From 37bb8e356841d86e2fbaf9fccfb40cedce3a1019 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 31 Oct 2014 19:48:32 +0100
Subject: [PATCH] More tests to guard against BAM query sorting error
---
.../tools/ExtractAlignedFastqUnitTest.scala | 29 ++++++++++++-------
1 file changed, 19 insertions(+), 10 deletions(-)
diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala
index e60af8466..1939d5351 100644
--- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala
+++ b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala
@@ -27,8 +27,11 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
private def resourcePath(p: String): String =
Paths.get(getClass.getResource(p).toURI).toString
- private def makeInterval(chr: String, start: Int, end: Int): Interval =
- new Interval(chr, start, end)
+ private def makeInterval(chr: String, start: Int, end: Int): Iterator[Interval] =
+ Iterator(new Interval(chr, start, end))
+
+ private def makeInterval(ivs: Iterable[(String, Int, Int)]): Iterator[Interval] =
+ ivs.map(x => new Interval(x._1, x._2, x._3)).toIterator
private def makeRecord(header: String): FastqRecord =
new FastqRecord(header, "ATGC", "", "HIHI")
@@ -106,15 +109,18 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
Array("partial overlap",
makeInterval("chrQ", 430, 460), sBam01, sFastq1, sFastq1Default.updated("r04", true)),
Array("enveloped",
- makeInterval("chrQ", 693, 698), sBam01, sFastq1, sFastq1Default.updated("r03", true))
+ makeInterval("chrQ", 693, 698), sBam01, sFastq1, sFastq1Default.updated("r03", true)),
+ Array("partial overlap and enveloped",
+ makeInterval(List(("chrQ", 693, 698), ("chrQ", 430, 460))), sBam01,
+ sFastq1, sFastq1Default.updated("r03", true).updated("r04", true))
)
}
@Test(dataProvider = "singleAlnProvider1")
- def testSingleBamDefault(name: String, feat: Interval, inAln: File,
+ def testSingleBamDefault(name: String, feats: Iterator[Interval], inAln: File,
fastqMap: Map[String, FastqInput], resultMap: Map[String, Boolean]) = {
require(resultMap.keySet == fastqMap.keySet)
- val memFunc = makeMembershipFunction(Iterator(feat), inAln)
+ val memFunc = makeMembershipFunction(feats, inAln)
for ((key, (rec1, rec2)) <- fastqMap) {
withClue(makeClue(name, inAln, key)) {
memFunc(rec1, rec2) shouldBe resultMap(key)
@@ -139,10 +145,10 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
}
@Test(dataProvider = "singleAlnProvider2")
- def testSingleBamMinMapQ(name: String, feat: Interval, inAln: File, minMapQ: Int,
+ def testSingleBamMinMapQ(name: String, feats: Iterator[Interval], inAln: File, minMapQ: Int,
fastqMap: Map[String, FastqInput], resultMap: Map[String, Boolean]) = {
require(resultMap.keySet == fastqMap.keySet)
- val memFunc = makeMembershipFunction(Iterator(feat), inAln, minMapQ)
+ val memFunc = makeMembershipFunction(feats, inAln, minMapQ)
for ((key, (rec1, rec2)) <- fastqMap) {
withClue(makeClue(name, inAln, key)) {
memFunc(rec1, rec2) shouldBe resultMap(key)
@@ -172,15 +178,18 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
Array("enveloped",
makeInterval("chrQ", 693, 698), pBam01, pFastq1, pFastq1Default.updated("r03", true)),
Array("in intron",
- makeInterval("chrQ", 900, 999), pBam01, pFastq1, pFastq1Default.updated("r05", true))
+ makeInterval("chrQ", 900, 999), pBam01, pFastq1, pFastq1Default.updated("r05", true)),
+ Array("partial overlap and enveloped",
+ makeInterval(List(("chrQ", 693, 698), ("chrQ", 430, 460))), pBam01,
+ pFastq1, pFastq1Default.updated("r03", true).updated("r04", true))
)
}
@Test(dataProvider = "pairAlnProvider1")
- def testPairBamDefault(name: String, feat: Interval, inAln: File,
+ def testPairBamDefault(name: String, feats: Iterator[Interval], inAln: File,
fastqMap: Map[String, FastqInput], resultMap: Map[String, Boolean]) = {
require(resultMap.keySet == fastqMap.keySet)
- val memFunc = makeMembershipFunction(Iterator(feat), inAln, commonSuffixLength = 2)
+ val memFunc = makeMembershipFunction(feats, inAln, commonSuffixLength = 2)
for ((key, (rec1, rec2)) <- fastqMap) {
withClue(makeClue(name, inAln, key)) {
memFunc(rec1, rec2) shouldBe resultMap(key)
--
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