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biopet.biopet
Commits
0d8c0531
Commit
0d8c0531
authored
May 01, 2015
by
Peter van 't Hof
Browse files
Fix flag handling and add some logging
parent
14c6c116
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
0d8c0531
...
...
@@ -80,6 +80,9 @@ object AnnotateVcfWithBed extends ToolCommand {
* @param args
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
...
...
@@ -92,17 +95,34 @@ object AnnotateVcfWithBed extends ToolCommand {
bedRecords(bedRecord.getChr) = (bedRecord.getStart, bedRecord.getEnd, bedRecord.getName) :: bedRecords.getOrElse(bedRecord.getChr, Nil)
}
*/
val
fieldType
=
commandArgs
.
fieldType
match
{
case
"Integer"
=>
VCFHeaderLineType
.
Integer
case
"Flag"
=>
VCFHeaderLineType
.
Flag
case
"Character"
=>
VCFHeaderLineType
.
Character
case
"Float"
=>
VCFHeaderLineType
.
Float
case
_
=>
VCFHeaderLineType
.
String
}
logger
.
info
(
"Reading bed file"
)
for
(
line
<-
Source
.
fromFile
(
commandArgs
.
bedFile
).
getLines
())
{
val
values
=
line
.
split
(
"\t"
)
if
(
values
.
size
>=
4
)
bedRecords
(
values
(
0
))
=
(
values
(
1
).
toInt
,
values
(
2
).
toInt
,
values
(
3
))
::
bedRecords
.
getOrElse
(
values
(
0
),
Nil
)
else
(
values
.
size
>=
3
&&
fieldType
==
VCFHeaderLineType
.
Flag
)
bedRecords
(
values
(
0
))
=
(
values
(
1
).
toInt
,
values
(
2
).
toInt
,
""
)
::
bedRecords
.
getOrElse
(
values
(
0
),
Nil
)
}
logger
.
info
(
"Sorting bed records"
)
// Sort records when needed
for
((
chr
,
record
)
<-
bedRecords
)
{
bedRecords
(
chr
)
=
record
.
sortBy
(
x
=>
(
x
.
_1
,
x
.
_2
))
}
logger
.
info
(
"Starting output file"
)
val
reader
=
new
VCFFileReader
(
commandArgs
.
inputFile
,
false
)
val
header
=
reader
.
getFileHeader
...
...
@@ -111,17 +131,12 @@ object AnnotateVcfWithBed extends ToolCommand {
setReferenceDictionary
(
header
.
getSequenceDictionary
).
build
)
val
fieldType
=
commandArgs
.
fieldType
match
{
case
"Integer"
=>
VCFHeaderLineType
.
Integer
case
"Flag"
=>
VCFHeaderLineType
.
Flag
case
"Character"
=>
VCFHeaderLineType
.
Character
case
"Float"
=>
VCFHeaderLineType
.
Float
case
_
=>
VCFHeaderLineType
.
String
}
header
.
addMetaDataLine
(
new
VCFInfoHeaderLine
(
commandArgs
.
fieldName
,
VCFHeaderLineCount
.
UNBOUNDED
,
fieldType
,
commandArgs
.
fieldDescription
))
writer
.
writeHeader
(
header
)
logger
.
info
(
"Start reading vcf records"
)
for
(
record
<-
reader
)
{
val
overlaps
=
bedRecords
.
getOrElse
(
record
.
getChr
,
Nil
).
filter
(
x
=>
{
record
.
getStart
<=
x
.
_2
&&
record
.
getEnd
>=
x
.
_1
...
...
@@ -130,11 +145,14 @@ object AnnotateVcfWithBed extends ToolCommand {
writer
.
add
(
record
)
}
else
{
val
builder
=
new
VariantContextBuilder
(
record
)
builder
.
attribute
(
commandArgs
.
fieldName
,
overlaps
.
map
(
_
.
_3
).
mkString
(
","
))
if
(
fieldType
==
VCFHeaderLineType
.
Flag
)
builder
.
attribute
(
commandArgs
.
fieldName
,
true
)
else
builder
.
attribute
(
commandArgs
.
fieldName
,
overlaps
.
map
(
_
.
_3
).
mkString
(
","
))
writer
.
add
(
builder
.
make
)
}
}
reader
.
close
writer
.
close
logger
.
info
(
"Done"
)
}
}
\ No newline at end of file
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