Skip to content
GitLab
Menu
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
2b9a6487
Commit
2b9a6487
authored
Jun 22, 2015
by
Peter van 't Hof
Browse files
All regions on 1 page now
parent
6e820b47
Changes
1
Show 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
(
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a 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