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biopet.biopet
Commits
75f13b0e
Commit
75f13b0e
authored
May 17, 2016
by
Peter van 't Hof
Browse files
Added testing for start from bam
parent
ec4eb7de
Changes
2
Hide whitespace changes
Inline
Side-by-side
mapping/src/test/resources/empty.sam
0 → 100644
View file @
75f13b0e
@HD VN:1.5 SO:coordinate
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
@RG ID:001 SM:sample3 LB:lib1
r02 0 chr1 210 60 10M * 0 0 TACGTACGTA EEFFGGHHII RG:Z:001
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
75f13b0e
...
...
@@ -30,6 +30,8 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
def
unmappedToGears
=
false
def
sample1
=
Array
(
true
,
false
)
def
sample2
=
Array
(
true
,
false
)
def
sample3
=
false
def
sample4
=
false
@DataProvider
(
name
=
"mappingOptions"
)
def
mappingOptions
=
{
...
...
@@ -44,6 +46,8 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
var
m
:
Map
[
String
,
Any
]
=
MultisampleMappingTestTrait
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample2
,
m
)
if
(
sample3
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample3
,
m
)
if
(
sample4
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample4
,
m
)
m
++
Map
(
"merge_strategy"
->
merge
.
toString
,
"bam_to_fastq"
->
bamToFastq
,
...
...
@@ -52,19 +56,23 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
)
}
if
(!
sample1
&&
!
sample2
)
{
// When no samples
if
(!
sample1
&&
!
sample2
&&
!
sample3
&&
!
sample4
)
{
// When no samples
intercept
[
IllegalArgumentException
]
{
initPipeline
(
map
).
script
()
}
}
else
if
(
sample4
&&
!
bamToFastq
&&
!
correctReadgroups
)
{
intercept
[
IllegalStateException
]
{
initPipeline
(
map
).
script
()
}
}
else
{
val
pipeline
=
initPipeline
(
map
)
pipeline
.
script
()
val
numberLibs
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
2
else
0
)
val
number
Fastq
Libs
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
2
else
0
)
+
(
if
(
sample3
&&
bamToFastq
)
1
else
0
)
+
(
if
(
sample4
&&
bamToFastq
)
1
else
0
)
val
numberSamples
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
1
else
0
)
import
MultisampleMapping.MergeStrategy
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
numberLibs
+
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
number
Fastq
Libs
+
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MarkDuplicates
||
merge
==
MergeStrategy
.
PreProcessMarkDuplicates
))
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MergeSam
||
merge
==
MergeStrategy
.
PreProcessMergeSam
))
1
else
0
))
...
...
@@ -84,6 +92,43 @@ class MultisampleMappingTest extends MultisampleMappingTestTrait {
override
def
sample1
=
Array
(
true
)
}
class
MultisampleMappingNoSamplesTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
false
)
override
def
sample2
=
Array
(
false
)
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
class
MultisampleMappingBamTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
false
)
override
def
sample2
=
Array
(
false
)
override
def
sample3
=
true
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
class
MultisampleMappingWrongBamTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
false
)
override
def
sample2
=
Array
(
false
)
override
def
sample4
=
true
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
class
MultisampleMappingCorrectBamTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
false
)
override
def
sample2
=
Array
(
false
)
override
def
correctReadgroups
=
true
override
def
sample4
=
true
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
class
MultisampleMappingBamToFastqTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
false
)
override
def
sample2
=
Array
(
false
)
override
def
bamToFastq
=
true
override
def
sample3
=
true
override
def
sample4
=
true
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
object
MultisampleMappingTestTrait
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
...
...
@@ -104,6 +149,7 @@ object MultisampleMappingTestTrait {
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
copyFile
(
"ref.fa.fai"
)
copyFile
(
"empty.sam"
)
val
config
=
Map
(
"name_prefix"
->
"test"
,
...
...
@@ -146,4 +192,20 @@ object MultisampleMappingTestTrait {
)
)
)))
val
sample3
=
Map
(
"samples"
->
Map
(
"sample3"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"bam"
->
(
outputDir
+
File
.
separator
+
"empty.sam"
)
)
)
)))
val
sample4
=
Map
(
"samples"
->
Map
(
"sample4"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"bam"
->
(
outputDir
+
File
.
separator
+
"empty.sam"
)
)
)
)))
}
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