Commit 05959d3b authored by bow's avatar bow
Browse files

Various small fixes for testing

parent 1e0a70bb
...@@ -5,6 +5,7 @@ ...@@ -5,6 +5,7 @@
package nl.lumc.sasc.biopet.core.apps package nl.lumc.sasc.biopet.core.apps
import java.io.{ File, IOException } import java.io.{ File, IOException }
import scala.collection.JavaConverters._
import scala.io.Source import scala.io.Source
import com.twitter.algebird.{ BF, BloomFilter } import com.twitter.algebird.{ BF, BloomFilter }
...@@ -35,7 +36,7 @@ object WipeReads { ...@@ -35,7 +36,7 @@ object WipeReads {
type OptionMap = Map[String, Any] type OptionMap = Map[String, Any]
private object Strand extends Enumeration { object Strand extends Enumeration {
type Strand = Value type Strand = Value
val Identical, Opposite, Both = Value val Identical, Opposite, Both = Value
} }
...@@ -112,9 +113,9 @@ object WipeReads { ...@@ -112,9 +113,9 @@ object WipeReads {
// TODO: how to chain initTargets to filteredTargets directly? // TODO: how to chain initTargets to filteredTargets directly?
val initTargets: Iterator[Vector[SAMRecord]] = for { 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 // 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 val filteredTargets: Iterator[SAMRecord] = initTargets.flatten
// filter on minimum MAPQ value // filter on minimum MAPQ value
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment