zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Moved some of the java to scala conversions from production to test code as it's not needed in production and slows down the code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5769 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-05-05 04:11:15 +00:00
parent 28b897d5de
commit 4d08d39849
3 changed files with 7 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
View File

@ -41,6 +41,6 @@ class ContigScatterFunction extends GATKScatterFunction with InProcessFunction {
def run() { def run() {
val gi = GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals) val gi = GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals)
IntervalUtils.scatterContigIntervals(gi.samFileHeader, gi.javaLocs, this.scatterOutputFiles) IntervalUtils.scatterContigIntervals(gi.samFileHeader, gi.locs, this.scatterOutputFiles)
} }
} }

8
scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
View File

@ -42,9 +42,7 @@ case class GATKIntervals(reference: File, intervals: List[String]) {
header header
} }
lazy val locs: List[GenomeLoc] = javaLocs.toList lazy val locs: java.util.List[GenomeLoc] = {
lazy val javaLocs: java.util.List[GenomeLoc] = {
val parser = new GenomeLocParser(referenceDataSource.getReference) val parser = new GenomeLocParser(referenceDataSource.getReference)
val parsedLocs = val parsedLocs =
if (intervals.isEmpty) if (intervals.isEmpty)
@ -55,11 +53,11 @@ case class GATKIntervals(reference: File, intervals: List[String]) {
Collections.unmodifiableList(parsedLocs) Collections.unmodifiableList(parsedLocs)
} }
lazy val contigs = locs.map(_.getContig).distinct lazy val contigs = locs.map(_.getContig).distinct.toList
def getSplits(size: Int) = { def getSplits(size: Int) = {
splitsBySize.getOrElse(size, { splitsBySize.getOrElse(size, {
val splits: java.util.List[java.lang.Integer] = IntervalUtils.splitFixedIntervals(javaLocs, size) val splits: java.util.List[java.lang.Integer] = IntervalUtils.splitFixedIntervals(locs, size)
splitsBySize += size -> splits splitsBySize += size -> splits
splits splits
}) })

6
scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
View File

@ -37,12 +37,12 @@ class GATKIntervalsUnitTest {
private final lazy val hg18Reference = new File(BaseTest.hg18Reference) private final lazy val hg18Reference = new File(BaseTest.hg18Reference)
private final lazy val hg18GenomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(hg18Reference)) private final lazy val hg18GenomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(hg18Reference))
private final lazy val hg18ReferenceLocs = GenomeLocSortedSet. private final lazy val hg18ReferenceLocs = GenomeLocSortedSet.
createSetFromSequenceDictionary(new ReferenceDataSource(hg18Reference).getReference.getSequenceDictionary).toList.toList createSetFromSequenceDictionary(new ReferenceDataSource(hg18Reference).getReference.getSequenceDictionary).toList
private final lazy val hg19Reference = new File(BaseTest.hg19Reference) private final lazy val hg19Reference = new File(BaseTest.hg19Reference)
private final lazy val hg19GenomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(hg19Reference)) private final lazy val hg19GenomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(hg19Reference))
private final lazy val hg19ReferenceLocs = GenomeLocSortedSet. private final lazy val hg19ReferenceLocs = GenomeLocSortedSet.
createSetFromSequenceDictionary(new ReferenceDataSource(hg19Reference).getReference.getSequenceDictionary).toList.toList createSetFromSequenceDictionary(new ReferenceDataSource(hg19Reference).getReference.getSequenceDictionary).toList
@Test @Test
def testWithIntervals() { def testWithIntervals() {
@ -51,7 +51,7 @@ class GATKIntervalsUnitTest {
val chr3 = hg18GenomeLocParser.parseGenomeInterval("chr3:3-5") val chr3 = hg18GenomeLocParser.parseGenomeInterval("chr3:3-5")
val gi = new GATKIntervals(hg18Reference, List("chr1:1-1", "chr2:2-3", "chr3:3-5")) val gi = new GATKIntervals(hg18Reference, List("chr1:1-1", "chr2:2-3", "chr3:3-5"))
Assert.assertEquals(gi.locs, List(chr1, chr2, chr3)) Assert.assertEquals(gi.locs.toList, List(chr1, chr2, chr3))
Assert.assertEquals(gi.contigs, List("chr1", "chr2", "chr3")) Assert.assertEquals(gi.contigs, List("chr1", "chr2", "chr3"))
Assert.assertEquals(gi.getSplits(2).toList, List(2, 3)) Assert.assertEquals(gi.getSplits(2).toList, List(2, 3))
Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3)) Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3))