From fd13448dba036ac7b0c2599e09c5e1bca76bde8c Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 31 Oct 2014 15:57:12 +0100
Subject: [PATCH] Code cleanup
---
.../nl/lumc/sasc/biopet/tools/WipeReads.scala | 4 ++--
.../sasc/biopet/tools/WipeReadsUnitTest.scala | 20 +++++++------------
2 files changed, 9 insertions(+), 15 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index f28f61256..704b203ec 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -378,11 +378,11 @@ object WipeReads extends ToolCommand {
opt[Long]("bloom_size") optional () action { (x, c) =>
c.copy(bloomSize = x)
- } text "expected maximum number of reads in target regions (default: 7e7)"
+ } text "Expected maximum number of reads in target regions (default: 7e7)"
opt[Double]("false_positive") optional () action { (x, c) =>
c.copy(bloomFp = x)
- } text "false positive rate (default: 4e-7)"
+ } text "False positive rate (default: 4e-7)"
note(
"""
diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
index 9523ba2bb..48f8a1c8d 100644
--- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
+++ b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
@@ -44,12 +44,6 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
private def makeSams(raws: String*): Seq[SAMRecord] =
raws.map(s => samP.parseLine(s))
- private def makeTempBam(): File =
- File.createTempFile("WipeReads", java.util.UUID.randomUUID.toString + ".bam")
-
- private def makeTempBamIndex(bam: File): File =
- new File(bam.getAbsolutePath.stripSuffix(".bam") + ".bai")
-
private def makeSamReader(f: File): SamReader = SamReaderFactory
.make()
.validationStringency(ValidationStringency.LENIENT)
@@ -144,15 +138,15 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testMakeIntervalFromRefFlat() = {
val intervals: List[Interval] = makeIntervalFromFile(RefFlatFile1)
intervals.length shouldBe 5
- intervals.last.getSequence should ===("chrQ")
- intervals.last.getStart shouldBe 100
- intervals.last.getEnd shouldBe 200
- intervals(2).getSequence should ===("chrQ")
- intervals(2).getStart shouldBe 800
- intervals(2).getEnd shouldBe 1000
intervals.head.getSequence should ===("chrS")
intervals.head.getStart shouldBe 100
intervals.head.getEnd shouldBe 500
+ intervals(2).getSequence should ===("chrQ")
+ intervals(2).getStart shouldBe 800
+ intervals(2).getEnd shouldBe 1000
+ intervals.last.getSequence should ===("chrQ")
+ intervals.last.getStart shouldBe 100
+ intervals.last.getEnd shouldBe 200
}
@Test def testSingleBamDefault() = {
@@ -282,7 +276,7 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
filterNotFunc(sBamRecs2(2)) shouldBe false
filterNotFunc(sBamRecs2(3)) shouldBe true
filterNotFunc(sBamRecs2(4)) shouldBe true
- // this r07 is not in since filterOuMulti is false
+ // this r07 is not in since filterOutMulti is false
filterNotFunc(sBamRecs2(5)) shouldBe false
filterNotFunc(sBamRecs2(6)) shouldBe false
filterNotFunc(sBamRecs2(7)) shouldBe false
--
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