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Change Some to Option to check for unmapped reads #225

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merged 1 commit into from
Apr 24, 2014
Merged

Change Some to Option to check for unmapped reads #225

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7 changes: 3 additions & 4 deletions adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@ import org.bdgenomics.adam.avro.{ ADAMRecord, ADAMGenotype, ADAMVariant, ADAMPil
import org.bdgenomics.adam.rdd.ADAMContext._
import com.esotericsoftware.kryo.{ Kryo, Serializer }
import com.esotericsoftware.kryo.io.{ Input, Output }
import Ordering.Option

object ReferencePositionWithOrientation {

Expand Down Expand Up @@ -80,9 +79,9 @@ object ReferencePosition {
* @return True if read is mapped and has a valid position, else false.
*/
def mappedPositionCheck(record: ADAMRecord): Boolean = {
val contig = Some(record.getContig)
val start = Some(record.getStart)
record.getReadMapped && (contig.isDefined && Some(contig.get.getContigName).isDefined) && start.isDefined
val contig = Option(record.getContig)
val start = Option(record.getStart)
record.getReadMapped && (contig.isDefined && Option(contig.get.getContigName).isDefined) && start.isDefined
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I know this is Scalic (what is the Scala equivalent of pythonic?), but wouldn't it be more efficient to just directly check vs. null? I think Options are more useful when used functionally (e.g., a foreach, flatmap, etc).

}

/**
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43 changes: 43 additions & 0 deletions adam-core/src/test/scala/org/bdgenomics/adam/models/ReferencePositionSuite.scala
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Expand Up @@ -51,6 +51,49 @@ class ReferencePositionSuite extends FunSuite {
assert(refPosOpt.isEmpty)
}

test("create reference position from mapped read but contig not specified") {
val read = ADAMRecord.newBuilder()
.setReadMapped(true)
.setStart(1L)
.build()

val refPosOpt = ReferencePosition(read)

assert(refPosOpt.isEmpty)
}

test("create reference position from mapped read but contig is underspecified") {
val contig = ADAMContig.newBuilder
// contigName is NOT set
//.setContigName("chr1")
.build

val read = ADAMRecord.newBuilder()
.setReadMapped(true)
.setStart(1L)
.setContig(contig)
.build()

val refPosOpt = ReferencePosition(read)

assert(refPosOpt.isEmpty)
}

test("create reference position from mapped read but start not specified") {
val contig = ADAMContig.newBuilder
.setContigName("chr1")
.build

val read = ADAMRecord.newBuilder()
.setReadMapped(true)
.setContig(contig)
.build()

val refPosOpt = ReferencePosition(read)

assert(refPosOpt.isEmpty)
}

test("create reference position from pileup") {
val contig = ADAMContig.newBuilder
.setContigName("chr2")
Expand Down