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biopet.biopet
Commits
fba9e593
Commit
fba9e593
authored
May 18, 2015
by
Peter van 't Hof
Browse files
Change method singature
parent
6111da8c
Changes
11
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
View file @
fba9e593
...
...
@@ -30,7 +30,7 @@ trait Summarizable {
def
summaryFiles
:
Map
[
String
,
File
]
/** Must returns stats to store into summary */
def
summaryStats
:
Map
[
String
,
Any
]
def
summaryStats
:
Any
/** Can be used to add additional Summarizable, this is executed at the start of WriteSummary*/
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
{}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
fba9e593
...
...
@@ -139,7 +139,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val
stats
=
summarizable
.
summaryStats
val
files
=
parseFiles
(
summarizable
.
summaryFiles
)
(
if
(
stats
.
isEmpty
)
Map
[
String
,
Any
]()
else
Map
(
"stats"
->
Map
(
name
->
stats
)))
++
(
Map
(
"stats"
->
Map
(
name
->
stats
)))
++
(
if
(
files
.
isEmpty
)
Map
[
String
,
Any
]()
else
Map
(
"files"
->
Map
(
name
->
files
)))
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
View file @
fba9e593
...
...
@@ -63,7 +63,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizabl
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
:
Any
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CalculateHsMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
View file @
fba9e593
...
...
@@ -66,7 +66,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectAlignmentSummaryMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
fba9e593
...
...
@@ -71,7 +71,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectGcBiasMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
View file @
fba9e593
...
...
@@ -75,7 +75,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
/** Returns files for summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output_histogram"
->
outputHistogram
)
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectInsertSizeMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
fba9e593
...
...
@@ -68,25 +68,25 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
:
Unit
=
{
program
.
foreach
(
p
=>
{
val
stats
:
Map
[
String
,
Any
]
=
p
match
{
val
stats
:
Any
=
p
match
{
case
_
if
p
==
Programs
.
CollectAlignmentSummaryMetrics
.
toString
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
)
).
getOrElse
(
Map
(
))
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
)
,
groupBy
=
Some
(
"CATEGORY"
))
case
_
if
p
==
Programs
.
CollectInsertSizeMetrics
.
toString
=>
Map
(
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
))
.
getOrElse
(
Map
())
,
"histogram"
->
Picard
.
get
Metrics
(
new
File
(
outputName
+
".insert_size_metrics"
)
,
"HISTOGRAM"
).
getOrElse
(
Map
()
)
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)),
"histogram"
->
Picard
.
get
Histogram
(
new
File
(
outputName
+
".insert_size_metrics"
))
)
case
_
if
p
==
Programs
.
QualityScoreDistribution
.
toString
=>
Picard
.
get
Metrics
(
new
File
(
outputName
+
".quality_distribution_metrics"
)
,
"HISTOGRAM"
).
getOrElse
(
Map
()
)
Picard
.
get
Histogram
(
new
File
(
outputName
+
".quality_distribution_metrics"
))
case
_
if
p
==
Programs
.
MeanQualityByCycle
.
toString
=>
Picard
.
get
Metrics
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
)
,
"HISTOGRAM"
).
getOrElse
(
Map
()
)
Picard
.
get
Histogram
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
))
case
_
if
p
==
Programs
.
CollectBaseDistributionByCycle
.
toString
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
))
.
getOrElse
(
Map
())
case
_
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
))
case
_
=>
None
}
val
sum
=
new
Summarizable
{
override
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
override
def
summaryStats
:
Map
[
String
,
Any
]
=
stats
override
def
summaryStats
=
stats
}
qscript
.
addSummarizable
(
sum
,
p
)
})
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
View file @
fba9e593
...
...
@@ -84,7 +84,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
"output_chart"
->
chartOutput
).
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
}
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
override
def
commandLine
=
super
.
commandLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
View file @
fba9e593
...
...
@@ -51,7 +51,7 @@ class CollectTargetedPcrMetrics(val root: Configurable) extends Picard with Summ
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectTargetedPcrMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
View file @
fba9e593
...
...
@@ -51,5 +51,5 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
View file @
fba9e593
...
...
@@ -100,7 +100,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
outputMetrics
).
getOrElse
(
Map
())
def
summaryStats
=
Picard
.
getMetrics
(
outputMetrics
).
getOrElse
(
Map
())
}
object
MarkDuplicates
{
/** Returns default MarkDuplicates */
...
...
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