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biopet.biopet
Commit b9a359c2 authored by Peter van 't Hof's avatar Peter van 't Hof
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Removed contigs storage in Stats class

parent 0d184280
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Showing with 92 additions and 169 deletions
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/SampleStats.scala
View file @ b9a359c2
......@@ -23,7 +23,7 @@ import scala.collection.mutable
* @param sampleToSample Stores sample to sample compare stats
*/
case class SampleStats(
genotypeStats: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map(),
genotypeStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map(),
sampleToSample: mutable.Map[String, SampleToSampleStats] = mutable.Map()) {
/** Add an other class */
......@@ -32,12 +32,10 @@ case class SampleStats(
if (this.sampleToSample.contains(key)) this.sampleToSample(key) += value
else this.sampleToSample(key) = value
}
for ((chr, chrMap) <- other.genotypeStats; (field, fieldMap) <- chrMap) {
if (!this.genotypeStats.contains(chr))
genotypeStats += (chr -> mutable.Map[String, mutable.Map[Any, Int]]())
val thisField = this.genotypeStats(chr).get(field)
for ((field, fieldMap) <- other.genotypeStats) {
val thisField = this.genotypeStats.get(field)
if (thisField.isDefined) Stats.mergeStatsMap(thisField.get, fieldMap)
else this.genotypeStats(chr) += field -> fieldMap
else this.genotypeStats += field -> fieldMap
}
}
}
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
View file @ b9a359c2
......@@ -16,9 +16,10 @@ package nl.lumc.sasc.biopet.tools.vcfstats
import java.io.{File, PrintWriter}
import scala.collection.mutable
import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.sampleDistributions
import nl.lumc.sasc.biopet.utils.sortAnyAny
import scala.collection.mutable
import nl.lumc.sasc.biopet.utils.{ConfigUtils, sortAnyAny}
/**
* General stats class to store vcf stats
......@@ -26,7 +27,7 @@ import nl.lumc.sasc.biopet.utils.sortAnyAny
* @param generalStats Stores are general stats
* @param samplesStats Stores all sample/genotype specific stats
*/
case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] =
case class Stats(generalStats: mutable.Map[String, mutable.Map[Any, Int]] =
mutable.Map(),
samplesStats: mutable.Map[String, SampleStats] = mutable.Map()) {
......@@ -36,12 +37,10 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
if (this.samplesStats.contains(key)) this.samplesStats(key) += value
else this.samplesStats(key) = value
}
for ((chr, chrMap) <- other.generalStats; (field, fieldMap) <- chrMap) {
if (!this.generalStats.contains(chr))
generalStats += (chr -> mutable.Map[String, mutable.Map[Any, Int]]())
val thisField = this.generalStats(chr).get(field)
for ((field, fieldMap) <- other.generalStats) {
val thisField = this.generalStats.get(field)
if (thisField.isDefined) Stats.mergeStatsMap(thisField.get, fieldMap)
else this.generalStats(chr) += field -> fieldMap
else this.generalStats += field -> fieldMap
}
this
}
......@@ -49,17 +48,13 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
/** Function to write 1 specific general field */
def writeField(field: String,
outputDir: File,
prefix: String = "",
chr: String = "total"): File = {
val file = (prefix, chr) match {
case ("", "total") => new File(outputDir, field + ".tsv")
case (_, "total") => new File(outputDir, prefix + "-" + field + ".tsv")
case ("", _) => new File(outputDir, chr + "-" + field + ".tsv")
case _ => new File(outputDir, prefix + "-" + chr + "-" + field + ".tsv")
prefix: String = ""): File = {
val file = prefix match {
case "" => new File(outputDir, field + ".tsv")
