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biopet.biopet
Commits
11fe02b4
Commit
11fe02b4
authored
Oct 29, 2015
by
Wai Yi Leung
Browse files
change pipeline test, not test on sambambaview, but on samtoolsview
parent
755b864d
Changes
1
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public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
View file @
11fe02b4
...
...
@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.sam
bamba.Sambamba
View
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
KrakenReportToJson
}
import
nl.lumc.sasc.biopet.extensions.sam
tools.Samtools
View
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
KrakenReportToJson
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
...
...
@@ -97,7 +97,8 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
// SamToFastq should have started if it was started from bam
gears
.
functions
.
count
(
_
.
isInstanceOf
[
SamToFastq
])
shouldBe
(
if
(
fromBam
)
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
SambambaView
])
shouldBe
(
if
(
fromBam
)
1
else
0
)
// gears.functions.count(_.isInstanceOf[SambambaView]) shouldBe (if (fromBam) 1 else 0)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
SamtoolsView
])
shouldBe
(
if
(
fromBam
)
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
FastqSync
])
shouldBe
(
if
(
fromBam
)
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
Kraken
])
shouldBe
1
...
...
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