)
}
amplicon
match
{
...
...
@@ -72,8 +75,14 @@ object ShivaReport extends MultisampleReportBuilder {
case
_
=>
}
if
(
regionPages
.
nonEmpty
)
Some
(
"Regions"
->
ReportPage
(
regionPages
.
keys
.
toList
.
sorted
.
map
(
x
=>
x
->
regionPages
(
x
)).
toMap
,
List
(),
Map
()))
else
None
if
(
regionPages
.
nonEmpty
)
Some
(
"Regions"
->
ReportPage
(
Map
(),
regionPages
.
map
(
p
=>
(
p
.
_1
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp"
,
Map
(
"target"
->
p
.
_1
.
stripSuffix
(
" (Amplicon)"
))
))).
toList
.
sortBy
(
_
.
_1
),
Map
())
)
else
None
}
def
filesPage
=
ReportPage
(
Map
(),
List
(
...
...
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