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biopet.biopet
Commits
c181bccd
Commit
c181bccd
authored
Jul 13, 2017
by
Peter van 't Hof
Browse files
Fixing compile and code warnings
parent
23f8f923
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
View file @
c181bccd
...
...
@@ -116,22 +116,22 @@ class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with Sc
outputIndex
=
VcfUtils
.
getVcfIndexFile
(
out
)
}
override
def
cmdLine
=
super
.
cmdLine
+
required
(
TaggedFile
.
formatCommandLineParameter
(
"-V"
,
variant
),
variant
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-snpEffFile"
,
snpEffFile
.
getOrElse
()),
snpEffFile
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
)),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-comp"
,
comp
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-resource"
,
resource
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-o"
,
out
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-A"
,
annotation
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-XA"
,
excludeAnnotation
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-G"
,
group
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-E"
,
expression
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
resourceAlleleConcordance
,
"-rac"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
useAllAnnotations
,
"-all"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
alwaysAppendDbsnpId
,
"-alwaysAppendDbsnpId"
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-mvq"
,
MendelViolationGenotypeQualityThreshold
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
MendelViolationGenotypeQualityThresholdFormat
)
+
conditional
(
filter_reads_with_N_cigar
,
"-filterRNC"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
override
def
cmdLine
:
String
=
super
.
cmdLine
+
required
(
TaggedFile
.
formatCommandLineParameter
(
"-V"
,
variant
),
variant
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-snpEffFile"
,
snpEffFile
.
getOrElse
(
new
File
(
"."
)
)),
snpEffFile
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
new
File
(
"."
))),
dbsnp
)
+
repeat
(
"-comp"
,
comp
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
)
+
repeat
(
"-resource"
,
resource
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
)
+
optional
(
"-o"
,
out
)
+
repeat
(
"-A"
,
annotation
)
+
repeat
(
"-XA"
,
excludeAnnotation
)
+
repeat
(
"-G"
,
group
)
+
repeat
(
"-E"
,
expression
)
+
conditional
(
resourceAlleleConcordance
,
"-rac"
)
+
conditional
(
useAllAnnotations
,
"-all"
)
+
conditional
(
alwaysAppendDbsnpId
,
"-alwaysAppendDbsnpId"
)
+
optional
(
"-mvq"
,
MendelViolationGenotypeQualityThreshold
,
format
=
MendelViolationGenotypeQualityThresholdFormat
)
+
conditional
(
filter_reads_with_N_cigar
,
"-filterRNC"
)
+
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
)
}
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala
View file @
c181bccd
...
...
@@ -28,7 +28,7 @@ object Question {
if
(
posibleValues
.
nonEmpty
)
println
(
s
"possible values: ${posibleValues.mkString("
,
")}"
)
default
.
foreach
(
x
=>
println
(
s
"Default value: $x"
))
print
(
s
"$name > "
)
(
Console
.
readLine
.
trim
,
default
)
match
{
(
scala
.
io
.
StdIn
.
readLine
.
trim
,
default
)
match
{
case
(
a
,
Some
(
d
))
if
a
.
isEmpty
=>
d
case
(
a
,
None
)
if
a
.
isEmpty
=>
println
(
"ERROR: Value is required"
)
...
...
@@ -50,7 +50,7 @@ object Question {
description
.
foreach
(
println
)
default
.
foreach
(
x
=>
println
(
s
"Default value: $x"
))
print
(
s
"$name (y/n) > "
)
Console
.
readLine
.
trim
.
toLowerCase
match
{
scala
.
io
.
StdIn
.
readLine
.
trim
.
toLowerCase
match
{
case
""
=>
default
match
{
case
Some
(
d
)
=>
d
...
...
@@ -75,7 +75,7 @@ object Question {
if
(
posibleValues
.
nonEmpty
)
println
(
s
"possible values: ${posibleValues.mkString("
,
")}"
)
default
.
foreach
(
x
=>
println
(
s
"Default value: $x"
))
print
(
s
"$name > "
)
(
Console
.
readLine
.
split
(
","
).
toList
.
map
(
_
.
trim
),
default
)
match
{
(
scala
.
io
.
StdIn
.
readLine
.
split
(
","
).
toList
.
map
(
_
.
trim
),
default
)
match
{
case
(
List
(
""
),
Some
(
d
))
=>
d
case
(
List
(
""
),
None
)
=>
println
(
"ERROR: Value is required"
)
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @
c181bccd
...
...
@@ -523,16 +523,14 @@ class SummaryDbWrite(val db: Database)(implicit val ec: ExecutionContext) extend
/** This method will create all tables */
def
createTables
()
:
Unit
=
{
try
{
val
setup
=
DBIO
.
seq
(
(
runs
.
schema
++
samples
.
schema
++
libraries
.
schema
++
pipelines
.
schema
++
modules
.
schema
++
stats
.
schema
++
settings
.
schema
++
files
.
schema
++
executables
.
schema
).
create
)
val
setupFuture
=
db
.
run
(
setup
)
Await
.
result
(
setupFuture
,
Duration
.
Inf
)
}
val
setup
=
DBIO
.
seq
(
(
runs
.
schema
++
samples
.
schema
++
libraries
.
schema
++
pipelines
.
schema
++
modules
.
schema
++
stats
.
schema
++
settings
.
schema
++
files
.
schema
++
executables
.
schema
).
create
)
val
setupFuture
=
db
.
run
(
setup
)
Await
.
result
(
setupFuture
,
Duration
.
