Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
c46b0592
Commit
c46b0592
authored
Nov 08, 2014
by
Peter van 't Hof
Browse files
Added MergeAlleles tool
parent
6b492ea4
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
0 → 100644
View file @
c46b0592
package
nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.reference.FastaSequenceFile
import
htsjdk.variant.variantcontext.Allele
import
htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.variantcontext.VariantContextBuilder
import
htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
import
htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import
htsjdk.variant.vcf.VCFFileReader
import
htsjdk.variant.vcf.VCFHeader
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommand
import
scala.collection.mutable.
{
Map
,
Set
}
import
scala.collection.JavaConversions._
object
MergeAlleles
extends
ToolCommand
{
case
class
Args
(
inputFiles
:
List
[
File
]
=
Nil
,
outputFile
:
File
=
null
,
reference
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputVcf"
)
minOccurs
(
2
)
required
()
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFiles
=
x
::
c
.
inputFiles
)
}
opt
[
File
](
'o'
,
"outputVcf"
)
required
()
unbounded
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
}
opt
[
File
](
'R'
,
"reference"
)
required
()
unbounded
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
reference
=
x
)
}
}
private
val
chunkSize
=
50000
/**
* @param args the command line arguments
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
referenceFile
=
new
FastaSequenceFile
(
commandArgs
.
reference
,
true
)
val
writer
=
new
AsyncVariantContextWriter
(
new
VariantContextWriterBuilder
().
setOutputFile
(
commandArgs
.
outputFile
).
build
)
val
header
=
new
VCFHeader
val
referenceDict
=
referenceFile
.
getSequenceDictionary
header
.
setSequenceDictionary
(
referenceDict
)
writer
.
writeHeader
(
header
)
for
(
chr
<-
referenceDict
.
getSequences
;
chunk
<-
(
0
to
(
chr
.
getSequenceLength
/
chunkSize
)))
{
val
readers
=
commandArgs
.
inputFiles
.
map
(
new
VCFFileReader
(
_
,
true
))
val
output
:
Map
[
Int
,
List
[
VariantContext
]]
=
Map
()
val
chrName
=
chr
.
getSequenceName
val
begin
=
chunk
*
chunkSize
+
1
val
end
=
{
val
e
=
(
chunk
+
1
)
*
chunkSize
if
(
e
>
chr
.
getSequenceLength
)
chr
.
getSequenceLength
else
e
}
for
(
reader
<-
readers
.
par
;
variant
<-
reader
.
query
(
chrName
,
begin
,
end
))
{
val
start
=
variant
.
getStart
if
(
output
.
contains
(
start
))
output
+=
variant
.
getStart
->
(
variant
::
output
(
start
))
else
output
+=
variant
.
getStart
->
List
(
variant
)
}
for
((
_
,
l
)
<-
output
)
{
writer
.
add
(
mergeAlleles
(
l
))
}
}
}
def
mergeAlleles
(
records
:
List
[
VariantContext
])
:
VariantContext
=
{
val
longestRef
=
{
var
l
:
Array
[
Byte
]
=
Array
()
for
(
a
<-
records
.
map
(
_
.
getReference
.
getBases
)
if
(
a
.
length
>
l
.
size
))
l
=
a
Allele
.
create
(
l
,
true
)
}
val
alleles
:
Set
[
Allele
]
=
Set
(
longestRef
)
val
builder
=
new
VariantContextBuilder
builder
.
chr
(
records
.
head
.
getChr
)
builder
.
start
(
records
.
head
.
getStart
)
for
(
record
<-
records
)
{
if
(
record
.
getReference
==
longestRef
)
alleles
++=
record
.
getAlternateAlleles
else
{
val
suffix
=
longestRef
.
getBaseString
.
stripPrefix
(
record
.
getReference
.
getBaseString
)
for
(
r
<-
record
.
getAlternateAlleles
)
alleles
+=
Allele
.
create
(
r
.
getBaseString
+
suffix
)
}
}
builder
.
alleles
(
alleles
.
toSeq
)
builder
.
make
}
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment