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biopet.biopet
Commits
2a838ba2
Commit
2a838ba2
authored
Mar 18, 2015
by
Peter van 't Hof
Browse files
Changes fraction of bins
parent
c9ef89f2
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
2a838ba2
...
...
@@ -15,6 +15,8 @@ import scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
htsjdk.samtools.util.Interval
import
scala.util.Random
/**
* Created by pjvan_thof on 1/10/15.
*/
...
...
@@ -326,8 +328,9 @@ object VcfStats extends ToolCommand {
logger
.
info
(
"total: "
+
variantCounter
+
" rows processed, "
+
fraction
+
"% done"
)
}
val
chrStats
=
for
(
intervals
<-
intervals
.
grouped
(
intervals
.
size
/
10
).
toList
.
par
)
yield
{
val
chunkStats
=
for
(
intervals
<-
intervals
.
grouped
(
10
))
yield
{
// Triple for loop to not keep all bins in memory
val
stats
=
(
for
(
intervals
<-
Random
.
shuffle
(
intervals
).
grouped
(
intervals
.
size
/
4
).
toList
.
par
)
yield
{
val
chunkStats
=
for
(
intervals
<-
intervals
.
grouped
(
25
))
yield
{
val
binStats
=
for
(
interval
<-
intervals
.
par
)
yield
{
val
reader
=
new
VCFFileReader
(
commandArgs
.
inputFile
,
true
)
var
chunkCounter
=
0
...
...
@@ -335,7 +338,7 @@ object VcfStats extends ToolCommand {
logger
.
info
(
"Starting on: "
+
interval
)
for
(
record
<-
reader
.
query
(
interval
.
getSequence
,
interval
.
getStart
,
interval
.
getEnd
)
record
<-
reader
.
query
(
interval
.
getSequence
,
interval
.
getStart
,
interval
.
getEnd
)
;
if
record
.
getStart
<=
interval
.
getEnd
)
{
mergeNestedStatsMap
(
stats
.
generalStats
,
checkGeneral
(
record
,
adInfoTags
))
...
...
@@ -366,9 +369,7 @@ object VcfStats extends ToolCommand {
binStats
.
toList
.
fold
(
createStats
)(
_
+=
_
)
}
chunkStats
.
toList
.
fold
(
createStats
)(
_
+=
_
)
}
val
stats
=
chrStats
.
toList
.
fold
(
createStats
)(
_
+=
_
)
}).
toList
.
fold
(
createStats
)(
_
+=
_
)
logger
.
info
(
"Done reading vcf records"
)
...
...
@@ -409,7 +410,7 @@ object VcfStats extends ToolCommand {
}
protected
def
writeWiggle
(
intervals
:
List
[
Interval
],
row
:
String
,
column
:
String
,
outputFile
:
File
,
genotype
:
Boolean
)
:
Unit
=
{
val
bla
=
intervals
.
groupBy
(
_
.
getSequence
).
map
{
case
(
k
,
v
)
=>
k
->
v
.
sortBy
(
_
.
getStart
)
}
val
bla
=
intervals
.
groupBy
(
_
.
getSequence
).
map
{
case
(
k
,
v
)
=>
k
->
v
.
sortBy
(
_
.
getStart
)
}
outputFile
.
getParentFile
.
mkdirs
()
val
writer
=
new
PrintWriter
(
outputFile
)
writer
.
println
(
"track type=wiggle_0"
)
...
...
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