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biopet.biopet
Commits
19236e6f
Commit
19236e6f
authored
Mar 14, 2016
by
Peter van 't Hof
Browse files
Added piping to freebayes
parent
cf10ac0c
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
19236e6f
...
...
@@ -149,7 +149,6 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
optional
(
"--contamination-estimates"
,
contamination_estimates
)
+
optional
(
"--variant-input"
,
variant_input
)
+
optional
(
"--haplotype-basis-alleles"
,
haplotype_basis_alleles
)
+
optional
(
"--vcf"
,
outputVcf
)
+
optional
(
"--pvar"
,
pvar
)
+
optional
(
"--theta"
,
theta
)
+
optional
(
"--ploidy"
,
ploidy
)
+
...
...
@@ -202,5 +201,7 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
conditional
(
harmonic_indel_quality
,
"--harmonic-indel-quality"
)
+
conditional
(
genotype_qualities
,
"--genotype-qualities"
)
+
conditional
(
debug
,
"--debug"
)
+
optional
(
"--haplotype-length"
,
haplotypeLength
)
optional
(
"--haplotype-length"
,
haplotypeLength
)
+
(
if
(
inputAsStdin
)
required
(
"--stdin"
)
else
""
)
+
(
if
(
outputAsStsout
)
""
else
optional
(
"--vcf"
,
outputVcf
))
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
View file @
19236e6f
...
...
@@ -14,15 +14,9 @@ class Freebayes(val root: Configurable) extends Variantcaller {
val
fb
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Freebayes
(
this
)
fb
.
bamfiles
=
inputBams
.
values
.
toList
fb
.
outputVcf
=
new
File
(
outputDir
,
namePrefix
+
".freebayes.vcf"
)
fb
.
isIntermediate
=
true
add
(
fb
)
//
fb.isIntermediate = true
add
(
fb
|
new
Bgzip
(
this
)
>
outputFile
)
//TODO: need piping for this, see also issue #114
val
bz
=
new
Bgzip
(
this
)
bz
.
input
=
List
(
fb
.
outputVcf
)
bz
.
output
=
outputFile
add
(
bz
)
add
(
Tabix
.
apply
(
this
,
bz
.
output
))
add
(
Tabix
.
apply
(
this
,
outputFile
))
}
}
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