case _ => new File(outputDir, prefix + "-" + field + ".tsv")
}
val data = this.generalStats
.getOrElse(chr, mutable.Map[String, mutable.Map[Any, Int]]())
.getOrElse(field, mutable.Map[Any, Int]())
file.getParentFile.mkdirs()
......@@ -73,10 +68,9 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
}
/** Function to write 1 specific general field */
def getField(field: String, chr: String = "total"): Map[String, Array[Any]] = {
def getField(field: String): Map[String, Array[Any]] = {
val data = this.generalStats
.getOrElse(chr, mutable.Map[String, mutable.Map[Any, Int]]())
.getOrElse(field, mutable.Map[Any, Int]())
val rows = for (key <- data.keySet.toArray.sortWith(sortAnyAny)) yield {
(key, data(key))
......@@ -88,13 +82,10 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
def writeGenotypeField(samples: List[String],
field: String,
outputDir: File,
prefix: String = "",
chr: String = "total"): Unit = {
val file = (prefix, chr) match {
case ("", "total") => new File(outputDir, field + ".tsv")
case (_, "total") => new File(outputDir, prefix + "-" + field + ".tsv")
case ("", _) => new File(outputDir, chr + "-" + field + ".tsv")
case _ => new File(outputDir, prefix + "-" + chr + "-" + field + ".tsv")
prefix: String = ""): Unit = {
val file = prefix match {
case "" => new File(outputDir, field + ".tsv")
case _ => new File(outputDir, prefix + "-" + field + ".tsv")
}
file.getParentFile.mkdirs()
......@@ -105,7 +96,6 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
this
.samplesStats(sample)
.genotypeStats
.getOrElse(chr, Map[String, Map[Any, Int]]())
.getOrElse(field, Map[Any, Int]())
.keySet).fold(Set[Any]())(_ ++ _)
for (key <- keySet.toList.sortWith(sortAnyAny)) {
......@@ -114,7 +104,6 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
this
.samplesStats(sample)
.genotypeStats
.getOrElse(chr, Map[String, Map[Any, Int]]())
.getOrElse(field, Map[Any, Int]())
.getOrElse(key, 0)
writer.println(values.mkString(key + "\t", "\t", ""))
......@@ -124,14 +113,12 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
/** Function to write 1 specific genotype field */
def getGenotypeField(samples: List[String],
field: String,
chr: String = "total"): Map[String, Map[String, Any]] = {
field: String): Map[String, Map[String, Any]] = {
val keySet = (for (sample <- samples)
yield
this
.samplesStats(sample)
.genotypeStats
.getOrElse(chr, Map[String, Map[Any, Int]]())
.getOrElse(field, Map[Any, Int]())
.keySet).fold(Set[Any]())(_ ++ _)
......@@ -144,7 +131,6 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
key.toString -> this
.samplesStats(sample)
.genotypeStats
.getOrElse(chr, Map[String, Map[Any, Int]]())
.getOrElse(field, Map[Any, Int]())
.get(key))
.filter(_._2.isDefined)
......@@ -153,19 +139,17 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
}
/** This will generate stats for one contig */
def getContigStats(contig: String,
samples: List[String],
def getStatsAsMap(samples: List[String],
genotypeFields: List[String] = Nil,
infoFields: List[String] = Nil,
sampleDistributions: List[String] = Nil): Map[String, Any] = {
Map(
"genotype" -> genotypeFields.map(f => f -> getGenotypeField(samples, f, contig)).toMap,
"info" -> infoFields.map(f => f -> getField(f, contig)).toMap,
"genotype" -> genotypeFields.map(f => f -> getGenotypeField(samples, f)).toMap,
"info" -> infoFields.map(f => f -> getField(f)).toMap,
"sample_distributions" -> sampleDistributions
.map(f => f -> getField("SampleDistribution-" + f, contig))
.map(f => f -> getField("SampleDistribution-" + f))
.toMap
) ++ (if (contig == "total")
Map(
) ++ Map(
"sample_compare" -> Map(
"samples" -> samples,
