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biopet.biopet
Commits
8265ffec
Commit
8265ffec
authored
Jan 05, 2017
by
Peter van 't Hof
Browse files
Renamed class because of decrapation
parent
bae8c53d
Changes
3
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
8265ffec
...
...
@@ -136,7 +136,7 @@ class BamMetrics(val root: Configurable) extends QScript
ampBedToInterval
.
isIntermediate
=
true
add
(
ampBedToInterval
)
val
chsMetrics
=
C
alculate
HsMetrics
(
this
,
inputBam
,
val
chsMetrics
=
C
ollect
HsMetrics
(
this
,
inputBam
,
List
(
ampIntervals
),
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
add
(
chsMetrics
)
addSummarizable
(
chsMetrics
,
"hs_metrics"
)
...
...
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
8265ffec
...
...
@@ -75,7 +75,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectRnaSeqMetrics
])
shouldBe
(
if
(
rna
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectWgsMetrics
])
shouldBe
(
if
(
wgs
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectMultipleMetrics
])
shouldBe
1
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
C
alculate
HsMetrics
])
shouldBe
(
if
(
amplicon
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
C
ollect
HsMetrics
])
shouldBe
(
if
(
amplicon
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectTargetedPcrMetrics
])
shouldBe
(
if
(
amplicon
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
BamStats
])
shouldBe
1
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/C
alculate
HsMetrics.scala
→
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/C
ollect
HsMetrics.scala
View file @
8265ffec
...
...
@@ -22,8 +22,8 @@ import nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/** Extension for picard CalculateHsMetrics */
class
C
alculate
HsMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
with
Reference
{
javaMainClass
=
new
picard
.
analysis
.
directed
.
C
alculate
HsMetrics
().
getClass
.
getName
class
C
ollect
HsMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
with
Reference
{
javaMainClass
=
new
picard
.
analysis
.
directed
.
C
ollect
HsMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
var
input
:
File
=
_
...
...
@@ -72,14 +72,14 @@ class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizabl
def
summaryStats
:
Any
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
C
alculate
HsMetrics
{
object
C
ollect
HsMetrics
{
/** Returns default CalculateHsMetrics */
def
apply
(
root
:
Configurable
,
input
:
File
,
baitIntervals
:
List
[
File
],
targetIntervals
:
List
[
File
],
outputDir
:
File
)
:
C
alculate
HsMetrics
=
{
val
calculateHsMetrics
=
new
C
alculate
HsMetrics
(
root
)
outputDir
:
File
)
:
C
ollect
HsMetrics
=
{
val
calculateHsMetrics
=
new
C
ollect
HsMetrics
(
root
)
calculateHsMetrics
.
input
=
input
calculateHsMetrics
.
baitIntervals
=
baitIntervals
calculateHsMetrics
.
targetIntervals
=
targetIntervals
...
...
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