Inf
)
}
/** This method will create a new run and return the runId */
...
...
tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala
View file @
c181bccd
...
...
@@ -68,14 +68,14 @@ class Tarmac(val parent: Configurable)
)
}
def
init
()
=
{}
def
init
()
:
Unit
=
{}
def
biopetScript
()
=
{
def
biopetScript
()
:
Unit
=
{
addSamplesJobs
()
addSummaryJobs
()
}
def
addMultiSampleJobs
()
=
{
def
addMultiSampleJobs
()
:
Unit
=
{
val
initRefMap
=
samples
map
{
case
(
sampleName
,
sample
)
=>
sample
->
getReferenceSamplesForSample
(
sampleName
)
}
...
...
@@ -383,7 +383,7 @@ class Tarmac(val parent: Configurable)
*/
def
createXhmmReferenceJobs
(
sample
:
Sample
,
referenceSamples
:
Set
[
Sample
],
outputDirectory
:
File
)
:
Tuple2
[
List
[
QFunction
]
,
File
]
=
{
outputDirectory
:
File
)
:
(
List
[
QFunction
],
File
)
=
{
/* XHMM requires refset including self */
val
totalSet
=
referenceSamples
+
sample
val
merger
=
new
XhmmMergeGatkDepths
(
this
)
...
...
@@ -431,7 +431,7 @@ class Tarmac(val parent: Configurable)
zscore
}
def
createXhmmZscore
(
sample
:
Sample
,
referenceMatrix
:
File
)
:
Tuple2
[
List
[
QFunction
]
,
File
]
=
{
def
createXhmmZscore
(
sample
:
Sample
,
referenceMatrix
:
File
)
:
(
List
[
QFunction
],
File
)
=
{
// the filtered and centered matrix
val
filtMatrix
=
new
XhmmMatrix
(
this
)
...
...
@@ -494,7 +494,7 @@ class Tarmac(val parent: Configurable)
protected
lazy
val
outputXhmmCountJob
:
String
\/
QFunction
=
{
val
outFile
=
new
File
(
xhmmDir
,
s
"$name.dcov"
)
(
inputXhmmCountFile
,
bamFile
)
match
{
case
(
Some
(
f
),
_
)
=>
{
case
(
Some
(
f
),
_
)
=>
if
(
bamFile
.
isDefined
)
{
logger
.
warn
(
s
"Both BAM and Xhmm count files are given for sample $name. The BAM file will be ignored"
)
...
...
@@ -503,11 +503,9 @@ class Tarmac(val parent: Configurable)
ln
.
input
=
f
ln
.
output
=
outFile
\/-(
ln
)
}
case
(
None
,
Some
(
bam
))
=>
{
case
(
None
,
Some
(
bam
))
=>
val
dcov
=
DepthOfCoverage
(
root
,
List
(
bam
),
outFile
,
List
(
targets
))
\/-(
dcov
)
}
case
_
=>
-\/(
s
"Cannot find bam file or xhmm count file for sample"
+
...
...
@@ -522,6 +520,7 @@ class Tarmac(val parent: Configurable)
case
\/-(
ln
:
Ln
)
=>
\/-(
ln
.
output
)
case
\/-(
doc
:
DepthOfCoverage
)
=>
\/-(
doc
.
intervalSummaryFile
)
case
-\/(
error
)
=>
-\/(
error
)
case
_
=>
throw
new
IllegalStateException
(
"This should not be reachable"
)
}
}
...
...
@@ -534,7 +533,7 @@ class Tarmac(val parent: Configurable)
protected
lazy
val
outputWisecondorCountJob
:
String
\/
QFunction
=
{
val
outFile
=
new
File
(
wisecondorDir
,
s
"$name.wisecondor.bed"
)
(
inputWisecondorCountFile
,
bamFile
)
match
{
case
(
Some
(
f
),
_
)
=>
{
case
(
Some
(
f
),
_
)
=>
if
(
bamFile
.
isDefined
)
{
logger
.
warn
(
s
"Both BAM and Wisecondor count files are given for sample $name. The BAM file will be ignored"
)
...
...
@@ -543,14 +542,12 @@ class Tarmac(val parent: Configurable)
ln
.
input
=
f
ln
.
output
=
outFile
\/-(
ln
)
}
case
(
None
,
Some
(
bam
))
=>
{
case
(
None
,
Some
(
bam
))
=>
val
counter
=
new
WisecondorCount
(
root
)
counter
.
inputBam
=
bam
counter
.
output
=
outFile
counter
.
binFile
=
Some
(
targets
)
\/-(
counter
)
}
case
_
=>
-\/(
s
"Cannot find bam file or wisecondor count for sample"
+
...
...
@@ -565,6 +562,7 @@ class Tarmac(val parent: Configurable)
case
\/-(
ln
:
Ln
)
=>
\/-(
ln
.
output
)
case
\/-(
count
:
WisecondorCount
)
=>
\/-(
count
.
output
)
case
-\/(
error
)
=>
-\/(
error
)
case
_
=>
throw
new
IllegalStateException
(
"This should not be reachable"
)
}
}
...
...
@@ -582,6 +580,7 @@ class Tarmac(val parent: Configurable)
outputWisecondorGccJob
match
{
case
\/-(
gcc
:
WisecondorGcCorrect
)
=>
\/-(
gcc
.
output
)
case
-\/(
error
)
=>
-\/(
error
)
case
_
=>
throw
new
IllegalStateException
(
"This should not be reachable"
)
}
}
...
...
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