diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index e8042553b5c32affee466c6372eeac29d1e5f7c6..57885eedfa68c7ac2c31312f1579f3b5fcda850b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -102,7 +102,7 @@ object ExtractAlignedFastq extends ToolCommand {
val queries: Array[QueryInterval] = iv.toList
// transform to QueryInterval
- .map(x => new QueryInterval(getSequenceIndex(x.getSequence), x.getStart, x.getEnd))
+ .map(x => new QueryInterval(getSequenceIndex(x.getContig), x.getStart, x.getEnd))
// sort Interval
.sortBy(x => (x.referenceIndex, x.start, x.end))
// cast to array
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index 7e3200d3e7d1525d53aeb4fa40abde0d0aecbaf8..d34e8cf9d99c7524c007799c67c04471ae0042f6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -358,7 +358,7 @@ object VcfStats extends ToolCommand {
logger.info("Starting on: " + interval)
for (
- record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd) if record.getStart <= interval.getEnd
+ record <- reader.query(interval.getContig, interval.getStart, interval.getEnd) if record.getStart <= interval.getEnd
) {
mergeNestedStatsMap(stats.generalStats, checkGeneral(record, adInfoTags))
for (sample1 <- samples) yield {
@@ -376,7 +376,7 @@ object VcfStats extends ToolCommand {
reader.close()
if (commandArgs.writeBinStats) {
- val binOutputDir = new File(commandArgs.outputDir, "bins" + File.separator + interval.getSequence)
+ val binOutputDir = new File(commandArgs.outputDir, "bins" + File.separator + interval.getContig)
writeGenotypeField(stats, samples, "general", binOutputDir, prefix = "genotype-" + interval.getStart + "-" + interval.getEnd)
writeField(stats, "general", binOutputDir, prefix = interval.getStart + "-" + interval.getEnd)
@@ -439,7 +439,7 @@ object VcfStats extends ToolCommand {
}
protected def writeWiggle(intervals: List[Interval], row: String, column: String, outputFile: File, genotype: Boolean): Unit = {
- val groupedIntervals = intervals.groupBy(_.getSequence).map { case (k, v) => k -> v.sortBy(_.getStart) }
+ val groupedIntervals = intervals.groupBy(_.getContig).map { case (k, v) => k -> v.sortBy(_.getStart) }
outputFile.getParentFile.mkdirs()
val writer = new PrintWriter(outputFile)
writer.println("track type=wiggle_0")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index 4060560236166e49d80d104b09a682d116afb16f..f010c1cc743a499fbfed63e3de32e8edeb7ac7de 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -149,12 +149,12 @@ object WipeReads extends ToolCommand {
throw new IllegalArgumentException("Unexpected interval file type: " + inFile.getPath)
iterFunc(inFile).toList
- .sortBy(x => (x.getSequence, x.getStart, x.getEnd))
+ .sortBy(x => (x.getContig, x.getStart, x.getEnd))
.foldLeft(List.empty[Interval])(
(acc, x) => {
acc match {
case head :: tail if x.intersects(head) =>
- new Interval(x.getSequence, min(x.getStart, head.getStart), max(x.getEnd, head.getEnd)) :: tail
+ new Interval(x.getContig, min(x.getStart, head.getStart), max(x.getEnd, head.getEnd)) :: tail
case _ => x :: acc
}
}
@@ -193,16 +193,16 @@ object WipeReads extends ToolCommand {
*/
def makeQueryInterval(in: SamReader, iv: Interval): Option[QueryInterval] = {
val getIndex = in.getFileHeader.getSequenceIndex _
- if (getIndex(iv.getSequence) > -1)
- Some(new QueryInterval(getIndex(iv.getSequence), iv.getStart, iv.getEnd))
- else if (iv.getSequence.startsWith("chr") && getIndex(iv.getSequence.substring(3)) > -1) {
+ if (getIndex(iv.getContig) > -1)
+ Some(new QueryInterval(getIndex(iv.getContig), iv.getStart, iv.getEnd))
+ else if (iv.getContig.startsWith("chr") && getIndex(iv.getContig.substring(3)) > -1) {
logger.warn("Removing 'chr' prefix from interval " + iv.toString)
- Some(new QueryInterval(getIndex(iv.getSequence.substring(3)), iv.getStart, iv.getEnd))
- } else if (!iv.getSequence.startsWith("chr") && getIndex("chr" + iv.getSequence) > -1) {
+ Some(new QueryInterval(getIndex(iv.getContig.substring(3)), iv.getStart, iv.getEnd))
+ } else if (!iv.getContig.startsWith("chr") && getIndex("chr" + iv.getContig) > -1) {
logger.warn("Adding 'chr' prefix to interval " + iv.toString)
- Some(new QueryInterval(getIndex("chr" + iv.getSequence), iv.getStart, iv.getEnd))
+ Some(new QueryInterval(getIndex("chr" + iv.getContig), iv.getStart, iv.getEnd))
} else {
- logger.warn("Sequence " + iv.getSequence + " does not exist in alignment")
