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biopet.biopet
Commits
af6b885e
Commit
af6b885e
authored
Aug 01, 2017
by
rhpvorderman
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Prepare for further defuturing of bammetrics
parent
58c2b606
Changes
1
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1 changed file
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109 additions
and
12 deletions
+109
-12
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+109
-12
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bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
af6b885e
...
@@ -74,7 +74,104 @@ object BammetricsReport extends ReportBuilder {
...
@@ -74,7 +74,104 @@ object BammetricsReport extends ReportBuilder {
sampleId
:
Option
[
Int
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
libId
:
Option
[
Int
],
metricsTag
:
String
=
"bammetrics"
)
:
Map
[
String
,
Any
]
=
{
metricsTag
:
String
=
"bammetrics"
)
:
Map
[
String
,
Any
]
=
{
Map
(
""
->
""
)
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"wgs"
,
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
val
rnaExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"rna"
,
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
val
insertsizeMetrics
=
summary
.
getStatKeys
(
runId
,
metricsTag
,
"CollectInsertSizeMetrics"
,
sampleId
.
map
(
SampleId
).
getOrElse
(
NoSample
),
libId
.
map
(
LibraryId
).
getOrElse
(
NoLibrary
),
Map
(
"metrics"
->
List
(
"metrics"
))
)
.
exists
(
_
.
_2
.
isDefined
)
val
targetSettings
=
summary
.
getSettingKeys
(
runId
,
metricsTag
,
NoModule
,
sample
=
sampleId
.
map
(
SampleId
).
getOrElse
(
NoSample
),
library
=
libId
.
map
(
LibraryId
).
getOrElse
(
NoLibrary
),
Map
(
"amplicon_name"
->
List
(
"amplicon_name"
),
"roi_name"
->
List
(
"roi_name"
))
)
val
targets
=
(
targetSettings
(
"amplicon_name"
),
targetSettings
(
"roi_name"
)
)
match
{
case
(
Some
(
amplicon
:
String
),
Some
(
roi
:
List
[
_
]))
=>
amplicon
::
roi
.
map
(
_
.
toString
)
case
(
_
,
Some
(
roi
:
List
[
_
]))
=>
roi
.
map
(
_
.
toString
)
case
_
=>
Nil
}
val
covstatsPlotValuesArray
=
ArrayBuffer
[(
String
,
Map
[
String
,
Any
])]()
for
(
t
<-
targets
)
{
covstatsPlotValuesArray
+=
Tuple2
(
t
,
BammetricsReportPage
.
covstatsPlotValues
(
summary
,
runId
,
sampleId
,
libId
,
Some
(
t
)))
}
val
covstatsPlotValuesList
=
covstatsPlotValuesArray
.
toList
val
alignmentSummaryReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
mappingQualityReportValues
=
BammetricsReportPage
.
mappingQualityValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
clippingReportValues
=
BammetricsReportPage
.
clippingValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
insertSizeReportValues
=
BammetricsReportPage
.
insertSizeValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
wgsHistogramReportValues
=
BammetricsReportPage
.
wgsHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
rnaHistogramReportValues
=
BammetricsReportPage
.
rnaHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
Map
(
"wgsExecuted"
->
wgsExecuted
,
"rnaExecuted"
->
rnaExecuted
,
"insertsizeMetrics"
->
insertsizeMetrics
,
"targetSettings"
->
targetSettings
,
"covstatsPlotValuesList"
->
covstatsPlotValuesList
,
"alignmentSummaryReportValues"
->
alignmentSummaryReportValues
,
"clippingReportValues"
->
clippingReportValues
,
"insertSizeReportValues"
->
insertSizeReportValues
,
"wgsHistogramReportValues"
->
wgsHistogramReportValues
,
"rnaHistogramReportValues"
->
rnaHistogramReportValues
)
}
}
/** Generates a page with alignment stats */
/** Generates a page with alignment stats */
...
@@ -83,18 +180,18 @@ object BammetricsReport extends ReportBuilder {
...
@@ -83,18 +180,18 @@ object BammetricsReport extends ReportBuilder {
libId
:
Option
[
Int
],
libId
:
Option
[
Int
],
metricsTag
:
String
=
"bammetrics"
)
:
Future
[
ReportPage
]
=
{
metricsTag
:
String
=
"bammetrics"
)
:
Future
[
ReportPage
]
=
{
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
val
wgsExecuted
:
Boolean
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
metricsTag
,
"wgs"
,
"wgs"
,
sample
=
sampleId
.
map
(
SampleId
),
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
library
=
libId
.
map
(
LibraryId
))
>=
1
val
rnaExecuted
=
summary
.
getStatsSize
(
runId
,
val
rnaExecuted
:
Boolean
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
metricsTag
,
"rna"
,
"rna"
,
sample
=
sampleId
.
map
(
SampleId
),
sample
=
sampleId
.
map
(
SampleId
),
library
=
libId
.
map
(
LibraryId
))
>=
1
library
=
libId
.
map
(
LibraryId
))
>=
1
val
insertsizeMetrics
=
summary
val
insertsizeMetrics
:
Boolean
=
summary
.
getStatKeys
(
.
getStatKeys
(
runId
,
runId
,
metricsTag
,
metricsTag
,
...
