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biopet.biopet
Commits
36b45eb4
Commit
36b45eb4
authored
Jul 25, 2017
by
Ruben Vorderman
Browse files
Completed sortableThemeBootstrap dictionary.
parent
c2d14321
Changes
2
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
36b45eb4
...
...
@@ -35,7 +35,7 @@
<%@ var trimCount: Int %>
<%@ var flexiprepReportPlotRead1: Option[Unit] %>
<%@ var flexiprepReportPlotRead2: Option[Unit] %>
<%@ var %>
<%@ var
sortableThemeBootstrap: scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Any]]]
%>
#if (showIntro)
<br/>
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
36b45eb4
...
...
@@ -302,7 +302,11 @@ object FlexiprepReadSummaryReportPage {
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
]
=
None
,
libId
:
Option
[
Int
]
=
None
,
showPlot
:
Boolean
=
false
)
=
{
showPlot
:
Boolean
=
false
,
showTable
:
Boolean
=
true
,
showIntro
:
Boolean
=
true
,
multisample
:
Boolean
=
true
)
=
{
val
settings
=
summary
.
getSettingsForLibraries
(
runId
,
"flexiprep"
,
keyValues
=
Map
(
"skip_trim"
->
List
(
"skip_trim"
),
"skip_clip"
->
List
(
"skip_clip"
),
"paired"
->
List
(
"paired"
)))
settings
.
count
(
_
.
_2
.
getOrElse
(
"skip_trim"
,
None
)
==
Some
(
true
))
...
...
@@ -316,16 +320,11 @@ object FlexiprepReadSummaryReportPage {
val
clipCount
=
settings
.
count
(
_
.
_2
.
getOrElse
(
"skip_clip"
,
None
)
==
Some
(
false
))
val
librariesCount
=
libraries
.
size
/* Todo: Map this conditionally */
if
(
showPlot
){
val
flexiprepReportPlotRead1
:
Option
[
Unit
]
=
Some
(
FlexiprepReport
.
readSummaryPlot
(
outputDir
,
"QC_Reads_R1"
,
"R1"
,
summary
,
sampleId
=
sampleId
))
if
(
paired
)
{
val
flexiprepReportPlotRead2
:
Option
[
Unit
]
=
Some
(
FlexiprepReport
.
readSummaryPlot
(
outputDir
,
"QC_Reads_R2"
,
"R2"
,
summary
,
sampleId
=
sampleId
))
else
val
flexiprepReportPlotRead2
:
Option
[
Unit
]
=
None
else
val
flexiprepReportPlotRead1
:
Option
[
Unit
]
=
None
}
val
flexiprepReportPlotRead1
:
Option
[
Unit
]
=
if
(
showPlot
){
Some
(
FlexiprepReport
.
readSummaryPlot
(
outputDir
,
"QC_Reads_R1"
,
"R1"
,
summary
,
sampleId
=
sampleId
))}
val
flexiprepReportPlotRead2
:
Option
[
Unit
]
=
if
(
showPlot
){
if
(
paired
){
Some
(
FlexiprepReport
.
readSummaryPlot
(
outputDir
,
"QC_Reads_R2"
,
"R2"
,
summary
,
sampleId
=
sampleId
))}}
}
val
sortableThemeBootstrapValues
=
sortableThemeBootstrap
(
samples
,
libraries
,
settings
,
summary
,
runId
)
Map
(
"summary"
->
summary
,
...
...
@@ -339,18 +338,23 @@ object FlexiprepReadSummaryReportPage {
"libraries"
->
libraries
,
"trimCount"
->
trimCount
,
"clipCount"
->
clipCount
,
"librariesCount"
->
librariesCount
"librariesCount"
->
librariesCount
,
"flexipreprReportPlotRead1"
->
flexiprepReportPlotRead1
,
"flexipreprReportPlotRead2"
->
flexiprepReportPlotRead2
,
"sortableThemeBootstrap"
->
sortableThemeBootstrapValues
)
}
/* Todo: Map these values to some iterable over map */
def
sortableThemeBootstrap
(
samples
:
Seq
[
Sample
],
libraries
:
Seq
[
Library
],
settings
:
Map
[(
Int
,
Int
)
,
Map
[
String
,
Option
[
Any
]]],
summary
:
SummaryDb
,
runId
:
Int
)
:
Unit
=
{
)
:
scala.collection.mutable.Map
[
Int
,
scala.collection.mutable.Map
[
Int
,
Map
[
String
,
Any
]]]
=
{
var
sortableThemeBootstrap
=
scala
.
collection
.
mutable
.
Map
[
Int
,
scala.collection.mutable.Map
[
Int
,
Map
[
String
,
Any
]]]()
/* iterable map */
for
(
sample
<-
samples
.
sortBy
(
_
.
name
))
{
val
sampleRowspan
=
{
libraries
.
filter
(
_
.
sampleId
==
sample
.
id
).
size
+
...
...
@@ -378,9 +382,23 @@ object FlexiprepReadSummaryReportPage {
val
clippingDiscardedToShort
=
clippingStats
(
"num_reads_discarded_too_short"
).
getOrElse
(
0
).
toString
.
toLong
val
clippingDiscardedToLong
=
clippingStats
(
"num_reads_discarded_too_long"
).
getOrElse
(
0
).
toString
.
toLong
val
trimmingDiscarded
=
trimmingStats
(
"num_reads_discarded"
).
getOrElse
(
0
).
toString
.
toLong
sortableThemeBootstrap
(
sample
.
id
)(
lib
.
id
)(
read
)
=
Map
(
"seqstatPaths"
->
seqstatPaths
,
"seqstatStats"
->
seqstatStats
,
"seqstatQcStats"
->
seqstatQcStats
,
"clippingPaths"
->
clippingPaths
,
"clippingStats"
->
clippingStats
,
"trimmingPaths"
->
trimmingPaths
,
"beforeTotal"
->
beforeTotal
,
"afterTotal"
->
afterTotal
,
"clippingDiscardedToShort"
->
clippingDiscardedToShort
,
"clippingDiscardedToLong"
->
clippingDiscardedToLong
,
"trimmingDiscarded"
->
trimmingDiscarded
)
}
}
}
sortableThemeBootstrap
}
}
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