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biopet.biopet
Commits
0425c5db
Commit
0425c5db
authored
Oct 14, 2014
by
Peter van 't Hof
Browse files
Changed arg parsing
parent
7ff8ef5d
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
0425c5db
...
...
@@ -5,6 +5,7 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import
htsjdk.variant.vcf.VCFFileReader
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
scala.collection.JavaConversions._
...
...
@@ -45,44 +46,45 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
conditional
(
filterRefCalls
,
"-filterRefCalls"
)
}
object
VcfFilter
{
var
inputVcf
:
File
=
_
var
outputVcf
:
File
=
_
var
minSampleDepth
=
-
1
var
minTotalDepth
=
-
1
var
minAlternateDepth
=
-
1
var
minSamplesPass
=
0
var
filterRefCalls
=
false
object
VcfFilter
extends
ToolCommand
{
case
class
Args
(
inputVcf
:
File
=
null
,
outputVcf
:
File
=
null
,
minSampleDepth
:
Int
=
-
1
,
minTotalDepth
:
Int
=
-
1
,
minAlternateDepth
:
Int
=
-
1
,
minSamplesPass
:
Int
=
0
,
filterRefCalls
:
Boolean
=
false
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputVcf"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
inputVcf
=
x
)
}
opt
[
File
](
'o'
,
"outputVcf"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputVcf
=
x
)
}
text
(
"output file, default to stdout"
)
opt
[
Int
](
"minSampleDepth"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minSampleDepth
=
x
)
}
opt
[
Int
](
"minTotalDepth"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minTotalDepth
=
x
)
}
opt
[
Int
](
"minAlternateDepth"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minAlternateDepth
=
x
)
}
opt
[
Int
](
"minSamplesPass"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minSamplesPass
=
x
)
}
opt
[
Boolean
](
"filterRefCalls"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
filterRefCalls
=
x
)
}
}
/**
* @param args the command line arguments
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
for
(
t
<-
0
until
args
.
size
)
{
args
(
t
)
match
{
case
"-I"
=>
inputVcf
=
new
File
(
args
(
t
+
1
))
case
"-o"
=>
outputVcf
=
new
File
(
args
(
t
+
1
))
case
"-minSampleDepth"
=>
minSampleDepth
=
args
(
t
+
1
).
toInt
case
"-minTotalDepth"
=>
minTotalDepth
=
args
(
t
+
1
).
toInt
case
"-minAlternateDepth"
=>
minAlternateDepth
=
args
(
t
+
1
).
toInt
case
"-minSamplesPass"
=>
minSamplesPass
=
args
(
t
+
1
).
toInt
case
"-filterRefCalls"
=>
filterRefCalls
=
true
case
_
=>
}
}
if
(
inputVcf
==
null
)
throw
new
IllegalStateException
(
"No inputVcf, use -I"
)
if
(
outputVcf
==
null
)
throw
new
IllegalStateException
(
"No outputVcf, use -o"
)
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
reader
=
new
VCFFileReader
(
inputVcf
,
false
)
val
writer
=
new
AsyncVariantContextWriter
(
new
VariantContextWriterBuilder
().
setOutputFile
(
outputVcf
).
build
)
val
reader
=
new
VCFFileReader
(
commandArgs
.
inputVcf
,
false
)
val
writer
=
new
AsyncVariantContextWriter
(
new
VariantContextWriterBuilder
().
setOutputFile
(
commandArgs
.
outputVcf
).
build
)
writer
.
writeHeader
(
reader
.
getFileHeader
)
for
(
record
<-
reader
)
{
val
genotypes
=
for
(
genotype
<-
record
.
getGenotypes
)
yield
{
genotype
.
getDP
>=
minSampleDepth
&&
List
(
genotype
.
getAD
:_
*
).
tail
.
count
(
_
>=
minAlternateDepth
)
>
0
&&
!(
filterRefCalls
&&
genotype
.
isHomRef
)
genotype
.
getDP
>=
commandArgs
.
minSampleDepth
&&
List
(
genotype
.
getAD
:_
*
).
tail
.
count
(
_
>=
commandArgs
.
minAlternateDepth
)
>
0
&&
!(
commandArgs
.
filterRefCalls
&&
genotype
.
isHomRef
)
}
if
(
record
.
getAttributeAsInt
(
"DP"
,
-
1
)
>=
minTotalDepth
&&
genotypes
.
count
(
_
==
true
)
>=
minSamplesPass
)
if
(
record
.
getAttributeAsInt
(
"DP"
,
-
1
)
>=
commandArgs
.
minTotalDepth
&&
genotypes
.
count
(
_
==
true
)
>=
commandArgs
.
minSamplesPass
)
writer
.
add
(
record
)
}
reader
.
close
...
...
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