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biopet.biopet
Commits
8263ea12
Commit
8263ea12
authored
Jul 25, 2017
by
Ruben Vorderman
Browse files
FlexiprepReadSummary.ssp defutured
parent
03fa2c53
Changes
1
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Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
8263ea12
...
...
@@ -351,9 +351,9 @@ object FlexiprepReadSummaryReportPage {
settings
:
Map
[(
Int
,
Int
)
,
Map
[
String
,
Option
[
Any
]]],
summary
:
SummaryDb
,
runId
:
Int
)
:
scala.collection.mutable.Map
[
Int
,
scala.collection.mutable.Map
[
Int
,
Map
[
String
,
Any
]]]
=
{
)
:
scala.collection.mutable.Map
[
Int
,
scala.collection.mutable.Map
[
Int
,
Map
[
String
,
Map
[
String
,
Long
]
]]]
=
{
var
sortableThemeBootstrap
=
scala
.
collection
.
mutable
.
Map
[
Int
,
scala.collection.mutable.Map
[
Int
,
Map
[
String
,
Any
]]]()
/* iterable map */
var
sortableThemeBootstrap
=
scala
.
collection
.
mutable
.
Map
[
Int
,
scala.collection.mutable.Map
[
Int
,
Map
[
String
,
Map
[
String
,
Long
]
]]]()
/* iterable map */
for
(
sample
<-
samples
.
sortBy
(
_
.
name
))
{
val
sampleRowspan
=
{
...
...
@@ -377,22 +377,16 @@ object FlexiprepReadSummaryReportPage {
val
trimmingPaths
=
Map
(
"num_reads_discarded"
->
List
(
"num_reads_discarded_total"
))
val
trimmingStats
=
summary
.
getStatKeys
(
runId
,
"flexiprep"
,
"trimming_"
+
read
,
sample
=
sample
.
id
,
library
=
lib
.
id
,
keyValues
=
trimmingPaths
)
val
beforeTotal
=
seqstatStats
(
"num_total"
).
getOrElse
(
0
).
toString
.
toLong
val
afterTotal
=
seqstatQcStats
(
"num_total"
).
getOrElse
(
0
).
toString
.
toLong
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
val
beforeTotal
:
Long
=
seqstatStats
(
"num_total"
).
getOrElse
(
0
).
toString
.
toLong
val
afterTotal
:
Long
=
seqstatQcStats
(
"num_total"
).
getOrElse
(
0
).
toString
.
toLong
val
clippingDiscardedTo
o
Short
:
Long
=
clippingStats
(
"num_reads_discarded_too_short"
).
getOrElse
(
0
).
toString
.
toLong
val
clippingDiscardedTo
oLong
:
Long
=
clippingStats
(
"num_reads_discarded_too_long"
).
getOrElse
(
0
).
toString
.
toLong
val
trimmingDiscarded
:
Long
=
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
,
"clippingDiscardedTo
o
Short"
->
clippingDiscardedTo
o
Short
,
"clippingDiscardedTo
o
Long"
->
clippingDiscardedTo
o
Long
,
"trimmingDiscarded"
->
trimmingDiscarded
)
}
...
...
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