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biopet.biopet
Commits
6104d68e
Commit
6104d68e
authored
May 11, 2016
by
Wai Yi Leung
Browse files
Update test
parent
39772398
Changes
1
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flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
View file @
6104d68e
...
...
@@ -73,11 +73,15 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
fqc
.
contaminants
=
Option
(
resourceFile
(
"fqc_contaminants_v0101.txt"
))
// found adapters also contain the adapters in reverse complement (done within flexiprep/fastqc only)
val
adapters
=
fqc
.
foundAdapters
// we find 1 adapter which comes with the Reverse Complement counterpart
adapters
.
size
shouldBe
2
adapters
.
head
.
name
shouldEqual
"TruSeq Adapter, Index 1_RC"
adapters
.
head
.
seq
shouldEqual
"CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC"
if
(
fqc
.
enableRCtrimming
)
{
// we find 1 adapter which comes with the Reverse Complement counterpart
adapters
.
size
shouldBe
2
adapters
.
head
.
name
shouldEqual
"TruSeq Adapter, Index 1_RC"
adapters
.
head
.
seq
shouldEqual
"CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC"
}
else
{
adapters
.
size
shouldBe
1
}
adapters
.
last
.
name
shouldEqual
"TruSeq Adapter, Index 1"
adapters
.
last
.
seq
shouldEqual
"GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
...
...
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