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biopet.biopet
Commits
2b4cb228
Commit
2b4cb228
authored
Nov 08, 2014
by
Peter van 't Hof
Browse files
Fix bugs on MergeAlleles
parent
c46b0592
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
2b4cb228
...
...
@@ -10,6 +10,8 @@ import htsjdk.variant.vcf.VCFFileReader
import
htsjdk.variant.vcf.VCFHeader
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommand
import
scala.collection.SortedMap
import
scala.collection.immutable.SortedSet
import
scala.collection.mutable.
{
Map
,
Set
}
import
scala.collection.JavaConversions._
...
...
@@ -37,6 +39,7 @@ object MergeAlleles extends ToolCommand {
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
readers
=
commandArgs
.
inputFiles
.
map
(
new
VCFFileReader
(
_
,
true
))
val
referenceFile
=
new
FastaSequenceFile
(
commandArgs
.
reference
,
true
)
val
writer
=
new
AsyncVariantContextWriter
(
new
VariantContextWriterBuilder
().
setOutputFile
(
commandArgs
.
outputFile
).
build
)
val
header
=
new
VCFHeader
...
...
@@ -45,7 +48,6 @@ object MergeAlleles extends ToolCommand {
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
...
...
@@ -55,16 +57,18 @@ object MergeAlleles extends ToolCommand {
if
(
e
>
chr
.
getSequenceLength
)
chr
.
getSequenceLength
else
e
}
for
(
reader
<-
readers
.
par
;
variant
<-
reader
.
query
(
chrName
,
begin
,
end
))
{
for
(
reader
<-
readers
;
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
))
for
((
k
,
v
)
<-
SortedMap
(
output
.
toSeq
:
_
*
)
)
{
writer
.
add
(
mergeAlleles
(
v
))
}
}
writer
.
close
readers
.
foreach
(
_
.
close
)
}
def
mergeAlleles
(
records
:
List
[
VariantContext
])
:
VariantContext
=
{
...
...
@@ -73,7 +77,7 @@ object MergeAlleles extends ToolCommand {
for
(
a
<-
records
.
map
(
_
.
getReference
.
getBases
)
if
(
a
.
length
>
l
.
size
))
l
=
a
Allele
.
create
(
l
,
true
)
}
val
alleles
:
Set
[
Allele
]
=
Set
(
longestRef
)
val
alleles
:
Set
[
Allele
]
=
Set
()
val
builder
=
new
VariantContextBuilder
builder
.
chr
(
records
.
head
.
getChr
)
builder
.
start
(
records
.
head
.
getStart
)
...
...
@@ -85,7 +89,8 @@ object MergeAlleles extends ToolCommand {
for
(
r
<-
record
.
getAlternateAlleles
)
alleles
+=
Allele
.
create
(
r
.
getBaseString
+
suffix
)
}
}
builder
.
alleles
(
alleles
.
toSeq
)
builder
.
alleles
(
longestRef
::
alleles
.
toList
)
builder
.
computeEndFromAlleles
(
longestRef
::
alleles
.
toList
,
records
.
head
.
getStart
)
builder
.
make
}
}
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