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Mirrors
biopet.biopet
Commits
14e2e355
Commit
14e2e355
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Fix unit testing
parent
9e21462b
Changes
12
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
View file @
14e2e355
...
...
@@ -42,7 +42,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
var
opt_front
:
Set
[
String
]
=
Set
()
if
(
config
.
contains
(
"front"
))
for
(
adapter
<-
config
(
"front"
).
asList
)
opt_front
+=
adapter
.
toString
var
opt_discard
:
Boolean
=
config
(
"discard"
)
var
opt_discard
:
Boolean
=
config
(
"discard"
,
default
=
false
)
var
opt_minimum_length
:
String
=
config
(
"minimum_length"
,
1
)
var
opt_maximum_length
:
String
=
config
(
"maximum_length"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
View file @
14e2e355
...
...
@@ -39,9 +39,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"fastqc"
)
var
java_exe
:
String
=
config
(
"exe"
,
default
=
"java"
,
submodule
=
"java"
,
freeVar
=
false
)
var
kmers
:
Option
[
Int
]
=
config
(
"kmers"
)
var
quiet
:
Boolean
=
config
(
"quiet"
)
var
noextract
:
Boolean
=
config
(
"noextract"
)
var
nogroup
:
Boolean
=
config
(
"nogroup"
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
var
noextract
:
Boolean
=
config
(
"noextract"
,
default
=
false
)
var
nogroup
:
Boolean
=
config
(
"nogroup"
,
default
=
false
)
var
extract
:
Boolean
=
config
(
"extract"
,
default
=
true
)
override
val
versionRegex
=
"""FastQC (.*)"""
.
r
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
View file @
14e2e355
...
...
@@ -42,10 +42,10 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var
iterations
:
Option
[
Int
]
=
config
(
"iterations"
)
var
minSnps
:
Option
[
Int
]
=
config
(
"min_snps"
)
var
convergeMethod
:
String
=
config
(
"converge_method"
)
var
useTimeStamp
:
Boolean
=
config
(
"use_time_stamp"
)
var
useTimeStamp
:
Boolean
=
config
(
"use_time_stamp"
,
default
=
false
)
var
prefix
:
String
=
config
(
"prefix"
)
var
verbose
:
Boolean
=
config
(
"verbose"
)
var
noCleanup
:
Boolean
=
config
(
"no_cleanup"
)
var
verbose
:
Boolean
=
config
(
"verbose"
,
default
=
false
)
var
noCleanup
:
Boolean
=
config
(
"no_cleanup"
,
default
=
false
)
override
def
afterGraph
:
Unit
=
{
super
.
afterGraph
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
14e2e355
...
...
@@ -46,9 +46,9 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
var
qualityType
:
String
=
config
(
"qualitytype"
)
var
qualityThreshold
:
Option
[
Int
]
=
config
(
"qualityThreshold"
)
var
lengthThreshold
:
Option
[
Int
]
=
config
(
"lengthThreshold"
)
var
noFiveprime
:
Boolean
=
config
(
"noFiveprime"
)
var
discardN
:
Boolean
=
config
(
"discardN"
)
var
quiet
:
Boolean
=
config
(
"quiet"
)
var
noFiveprime
:
Boolean
=
config
(
"noFiveprime"
,
default
=
false
)
var
discardN
:
Boolean
=
config
(
"discardN"
,
default
=
false
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
var
defaultQualityType
:
String
=
config
(
"defaultqualitytype"
,
default
=
"sanger"
)
override
val
versionRegex
=
"""sickle version (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala
View file @
14e2e355
...
...
@@ -36,7 +36,7 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
var
R
:
String
=
config
(
"R"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
r
:
Option
[
Float
]
=
config
(
"r"
)
var
S
:
Boolean
=
config
(
"S"
)
var
S
:
Boolean
=
config
(
"S"
,
default
=
false
)
var
M
:
Boolean
=
config
(
"M"
,
default
=
true
)
var
w
:
Option
[
Int
]
=
config
(
"w"
)
var
d
:
Option
[
Int
]
=
config
(
"d"
)
...
...
@@ -44,8 +44,8 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
var
D
:
Option
[
Float
]
=
config
(
"D"
)
var
W
:
Option
[
Int
]
=
config
(
"W"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
P
:
Boolean
=
config
(
"P"
)
var
e
:
Boolean
=
config
(
"e"
)
var
P
:
Boolean
=
config
(
"P"
,
default
=
false
)
var
e
:
Boolean
=
config
(
"e"
,
default
=
false
)
var
A
:
Option
[
Int
]
=
config
(
"A"
)
var
B
:
Option
[
Int
]
=
config
(
"B"
)
var
O
:
String
=
config
(
"O"
)
...
...
@@ -53,13 +53,13 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
var
L
:
String
=
config
(
"L"
)
var
U
:
Option
[
Int
]
=
config
(
"U"
)
var
x
:
String
=
config
(
"x"
)
var
p
:
Boolean
=
config
(
"p"
)
var
p
:
Boolean
=
config
(
"p"
,
default
=
false
)
var
v
:
Option
[
Int
]
=
config
(
"v"
)
var
T
:
Option
[
Int
]
=
config
(
"T"
)
var
h
:
Option
[
Int
]
=
config
(
"h"
)
var
a
:
Boolean
=
config
(
"a"
)
var
C
:
Boolean
=
config
(
"C"
)
var
Y
:
Boolean
=
config
(
"Y"
)
var
a
:
Boolean
=
config
(
"a"
,
default
=
false
)
var
C
:
Boolean
=
config
(
"C"
,
default
=
false
)
var
Y
:
Boolean
=
config
(
"Y"
,
default
=
false
)
var
I
:
String
=
config
(
"I"
)
executable
=
config
(
"exe"
,
default
=
"bwa"
,
freeVar
=
false
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
View file @
14e2e355
...
...
@@ -29,7 +29,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
var
maxInstertSize
:
Option
[
Int
]
=
config
(
"maxInstertSize"
)
@Argument
(
doc
=
"ADAPTER_SEQUENCE"
,
required
=
false
)
var
adapterSequence
:
List
[
String
]
=
config
(
"adapterSequence"
)
var
adapterSequence
:
List
[
String
]
=
config
(
"adapterSequence"
,
default
=
Nil
)
@Argument
(
doc
=
"IS_BISULFITE_SEQUENCED"
,
required
=
false
)
var
isBisulfiteSequenced
:
Option
[
Boolean
]
=
config
(
"isBisulfiteSequenced"
)
...
...
@@ -44,7 +44,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
var
assumeSorted
:
Boolean
=
config
(
"assumeSorted"
,
default
=
true
)
@Argument
(
doc
=
"METRIC_ACCUMULATION_LEVEL"
,
required
=
false
)
var
metricAccumulationLevel
:
List
[
String
]
=
config
(
"metricaccumulationlevel"
)
var
metricAccumulationLevel
:
List
[
String
]
=
config
(
"metricaccumulationlevel"
,
default
=
Nil
)
@Argument
(
doc
=
"STOP_AFTER"
,
required
=
false
)
var
stopAfter
:
Option
[
Long
]
=
config
(
"stopAfter"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
View file @
14e2e355
...
...
@@ -19,6 +19,8 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
scala.collection.immutable.Nil
class
CollectInsertSizeMetrics
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"picard.analysis.CollectInsertSizeMetrics"
...
...
@@ -47,7 +49,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
var
stopAfter
:
Option
[
Long
]
=
config
(
"stopAfter"
)
@Argument
(
doc
=
"METRIC_ACCUMULATION_LEVEL"
,
required
=
false
)
var
metricAccumulationLevel
:
List
[
String
]
=
config
(
"metricaccumulationlevel"
)
var
metricAccumulationLevel
:
List
[
String
]
=
config
(
"metricaccumulationlevel"
,
default
=
Nil
)
@Argument
(
doc
=
"HISTOGRAM_WIDTH"
,
required
=
false
)
var
histogramWidth
:
Option
[
Int
]
=
config
(
"histogramWidth"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
View file @
14e2e355
...
...
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract
class
Samtools
extends
BiopetCommandLineFunction
{
override
def
subPath
=
"samtools"
::
super
.
subPath
executable
=
config
(
"exe"
,
default
=
"samtools"
,
freeVar
=
false
)
executable
=
config
(
"exe"
,
default
=
"samtools"
)
override
def
versionCommand
=
executable
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
View file @
14e2e355
...
...
@@ -58,28 +58,28 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
var
L
:
Option
[
Int
]
=
config
(
"L"
)
/** mask complement region (effective with -M) */
var
c
:
Boolean
=
config
(
"c"
)
var
c
:
Boolean
=
config
(
"c"
,
default
=
false
)
/** reverse complement */
var
r
:
Boolean
=
config
(
"r"
)
var
r
:
Boolean
=
config
(
"r"
,
default
=
false
)
/** force FASTA output (discard quality) */
var
A
:
Boolean
=
config
(
"A"
)
var
A
:
Boolean
=
config
(
"A"
,
default
=
false
)
/** drop comments at the header lines */
var
C
:
Boolean
=
config
(
"C"
)
var
C
:
Boolean
=
config
(
"C"
,
default
=
false
)
/** drop sequences containing ambiguous bases */
var
N
:
Boolean
=
config
(
"N"
)
var
N
:
Boolean
=
config
(
"N"
,
default
=
false
)
/** output the 2n-1 reads only */
var
flag1
:
Boolean
=
config
(
"1"
)
var
flag1
:
Boolean
=
config
(
"1"
,
default
=
false
)
/** output the 2n reads only */
var
flag2
:
Boolean
=
config
(
"2"
)
var
flag2
:
Boolean
=
config
(
"2"
,
default
=
false
)
/** shift quality by '(-Q) - 33' */
var
V
:
Boolean
=
config
(
"V"
)
var
V
:
Boolean
=
config
(
"V"
,
default
=
false
)
def
cmdLine
=
{
required
(
executable
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
14e2e355
...
