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biopet.biopet
Commits
bffd796d
Commit
bffd796d
authored
May 10, 2016
by
bow
Browse files
Merge branch 'fix-tagged_files' into 'develop'
Fixed tagged files Fixes #339 See merge request !394
parents
59c78525
e7aeabf3
Changes
7
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
View file @
bffd796d
...
...
@@ -69,7 +69,7 @@ class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterG
override
def
cmdLine
=
super
.
cmdLine
+
repeat
(
"-A"
,
annotation
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-G"
,
group
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
null
)
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-V"
,
variant
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-o"
,
out
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
convertToBasePairResolution
,
"-bpResolution"
,
escape
=
true
,
format
=
"%s"
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
View file @
bffd796d
...
...
@@ -129,7 +129,7 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
optional
(
"-ploidy"
,
sample_ploidy
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-A"
,
annotation
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-G"
,
group
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
null
)
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
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"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
bffd796d
...
...
@@ -419,7 +419,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional
(
"-o"
,
out
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-likelihoodEngine"
,
likelihoodCalculationEngine
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-hksr"
,
heterogeneousKmerSizeResolution
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
null
)
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
dontTrimActiveRegions
,
"-dontTrimActiveRegions"
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-maxDiscARExtension"
,
maxDiscARExtension
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-maxGGAARExtension"
,
maxGGAARExtension
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
@@ -444,7 +444,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
repeat
(
"-inputPrior"
,
input_prior
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-ploidy"
,
sample_ploidy
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-gt_mode"
,
genotyping_mode
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-alleles"
,
alleles
),
alleles
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-alleles"
,
alleles
.
getOrElse
(
null
)
),
alleles
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-contamination"
,
contamination_fraction_to_filter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
contamination_fraction_to_filterFormat
)
+
optional
(
"-contaminationFile"
,
contamination_fraction_per_sample_file
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-pnrm"
,
p_nonref_model
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
View file @
bffd796d
...
...
@@ -218,8 +218,8 @@ class SelectVariants(val root: Configurable) extends CommandLineGATK with Scatte
override
def
cmdLine
=
super
.
cmdLine
+
required
(
TaggedFile
.
formatCommandLineParameter
(
"-V"
,
variant
),
variant
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-disc"
,
discordance
),
discordance
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-conc"
,
concordance
),
concordance
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-disc"
,
discordance
.
getOrElse
(
null
)
),
discordance
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-conc"
,
concordance
.
getOrElse
(
null
)
),
concordance
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-o"
,
out
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-sn"
,
sample_name
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-se"
,
sample_expressions
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
View file @
bffd796d
...
...
@@ -276,7 +276,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
conditional
(
ignoreSNPAlleles
,
"-ignoreSNPAlleles"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
allReadsSP
,
"-dl"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
ignoreLaneInfo
,
"-ignoreLane"
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-referenceCalls"
,
reference_sample_calls
),
reference_sample_calls
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-referenceCalls"
,
reference_sample_calls
.
getOrElse
(
null
)
),
reference_sample_calls
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-refsample"
,
reference_sample_name
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-minqs"
,
min_quality_score
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-maxqs"
,
max_quality_score
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
@@ -291,14 +291,14 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
repeat
(
"-inputPrior"
,
input_prior
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-ploidy"
,
sample_ploidy
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-gt_mode"
,
genotyping_mode
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-alleles"
,
alleles
),
alleles
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-alleles"
,
alleles
.
getOrElse
(
null
)
),
alleles
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-contamination"
,
contamination_fraction_to_filter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
contamination_fraction_to_filterFormat
)
+
optional
(
"-contaminationFile"
,
contamination_fraction_per_sample_file
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-pnrm"
,
p_nonref_model
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-logExactCalls"
,
exactcallslog
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-out_mode"
,
output_mode
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
allSitePLs
,
"-allSitePLs"
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
null
)
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-comp"
,
comp
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-o"
,
out
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-onlyEmitSamples"
,
onlyEmitSamples
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
View file @
bffd796d
...
...
@@ -104,8 +104,8 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
override
def
cmdLine
=
super
.
cmdLine
+
required
(
TaggedFile
.
formatCommandLineParameter
(
"-V"
,
variant
),
variant
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-snpEffFile"
,
snpEffFile
),
snpEffFile
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
),
dbsnp
,
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"
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
View file @
bffd796d
...
...
@@ -135,8 +135,8 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
optional
(
"-o"
,
out
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-eval"
,
eval
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-comp"
,
comp
,
formatPrefix
=
TaggedFile
.
formatCommandLineParameter
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-gold"
,
goldStandard
),
goldStandard
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-D"
,
dbsnp
.
getOrElse
(
null
)
),
dbsnp
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
TaggedFile
.
formatCommandLineParameter
(
"-gold"
,
goldStandard
.
getOrElse
(
null
)
),
goldStandard
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-select"
,
select_exps
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-selectName"
,
select_names
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-sn"
,
sample
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
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