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biopet.biopet
Commits
d1e7b1f9
Commit
d1e7b1f9
authored
Oct 24, 2016
by
Peter van 't Hof
Browse files
Changed var name
parent
5ecbd595
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
View file @
d1e7b1f9
...
...
@@ -66,19 +66,19 @@ object FindOverlapMatch extends ToolCommand {
case
_
=>
sys
.
process
.
stdout
}
for
(
i1
<-
samplesColumnHeader
if
cmdArgs
.
columnSampleRegex
.
map
(
_
.
findFirstIn
(
i1
.
_1
).
isDefined
).
getOrElse
(
true
))
{
for
(
columnSample
<-
samplesColumnHeader
if
cmdArgs
.
columnSampleRegex
.
map
(
_
.
findFirstIn
(
columnSample
.
_1
).
isDefined
).
getOrElse
(
true
))
{
val
buffer
=
ListBuffer
[(
String
,
Double
)]()
for
(
i2
<-
samplesRowHeader
if
cmdArgs
.
rowSampleRegex
.
map
(
_
.
findFirstIn
(
i2
.
_1
).
isDefined
).
getOrElse
(
true
))
{
val
value
=
data
(
i1
.
_2
)(
i2
.
_2
).
toDouble
if
(
value
>=
cmdArgs
.
cutoff
&&
(!
cmdArgs
.
filterSameNames
||
i1
.
_2
!=
i2
.
_2
))
{
buffer
.+=((
i2
.
_1
,
value
))
for
(
rowSample
<-
samplesRowHeader
if
cmdArgs
.
rowSampleRegex
.
map
(
_
.
findFirstIn
(
rowSample
.
_1
).
isDefined
).
getOrElse
(
true
))
{
val
value
=
data
(
columnSample
.
_2
)(
rowSample
.
_2
).
toDouble
if
(
value
>=
cmdArgs
.
cutoff
&&
(!
cmdArgs
.
filterSameNames
||
columnSample
.
_2
!=
rowSample
.
_2
))
{
buffer
.+=((
rowSample
.
_1
,
value
))
}
}
if
(
buffer
.
nonEmpty
)
overlap
+=
1
else
noOverlap
+=
1
if
(
buffer
.
size
>
1
)
multiOverlap
+=
1
writer
.
println
(
s
"${
i1
._1}\t${buffer.mkString("
\
t
")}"
)
writer
.
println
(
s
"${
columnSample
._1}\t${buffer.mkString("
\
t
")}"
)
}
logger
.
info
(
s
"$overlap found"
)
logger
.
info
(
s
"no $noOverlap found"
)
...
...
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