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biopet.biopet
Commits
99b31701
Commit
99b31701
authored
Jul 21, 2016
by
Peter van 't Hof
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Fixed number of bins
parent
6d39308c
Changes
2
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2 changed files
with
5 additions
and
4 deletions
+5
-4
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+3
-2
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
...elines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
+2
-2
No files found.
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
View file @
99b31701
...
...
@@ -109,9 +109,10 @@ object BamStats extends ToolCommand {
def
processContig
(
region
:
BedRecord
,
bamFile
:
File
,
binSize
:
Int
,
threadBinSize
:
Int
,
outputDir
:
File
)
:
Stats
=
{
val
scattersFutures
=
region
.
scatter
(
binSize
)
.
grouped
((
region
.
length
.
toDouble
/
threadBinSize
).
ceil
.
toInt
)
.
grouped
((
region
.
length
.
toDouble
/
binSize
).
ceil
.
toInt
/
(
region
.
length
.
toDouble
/
threadBinSize
).
ceil
.
toInt
)
.
map
(
scatters
=>
Future
{
processThread
(
scatters
,
bamFile
)
})
val
stats
=
waitOnFutures
(
scattersFutures
.
toList
,
Some
(
region
.
chr
))
.
toList
val
stats
=
waitOnFutures
(
scattersFutures
,
Some
(
region
.
chr
))
val
contigDir
=
new
File
(
outputDir
,
"contigs"
+
File
.
separator
+
region
.
chr
)
contigDir
.
mkdirs
()
stats
.
writeStatsToFiles
(
contigDir
)
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
View file @
99b31701
...
...
@@ -7,8 +7,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by Sander Bollen on 13-7-16.
*/
* Created by Sander Bollen on 13-7-16.
*/
class
HaploTypeCallerGvcfTest
extends
TestNGSuite
with
Matchers
{
@Test
...
...
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