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biopet.biopet
Commits
05959d3b
Commit
05959d3b
authored
Oct 02, 2014
by
bow
Browse files
Various small fixes for testing
parent
1e0a70bb
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
05959d3b
...
...
@@ -5,6 +5,7 @@
package
nl.lumc.sasc.biopet.core.apps
import
java.io.
{
File
,
IOException
}
import
scala.collection.JavaConverters._
import
scala.io.Source
import
com.twitter.algebird.
{
BF
,
BloomFilter
}
...
...
@@ -35,7 +36,7 @@ object WipeReads {
type
OptionMap
=
Map
[
String
,
Any
]
private
object
Strand
extends
Enumeration
{
object
Strand
extends
Enumeration
{
type
Strand
=
Value
val
Identical
,
Opposite
,
Both
=
Value
}
...
...
@@ -112,9 +113,9 @@ object WipeReads {
// TODO: how to chain initTargets to filteredTargets directly?
val
initTargets
:
Iterator
[
Vector
[
SAMRecord
]]
=
for
{
x
<-
firstBAM
.
queryOverlapping
(
iv
.
toArray
)
;
x
<-
firstBAM
.
queryOverlapping
(
iv
.
toArray
)
.
asScala
// TODO: can we do without Vector here? It's only so we can flatten it later
}
yield
Vector
(
x
,
monadicMateQuery
(
secondBAM
,
x
)).
flatten
}
yield
Vector
(
Some
(
x
)
,
monadicMateQuery
(
secondBAM
,
x
)).
flatten
val
filteredTargets
:
Iterator
[
SAMRecord
]
=
initTargets
.
flatten
// filter on minimum MAPQ value
...
...
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