...
@@ -40,7 +40,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
var
minTotalDepth
:
Option
[
Int
]
=
config
(
"min_total_depth"
)
var
minAlternateDepth
:
Option
[
Int
]
=
config
(
"min_alternate_depth"
)
var
minSamplesPass
:
Option
[
Int
]
=
config
(
"min_samples_pass"
)
var
filterRefCalls
:
Boolean
=
config
(
"filter_ref_calls"
)
var
filterRefCalls
:
Boolean
=
config
(
"filter_ref_calls"
,
default
=
false
)
override
val
defaultVmem
=
"8G"
memoryLimit
=
Option
(
4.0
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
View file @
14e2e355
...
...
@@ -354,7 +354,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2long
(
value
:
ConfigValue
)
:
Long
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2long
(
value
.
value
)
else
0
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2long
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -372,7 +373,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2int
(
value
:
ConfigValue
)
:
Int
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2int
(
value
.
value
)
else
0
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2int
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -390,7 +392,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2double
(
value
:
ConfigValue
)
:
Double
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2double
(
value
.
value
)
else
0
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2double
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -408,7 +411,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2float
(
value
:
ConfigValue
)
:
Float
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2float
(
value
.
value
)
else
0
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2float
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -426,7 +430,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2boolean
(
value
:
ConfigValue
)
:
Boolean
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2boolean
(
value
.
value
)
else
false
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2boolean
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -444,7 +449,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2list
(
value
:
ConfigValue
)
:
List
[
Any
]
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2list
(
value
.
value
)
else
null
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2list
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -453,7 +459,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2stringList
(
value
:
ConfigValue
)
:
List
[
String
]
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2stringList
(
value
.
value
)
else
null
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2stringList
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -462,7 +469,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2stringSet
(
value
:
ConfigValue
)
:
Set
[
String
]
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2stringList
(
value
.
value
).
toSet
else
null
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2stringList
(
value
.
value
).
toSet
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
/**
...
...
@@ -471,7 +479,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit
def
configValue2map
(
value
:
ConfigValue
)
:
Map
[
String
,
Any
]
=
{
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2map
(
value
.
value
)
else
null
if
(
value
!=
null
&&
value
.
value
!=
null
&&
value
.
value
!=
None
)
any2map
(
value
.
value
)
else
throw
new
IllegalStateException
(
"Value does not exist"
)
}
}
}
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
View file @
14e2e355
...
...
@@ -169,17 +169,20 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
@Test
def
testImplicits
:
Unit
=
{
val
index
=
ConfigValueIndex
(
"test"
,
Nil
,
"test"
)
new
ImplicitConversions
{
var
map
:
Map
[
String
,
Any
]
=
ConfigValue
(
index
,
index
,
Map
())
map
=
ConfigValue
(
index
,
index
,
null
)
configValue2list
(
ConfigValue
(
index
,
index
,
List
(
""
)))
shouldBe
List
(
""
)
configValue2list
(
ConfigValue
(
index
,
index
,
null
))
shouldBe
null
intercept
[
IllegalStateException
]
{
configValue2list
(
ConfigValue
(
index
,
index
,
null
))
}
configValue2stringList
(
ConfigValue
(
index
,
index
,
List
(
""
)))
shouldBe
List
(
""
)
configValue2stringList
(
ConfigValue
(
index
,
index
,
null
))
shouldBe
null
intercept
[
IllegalStateException
]
{
configValue2stringList
(
ConfigValue
(
index
,
index
,
null
))
}
configValue2stringSet
(
ConfigValue
(
index
,
index
,
List
(
""
)))
shouldBe
Set
(
""
)
configValue2stringSet
(
ConfigValue
(
index
,
index
,
null
))
shouldBe
null
intercept
[
IllegalStateException
]
{
configValue2stringSet
(
ConfigValue
(
index
,
index
,
null
))
}
var
int
:
Int
=
ConfigValue
(
index
,
index
,
1
)
intercept
[
IllegalStateException
]
{
...
...
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