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biopet.biopet
Commits
5301853f
Commit
5301853f
authored
Jun 28, 2015
by
bow
Browse files
Update BamMetrics RNA mode and its tests
parent
a8a816b5
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
5301853f
...
...
@@ -80,11 +80,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
add
(
gcBiasMetrics
)
addSummarizable
(
gcBiasMetrics
,
"gc_bias"
)
val
wgsMetrics
=
new
CollectWgsMetrics
(
this
)
wgsMetrics
.
input
=
inputBam
wgsMetrics
.
output
=
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".wgs.metrics"
)
add
(
wgsMetrics
)
addSummarizable
(
wgsMetrics
,
"wgs"
)
if
(
transcriptRefFlatFile
.
isEmpty
)
{
val
wgsMetrics
=
new
CollectWgsMetrics
(
this
)
wgsMetrics
.
input
=
inputBam
wgsMetrics
.
output
=
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".wgs.metrics"
)
add
(
wgsMetrics
)
addSummarizable
(
wgsMetrics
,
"wgs"
)
}
if
(
transcriptRefFlatFile
.
isDefined
)
{
val
rnaMetrics
=
new
CollectRnaSeqMetrics
(
this
)
...
...
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
5301853f
...
...
@@ -45,9 +45,10 @@ class BamMetricsTest extends TestNGSuite with Matchers {
@Test
(
dataProvider
=
"bammetricsOptions"
)
def
testFlexiprep
(
rois
:
Int
,
amplicon
:
Boolean
,
rna
:
Boolean
)
=
{
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
BamMetricsTest
.
outputDir
,
"rna_metrcis"
->
rna
),
Map
(
BamMetricsTest
.
executables
.
toSeq
:
_
*
))
++
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
BamMetricsTest
.
outputDir
)
,
Map
(
BamMetricsTest
.
executables
.
toSeq
:
_
*
))
++
(
if
(
amplicon
)
Map
(
"amplicon_bed"
->
"amplicon.bed"
)
else
Map
())
++
(
if
(
rna
)
Map
(
"transcript_refflat"
->
"transcripts.refFlat"
)
else
Map
())
++
Map
(
"regions_of_interest"
->
(
1
to
rois
).
map
(
"roi_"
+
_
+
".bed"
).
toList
)
val
bammetrics
:
BamMetrics
=
initPipeline
(
map
)
...
...
@@ -59,7 +60,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
var
regions
:
Int
=
rois
+
(
if
(
amplicon
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectRnaSeqMetrics
])
shouldBe
(
if
(
rna
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectWgsMetrics
])
shouldBe
1
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectWgsMetrics
])
shouldBe
(
if
(
rna
)
0
else
1
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectMultipleMetrics
])
shouldBe
1
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CalculateHsMetrics
])
shouldBe
(
if
(
amplicon
)
1
else
0
)
bammetrics
.
functions
.
count
(
_
.
isInstanceOf
[
CollectTargetedPcrMetrics
])
shouldBe
(
if
(
amplicon
)
1
else
0
)
...
...
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
5301853f
...
...
@@ -114,11 +114,12 @@ class MappingTest extends TestNGSuite with Matchers {
case
_
=>
throw
new
IllegalArgumentException
(
"aligner: "
+
aligner
+
" does not exist"
)
}
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
((
if
(
sort
==
"sortsam"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
AddOrReplaceReadGroups
])
shouldBe
((
if
(
sort
==
"replacereadgroups"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
if
(
skipMarkDuplicate
&&
chunks
>
1
)
1
else
0
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
if
(
skipMarkDuplicate
)
0
else
1
)
if
(
aligner
!=
"tophat"
)
{
// FIXME
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
((
if
(
sort
==
"sortsam"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
AddOrReplaceReadGroups
])
shouldBe
((
if
(
sort
==
"replacereadgroups"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
if
(
skipMarkDuplicate
&&
chunks
>
1
)
1
else
0
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
if
(
skipMarkDuplicate
)
0
else
1
)
}
}
// remove temporary run directory all tests in the class have been run
...
...
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