From 94a2b3ddc7f9890bbbdaf26bdb105d756d2b137a Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 31 Oct 2014 13:41:43 +0100
Subject: [PATCH] Add test for different chromosome overlap
---
.../src/test/resources/single05.bam | Bin 0 -> 318 bytes
.../src/test/resources/single05.bam.bai | Bin 0 -> 176 bytes
.../src/test/resources/single05.sam | 9 +++++++
.../sasc/biopet/tools/WipeReadsUnitTest.scala | 23 ++++++++++++++++++
4 files changed, 32 insertions(+)
create mode 100644 biopet-framework/src/test/resources/single05.bam
create mode 100644 biopet-framework/src/test/resources/single05.bam.bai
create mode 100644 biopet-framework/src/test/resources/single05.sam
diff --git a/biopet-framework/src/test/resources/single05.bam b/biopet-framework/src/test/resources/single05.bam
new file mode 100644
index 0000000000000000000000000000000000000000..e9fab38e6a945bf942921353d4a443cee881de2e
GIT binary patch
literal 318
zcmb2|=3rp}f&Xj_PR>jWlNgGNzNG4;CnOYnD0s;8d9%?K;|Dz7wtJmBukUs8jJJ;G
z(;^POCp_Oad!5tZdh&%)%YcDN<)8u(mHYXNYcn%D`%O<+{pie|FLOffUfCnky6DQ0
zDM{xN;#Yq-({x2aKwV|)jw6;EEv9yJW|(RVH20(n1hf}79gt!0-f%i_F3=_NXin;5
z*qq$J;H;3g@uNsmia^2xrcM8y89mmWIM9*EI3X{D(NQ!s)YP=Jl($#my9Uq!Y}P9{
z=SwE486+4UWXWMV!jPk8uxJP4Y|b{8I|n)*vE}SDV4MBm(IX9w6>RJQ!fPgkY&NLi
lU_5&;sY$b$g=0nb0fi8AhNbQnN8A`Oog>Y_3=S|50RRKrZ-M{-
literal 0
HcmV?d00001
diff --git a/biopet-framework/src/test/resources/single05.bam.bai b/biopet-framework/src/test/resources/single05.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..7a081f4700900bd7f3da6634d39b676b5547130a
GIT binary patch
literal 176
zcmZ>A^kigWU|;}YPay^dMj*|=Fd0m?KxwZ@5P5WQkRD`!tQXllm^mDb5OZPXp^IZP
L52glUHUk3yao`KH
literal 0
HcmV?d00001
diff --git a/biopet-framework/src/test/resources/single05.sam b/biopet-framework/src/test/resources/single05.sam
new file mode 100644
index 000000000..b5fe7ceae
--- /dev/null
+++ b/biopet-framework/src/test/resources/single05.sam
@@ -0,0 +1,9 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chrQ LN:10000
+@SQ SN:chrR LN:10000
+@RG ID:001 DS:single-end reads SM:WipeReadsTestCase
+r02 16 chrQ 50 60 10M * 0 0 TACGTACGTA EEFFGGHHII RG:Z:001
+r04 0 chrQ 500 60 10M * 0 0 CGTACGTACG EEFFGGHHII RG:Z:001
+r01 0 chrR 50 60 10M * 0 0 TACGTACGTA EEFFGGHHII RG:Z:001
+r03 16 chrR 500 60 10M * 0 0 GGGGGAAAAA GGGGGGGGGG RG:Z:001
+r05 4 * 0 0 * * 0 0 ATATATATAT HIHIHIHIHI RG:Z:001
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 772ed6295..f05b34219 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
@@ -35,6 +35,7 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
private val samP: SAMLineParser = {
val samh = new SAMFileHeader
samh.addSequence(new SAMSequenceRecord("chrQ", 10000))
+ samh.addSequence(new SAMSequenceRecord("chrR", 10000))
samh.addReadGroup(new SAMReadGroupRecord("001"))
samh.addReadGroup(new SAMReadGroupRecord("002"))
new SAMLineParser(samh)
@@ -83,6 +84,15 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
val sBamFile3 = new File(resourcePath("/single03.bam"))
val sBamFile4 = new File(resourcePath("/single04.bam"))
+ val sBamFile5 = new File(resourcePath("/single05.bam"))
+ val sBamRecs5 = makeSams(
+ "r02\t16\tchrR\t50\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001",
+ "r04\t0\tchrQ\t500\t60\t10M\t*\t0\t0\tCGTACGTACG\tEEFFGGHHII\tRG:Z:001",
+ "r01\t0\tchrR\t50\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001",
+ "r03\t16\tchrQ\t500\t60\t10M\t*\t0\t0\tGGGGGAAAAA\tGGGGGGGGGG\tRG:Z:001",
+ "r05\t4\t*\t0\t0\t*\t*\t0\t0\tATATATATAT\tHIHIHIHIHI\tRG:Z:001"
+ )
+
val pBamFile1 = new File(resourcePath("/paired01.bam"))
val pBamRecs1 = makeSams(
"r02\t99\tchrQ\t50\t60\t10M\t=\t90\t50\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001",
@@ -196,6 +206,19 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
filterNotFunc(sBamRecs1(6)) shouldBe false
}
+ @Test def testSingleBamDifferentChromosomes() = {
+ val intervals: List[Interval] = List(
+ new Interval("chrQ", 50, 55),
+ new Interval("chrR", 500, 505)
+ )
+ val filterNotFunc = makeFilterNotFunction(intervals, sBamFile5, bloomSize = bloomSize, bloomFp = bloomFp)
+ filterNotFunc(sBamRecs5(0)) shouldBe true
+ filterNotFunc(sBamRecs5(1)) shouldBe false
+ filterNotFunc(sBamRecs5(2)) shouldBe false
+ filterNotFunc(sBamRecs5(3)) shouldBe true
+ filterNotFunc(sBamRecs5(4)) shouldBe false
+ }
+
@Test def testSingleBamFilterOutMultiNotSet() = {
val intervals: List[Interval] = List(
new Interval("chrQ", 291, 320), // overlaps r01, second hit,
--
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