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biopet.biopet
Commits
e859f656
Commit
e859f656
authored
Jul 24, 2017
by
Ruben Vorderman
Browse files
Started on flexiprepReadSummary.ssp
parent
eceab944
Changes
2
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
e859f656
...
...
@@ -24,26 +24,17 @@
<%@ var settings: Map[(Int, Int), Map[String, Option[Any]]] %>
<%@ var paired: Boolean %>
<%@ var seqstatPaths: Map[String, List[String]] %>
<%@ var seqstatPaths: Map[String, List[String]] %>
<%@ var seqstatStats: Map[String, Option[Any]] %>
<%@ var seqstatQcStats: Map[String, Option[Any]] %>
<%@ var clippingStats: Map[String, Option[Any]] %>
<%@ var trimmingStats: Map[String, Option[Any]] %>
<%@ var samples: Seq[Sample] %>
<%@ var libraries: Seq[Library] %>
<%@ var librariesCount: Int %>
<%@ var clipCount: Int %>
<%@ var trimCount: Int %>
<%@ var %>
#{
val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
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))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(false))
val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false))
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
#if (showIntro)
<br/>
<div class="row">
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
e859f656
...
...
@@ -293,3 +293,47 @@ object FlexiprepReadSummary {
}
}
}
object
FlexiprepReadSummaryReportPage
{
def
values
(
summary
:
SummaryDb
,
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
]
=
None
,
libId
:
Option
[
Int
]
=
None
)
=
{
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
))
val
paired
=
if
(
sampleId
.
isDefined
&&
libId
.
isDefined
){
summary
.
getSettingKeys
(
runId
,
"flexiprep"
,
NoModule
,
SampleId
(
sampleId
.
get
),
LibraryId
(
libId
.
get
),
keyValues
=
Map
(
"paired"
->
List
(
"paired"
))).
getOrElse
(
"paired"
,
None
)
==
Some
(
true
)}
else
settings
.
count
(
_
.
_2
.
getOrElse
(
"paired"
,
None
)
==
Some
(
true
))
>=
1
val
samples
=
sampleId
.
map
(
id
=>
allSamples
.
filter
(
_
.
id
==
id
)).
getOrElse
(
allSamples
)
val
libraries
=
libId
.
map
(
id
=>
allLibraries
.
filter
(
_
.
id
==
id
)).
getOrElse
(
allLibraries
)
val
trimCount
=
settings
.
count
(
_
.
_2
.
getOrElse
(
"skip_trim"
,
None
)
==
Some
(
false
))
val
clipCount
=
settings
.
count
(
_
.
_2
.
getOrElse
(
"skip_clip"
,
None
)
==
Some
(
false
))
val
librariesCount
=
libraries
.
size
Map
(
"summary"
->
summary
,
"runId"
->
runId
,
"sampleId"
->
sampleId
,
"libId"
->
libId
,
"settings"
->
settings
,
"samples"
->
samples
,
"libraries"
->
libraries
,
"trimCount"
->
trimCount
,
"clipCount"
->
clipCount
,
"librariesCount"
->
librariesCount
)
}
def
settings
(
summary
:
SummaryDb
,
runId
:
Int
)
=
{
}
def
paired
(
summary
:
SummaryDb
,
runId
:
Int
,
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
])
=
}
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