@@ -105,7 +202,7 @@ object BammetricsReport extends ReportBuilder {
...
@@ -105,7 +202,7 @@ object BammetricsReport extends ReportBuilder {
)
)
.
exists
(
_
.
_2
.
isDefined
)
.
exists
(
_
.
_2
.
isDefined
)
val
targetSettings
=
summary
.
getSettingKeys
(
val
targetSettings
:
Map
[
String
,
Option
[
Any
]]
=
summary
.
getSettingKeys
(
runId
,
runId
,
metricsTag
,
metricsTag
,
NoModule
,
NoModule
,
...
@@ -126,9 +223,9 @@ object BammetricsReport extends ReportBuilder {
...
@@ -126,9 +223,9 @@ object BammetricsReport extends ReportBuilder {
for
(
t
<-
targets
)
{
for
(
t
<-
targets
)
{
covstatsPlotValuesArray
+=
Tuple2
(
t
,
BammetricsReportPage
.
covstatsPlotValues
(
summary
,
runId
,
sampleId
,
libId
,
Some
(
t
)))
covstatsPlotValuesArray
+=
Tuple2
(
t
,
BammetricsReportPage
.
covstatsPlotValues
(
summary
,
runId
,
sampleId
,
libId
,
Some
(
t
)))
}
}
val
covstatsPlotValuesList
=
covstatsPlotValuesArray
.
toList
val
covstatsPlotValuesList
:
List
[(
String
,
Map
[
String
,
Any
])]
=
covstatsPlotValuesArray
.
toList
val
alignmentSummaryReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
val
alignmentSummaryReportValues
:
Map
[
String
,
Any
]
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
summary
,
runId
,
runId
,
samples
,
samples
,
...
@@ -136,7 +233,7 @@ object BammetricsReport extends ReportBuilder {
...
@@ -136,7 +233,7 @@ object BammetricsReport extends ReportBuilder {
sampleId
,
sampleId
,
libId
libId
)
)
val
mappingQualityReportValues
=
BammetricsReportPage
.
mappingQualityValues
(
val
mappingQualityReportValues
:
Map
[
String
,
Any
]
=
BammetricsReportPage
.
mappingQualityValues
(
summary
,
summary
,
runId
,
runId
,
samples
,
samples
,
...
@@ -145,7 +242,7 @@ object BammetricsReport extends ReportBuilder {
...
@@ -145,7 +242,7 @@ object BammetricsReport extends ReportBuilder {
libId
,
libId
,
showPlot
=
true
showPlot
=
true
)
)
val
clippingReportValues
=
BammetricsReportPage
.
clippingValues
(
val
clippingReportValues
:
Map
[
String
,
Any
]
=
BammetricsReportPage
.
clippingValues
(
summary
,
summary
,
runId
,
runId
,
samples
,
samples
,
...
@@ -154,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
...
@@ -154,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
libId
,
libId
,
showPlot
=
true
showPlot
=
true
)
)
val
insertSizeReportValues
=
BammetricsReportPage
.
insertSizeValues
(
val
insertSizeReportValues
:
Map
[
String
,
Any
]
=
BammetricsReportPage
.
insertSizeValues
(
summary
,
summary
,
runId
,
runId
,
samples
,
samples
,
...
@@ -163,10 +260,10 @@ object BammetricsReport extends ReportBuilder {
...
@@ -163,10 +260,10 @@ object BammetricsReport extends ReportBuilder {
libId
,
libId
,
showPlot
=
true
showPlot
=
true
)
)
val
wgsHistogramReportValues
=
BammetricsReportPage
.
wgsHistogramValues
(
val
wgsHistogramReportValues
:
Map
[
String
,
Any
]
=
BammetricsReportPage
.
wgsHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
)
val
rnaHistogramReportValues
=
BammetricsReportPage
.
rnaHistogramValues
(
val
rnaHistogramReportValues
:
Map
[
String
,
Any
]
=
BammetricsReportPage
.
rnaHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
)
Future
{
Future
{
...
...
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