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biopet.biopet
Commits
505e9ae6
Commit
505e9ae6
authored
Jul 31, 2017
by
Ruben Vorderman
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Defutured wgsHistogramPlot
parent
fc410e94
Changes
1
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1 changed file
with
69 additions
and
68 deletions
+69
-68
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+69
-68
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
505e9ae6
...
...
@@ -341,16 +341,15 @@ object BammetricsReport extends ReportBuilder {
"insert_size"
->
List
(
"histogram"
,
"insert_size"
),
"count"
->
List
(
"histogram"
,
"All_Reads.fr_count"
)
)
val
plotTables
=
summaryForPlot
(
summary
,
statsPaths
,
"insert_size"
::
Nil
,
"count"
::
Nil
,
"bammetrics"
,
"CollectInsertSizeMetrics"
,
libraryLevel
,
sampleId
,
libraryId
)
plotTables
summaryForPlot
(
summary
,
statsPaths
,
"insert_size"
::
Nil
,
"count"
::
Nil
,
"bammetrics"
,
"CollectInsertSizeMetrics"
,
libraryLevel
,
sampleId
,
libraryId
)
}
/**
...
...
@@ -381,16 +380,15 @@ object BammetricsReport extends ReportBuilder {
"mapping_quality"
->
List
(
"mapping_quality"
,
"histogram"
,
"values"
),
"count"
->
List
(
"mapping_quality"
,
"histogram"
,
"counts"
)
)
val
plotTables
=
summaryForPlot
(
summary
,
statsPaths
,
"mapping_quality"
::
Nil
,
"count"
::
Nil
,
"bammetrics"
,
"bamstats"
,
libraryLevel
,
sampleId
,
libraryId
)
plotTables
summaryForPlot
(
summary
,
statsPaths
,
"mapping_quality"
::
Nil
,
"count"
::
Nil
,
"bammetrics"
,
"bamstats"
,
libraryLevel
,
sampleId
,
libraryId
)
}
def
mappingQualityPlot
(
outputDir
:
File
,
...
...
@@ -405,37 +403,57 @@ object BammetricsReport extends ReportBuilder {
"Reads"
,
"Mapping Quality"
)
}
def
clippingPlotTables
(
summary
:
SummaryDb
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
Array
[
Map
[
String
,
Array
[
Any
]]]
=
{}
def
clippingPlot
(
outputDir
:
File
,
prefix
:
String
,
clippingPlotTables
:
Array
[
Map
[
String
,
Array
[
Any
]]],
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
Unit
=
{
libraryId
:
Option
[
Int
]
=
None
)
:
Array
[
Map
[
String
,
Array
[
Any
]]]
=
{
val
statsPaths
=
Map
(
"clipping"
->
List
(
"clipping"
,
"histogram"
,
"values"
),
"count"
->
List
(
"clipping"
,
"histogram"
,
"counts"
)
)
summaryForPlot
(
summary
,
statsPaths
,
"clipping"
::
Nil
,
"count"
::
Nil
,
"bammetrics"
,
"bamstats"
,
libraryLevel
,
sampleId
,
libraryId
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"clipping"
::
Nil
,
"count"
::
Nil
,
"bammetrics"
,
"bamstats"
,
"Clipping"
,
"Reads"
,
"Clipping"
}
def
clippingPlot
(
outputDir
:
File
,
prefix
:
String
,
clippingPlotTables
:
Array
[
Map
[
String
,
Array
[
Any
]]])
:
Unit
=
{
writePlotFromSummary
(
outputDir
,
prefix
,
clippingPlotTables
,
"clipping"
::
Nil
,
"count"
::
Nil
,
"Clipping"
,
"Reads"
,
"Clipping"
)
}
def
wgsHistogramPlotTables
(
summary
:
SummaryDb
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
Array
[
Map
[
String
,
Array
[
Any
]]]
=
{
val
statsPaths
=
Map
(
"coverage"
->
List
(
"histogram"
,
"coverage"
),
"count"
->
List
(
"histogram"
,
"count"
),
"high_quality_coverage_count"
->
List
(
"histogram"
,
"high_quality_coverage_count"
)
)
summaryForPlot
(
summary
,
statsPaths
,
"coverage"
::
Nil
,
"count"
::
"high_quality_coverage_count"
::
Nil
,
"bammetrics"
,
"wgs"
,
libraryLevel
,
sampleId
,
libraryId
)
}
/**
...
...
@@ -449,32 +467,15 @@ object BammetricsReport extends ReportBuilder {
*/
def
wgsHistogramPlot
(
outputDir
:
File
,
prefix
:
String
,
tables
:
Array
[
Map
[
String
,
Array
[
Any
]]],
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
Unit
=
{
val
statsPaths
=
Map
(
"coverage"
->
List
(
"histogram"
,
"coverage"
),
"count"
->
List
(
"histogram"
,
"count"
),
"high_quality_coverage_count"
->
List
(
"histogram"
,
"high_quality_coverage_count"
)
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"coverage"
::
Nil
,
"count"
::
"high_quality_coverage_count"
::
Nil
,
"bammetrics"
,
"wgs"
,
"Coverage"
,
"Bases"
,
"Whole genome coverage"
)
wgsHistogramPlotTables
:
Array
[
Map
[
String
,
Array
[
Any
]]])
:
Unit
=
{
writePlotFromSummary
(
outputDir
,
prefix
,
wgsHistogramPlotTables
,
"coverage"
::
Nil
,
"count"
::
"high_quality_coverage_count"
::
Nil
,
"Coverage"
,
"Bases"
,
"Whole genome coverage"
)
}
/**
...
...
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