+ logger.warn("Sequence " + iv.getContig + " does not exist in alignment")
None
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
index 9b4958b4538c11693d1a91f4bfcb0c82427445ba..c62c6bd19c5980c0ffcba55223a974b78a946c24 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
@@ -58,7 +58,7 @@ class ExtractAlignedFastqTest extends TestNGSuite with MockitoSugar with Matcher
@Test def testIntervalStartEnd() = {
val obs = makeIntervalFromString(List("chr5:1000-1100")).next()
val exp = new Interval("chr5", 1000, 1100)
- obs.getSequence should ===(exp.getSequence)
+ obs.getContig should ===(exp.getContig)
obs.getStart should ===(exp.getStart)
obs.getEnd should ===(exp.getEnd)
}
@@ -66,7 +66,7 @@ class ExtractAlignedFastqTest extends TestNGSuite with MockitoSugar with Matcher
@Test def testIntervalStartEndComma() = {
val obs = makeIntervalFromString(List("chr5:1,000-1,100")).next()
val exp = new Interval("chr5", 1000, 1100)
- obs.getSequence should ===(exp.getSequence)
+ obs.getContig should ===(exp.getContig)
obs.getStart should ===(exp.getStart)
obs.getEnd should ===(exp.getEnd)
}
@@ -74,7 +74,7 @@ class ExtractAlignedFastqTest extends TestNGSuite with MockitoSugar with Matcher
@Test def testIntervalStartEndDot() = {
val obs = makeIntervalFromString(List("chr5:1.000-1.100")).next()
val exp = new Interval("chr5", 1000, 1100)
- obs.getSequence should ===(exp.getSequence)
+ obs.getContig should ===(exp.getContig)
obs.getStart should ===(exp.getStart)
obs.getEnd should ===(exp.getEnd)
}
@@ -82,7 +82,7 @@ class ExtractAlignedFastqTest extends TestNGSuite with MockitoSugar with Matcher
@Test def testIntervalStart() = {
val obs = makeIntervalFromString(List("chr5:1000")).next()
val exp = new Interval("chr5", 1000, 1000)
- obs.getSequence should ===(exp.getSequence)
+ obs.getContig should ===(exp.getContig)
obs.getStart should ===(exp.getStart)
obs.getEnd should ===(exp.getEnd)
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
index 4b98bba0c873a0ec5aa9c48a51c36475280adbfb..4919486d601415c307b44e4f016bd80fb05a97e8 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
@@ -140,10 +140,10 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testMakeIntervalFromBed() = {
val intervals: List[Interval] = makeIntervalFromFile(BedFile1)
intervals.length shouldBe 3
- intervals.head.getSequence should ===("chrQ")
+ intervals.head.getContig should ===("chrQ")
intervals.head.getStart shouldBe 991
intervals.head.getEnd shouldBe 1000
- intervals.last.getSequence should ===("chrQ")
+ intervals.last.getContig should ===("chrQ")
intervals.last.getStart shouldBe 291
intervals.last.getEnd shouldBe 320
}
@@ -151,13 +151,13 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testMakeIntervalFromRefFlat() = {
val intervals: List[Interval] = makeIntervalFromFile(RefFlatFile1)
intervals.length shouldBe 5
- intervals.head.getSequence should ===("chrS")
+ intervals.head.getContig should ===("chrS")
intervals.head.getStart shouldBe 101
intervals.head.getEnd shouldBe 500
- intervals(2).getSequence should ===("chrQ")
+ intervals(2).getContig should ===("chrQ")
intervals(2).getStart shouldBe 801
intervals(2).getEnd shouldBe 1000
- intervals.last.getSequence should ===("chrQ")
+ intervals.last.getContig should ===("chrQ")
intervals.last.getStart shouldBe 101
intervals.last.getEnd shouldBe 200
}
@@ -165,10 +165,10 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testMakeIntervalFromGtf() = {
val intervals: List[Interval] = makeIntervalFromFile(GtfFile1, "exon")
intervals.length shouldBe 3
- intervals.head.getSequence should ===("chrQ")
+ intervals.head.getContig should ===("chrQ")
intervals.head.getStart shouldBe 669
intervals.head.getEnd shouldBe 778
- intervals.last.getSequence should ===("chrP")
+ intervals.last.getContig should ===("chrP")
intervals.last.getStart shouldBe 2949
intervals.last.getEnd shouldBe 3063
}
@@ -176,10 +176,10 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testMakeIntervalFromBedOverlap() = {
val intervals: List[Interval] = makeIntervalFromFile(BedFile2)
intervals.length shouldBe 4
- intervals.head.getSequence should ===("chrQ")
+ intervals.head.getContig should ===("chrQ")
intervals.head.getStart shouldBe 451
intervals.head.getEnd shouldBe 480
- intervals.last.getSequence should ===("chrQ")
+ intervals.last.getContig should ===("chrQ")
intervals.last.getStart shouldBe 2
intervals.last.getEnd shouldBe 250
}