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biopet.biopet
Commits
2757c868
Commit
2757c868
authored
Feb 06, 2015
by
Peter van 't Hof
Browse files
Refactor code
parent
4d20276b
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
2757c868
...
...
@@ -145,10 +145,8 @@ object VcfFilter extends ToolCommand {
val
writer
=
new
AsyncVariantContextWriter
(
new
VariantContextWriterBuilder
().
setOutputFile
(
commandArgs
.
outputVcf
).
build
)
writer
.
writeHeader
(
header
)
val
invertedWriter
=
if
(
commandArgs
.
invertedOutputVcf
.
isDefined
)
Some
(
new
AsyncVariantContextWriter
(
new
VariantContextWriterBuilder
().
setOutputFile
(
commandArgs
.
invertedOutputVcf
.
get
).
build
))
else
None
if
(
invertedWriter
.
isDefined
)
invertedWriter
.
get
.
writeHeader
(
header
)
val
invertedWriter
=
commandArgs
.
invertedOutputVcf
.
collect
{
case
x
=>
new
VariantContextWriterBuilder
().
setOutputFile
(
x
).
build
}
invertedWriter
.
foreach
(
_
.
writeHeader
(
header
))
var
counterTotal
=
0
var
counterLeft
=
0
...
...
@@ -167,16 +165,15 @@ object VcfFilter extends ToolCommand {
inIdSet
(
record
))
{
writer
.
add
(
record
)
counterLeft
+=
1
}
else
{
if
(
invertedWriter
.
isDefined
)
invertedWriter
.
get
.
add
(
record
)
}
}
else
invertedWriter
.
foreach
(
_
.
add
(
record
))
counterTotal
+=
1
if
(
counterTotal
%
100000
==
0
)
logger
.
info
(
counterTotal
+
" variants processed, "
+
counterLeft
+
" left"
)
}
logger
.
info
(
counterTotal
+
" variants processed, "
+
counterLeft
+
" left"
)
reader
.
close
writer
.
close
if
(
invertedWriter
.
isDefined
)
invertedWriter
.
get
.
close
()
invertedWriter
.
foreach
(
_
.
close
()
)
logger
.
info
(
"Done"
)
}
...
...
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