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biopet.biopet
Commits
38103728
Commit
38103728
authored
Jul 15, 2017
by
Peter van 't Hof
Browse files
Fixing some compile issues
parent
962887bc
Changes
2
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @
38103728
...
...
@@ -643,8 +643,6 @@ object VcfStats extends ToolCommand {
val
absFile
=
new
File
(
prefix
+
".abs.tsv"
)
val
relFile
=
new
File
(
prefix
+
".rel.tsv"
)
stats
.
getContigStats
()
absFile
.
getParentFile
.
mkdirs
()
val
absWriter
=
new
PrintWriter
(
absFile
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsSpark.scala
View file @
38103728
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.tools.vcfstats
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.
{
cmdArgs
,
_
}
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.
_
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
FastaUtils
,
ToolCommand
,
VcfUtils
}
import
nl.lumc.sasc.biopet.utils.intervals.
{
BedRecord
,
BedRecordList
}
import
org.apache.spark.
{
SparkConf
,
SparkContext
}
...
...
@@ -137,7 +137,7 @@ object VcfStatsSpark extends ToolCommand {
val
regionStats
=
sc
.
parallelize
(
regions
,
regions
.
size
).
groupBy
(
_
.
chr
).
map
{
case
(
contig
,
records
)
=>
contig
->
records
.
map
(
readBin
(
_
,
samples
,
cmdArgs
,
adInfoTags
,
adGenotypeTags
))}
val
chrStats
=
regionStats
.
map
{
case
(
contig
,
stats
)
=>
contig
->
stats
.
reduce
(
_
+=
_
)}
.
cache
()
val
chrStats
=
regionStats
.
map
{
case
(
contig
,
stats
)
=>
contig
->
stats
.
reduce
(
_
+=
_
)}
val
totalStats
=
chrStats
.
values
.
reduce
(
_
+=
_
)
...
...
@@ -163,8 +163,6 @@ object VcfStatsSpark extends ToolCommand {
cmdArgs
.
outputDir
+
"/sample_compare/allele_overlap"
,
samples
)
Thread
.
sleep
(
1000000
)
sc
.
stop
logger
.
info
(
"Done"
)
}
...
...
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