"genotype_overlap" -> samples.map(sample1 =>
......@@ -176,29 +160,21 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
samplesStats(sample1).sampleToSample(sample2).alleleOverlap))
)
)
else Map())
}
/** This will generate stats for total */
def getTotalStats(samples: List[String],
genotypeFields: List[String] = Nil,
infoFields: List[String] = Nil,
sampleDistributions: List[String] = Nil): Map[String, Any] =
getContigStats("total", samples, genotypeFields, infoFields, sampleDistributions)
/** This will generate stats for total and contigs separated */
def getAllStats(contigs: List[String],
def writeToFile(outputFile: File,
samples: List[String],
genotypeFields: List[String] = Nil,
infoFields: List[String] = Nil,
sampleDistributions: List[String] = Nil): Map[String, Any] = {
Map(
"contigs" -> contigs
.map(c => c -> getContigStats(c, samples, genotypeFields, infoFields, sampleDistributions))
.toMap,
"total" -> getTotalStats(samples, genotypeFields, infoFields, sampleDistributions)
)
sampleDistributions: List[String] = Nil): Unit = {
val allWriter = new PrintWriter(outputFile)
val json = ConfigUtils.mapToJson(
this.getStatsAsMap(samples, genotypeFields, infoFields, sampleDistributions))
allWriter.println(json.nospaces)
allWriter.close()
}
}
object Stats {
......@@ -222,17 +198,15 @@ object Stats {
}
/** Merge m2 into m1 */
def mergeNestedStatsMap(m1: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]],
m2: Map[String, Map[String, Map[Any, Int]]]): Unit = {
for ((chr, chrMap) <- m2; (field, fieldMap) <- chrMap) {
if (m1.contains(chr)) {
if (m1(chr).contains(field)) {
for ((key, value) <- fieldMap) {
if (m1(chr)(field).contains(key)) m1(chr)(field)(key) += value
else m1(chr)(field)(key) = value
}
} else m1(chr)(field) = mutable.Map(fieldMap.toList: _*)
} else m1(chr) = mutable.Map(field -> mutable.Map(fieldMap.toList: _*))
def mergeNestedStatsMap(m1: mutable.Map[String, mutable.Map[Any, Int]],
m2: Map[String, Map[Any, Int]]): Unit = {
for ((field, fieldMap) <- m2) {
if (m1.contains(field)) {
for ((key, value) <- fieldMap) {
if (m1(field).contains(key)) m1(field)(key) += value
else m1(field)(key) = value
}
} else m1(field) = mutable.Map(fieldMap.toList: _*)
}
}
}
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @ b9a359c2
......@@ -6,7 +6,7 @@ import java.net.URLClassLoader
import htsjdk.variant.variantcontext.{Genotype, VariantContext}
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand, VcfUtils}
import nl.lumc.sasc.biopet.utils.{ToolCommand, VcfUtils}
import org.apache.spark.{SparkConf, SparkContext}
import scala.collection.JavaConversions._
......@@ -83,13 +83,7 @@ object VcfStats extends ToolCommand {
val totalStats = regionStats.reduce(_ += _)
val allWriter = new PrintWriter(new File(cmdArgs.outputDir, "stats.json"))
val json = ConfigUtils.mapToJson(
totalStats.getAllStats(contigs, samples, adGenotypeTags, adInfoTags, sampleDistributions))
allWriter.println(json.nospaces)
allWriter.close()
//TODO: write wig files
totalStats.writeToFile(new File(cmdArgs.outputDir, "stats.json"), samples, adGenotypeTags, adInfoTags, sampleDistributions)
writeOverlap(totalStats,
_.genotypeOverlap,
......@@ -240,7 +234,7 @@ object VcfStats extends ToolCommand {
protected[tools] def checkGenotype(
record: VariantContext,
genotype: Genotype,
additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
additionalTags: List[String]): Map[String, Map[Any, Int]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
......@@ -288,13 +282,13 @@ object VcfStats extends ToolCommand {
else addToBuffer(tag, value, found = true)
}
Map(record.getContig -> buffer.toMap, "total" -> buffer.toMap)
buffer.toMap
}
/** Function to check all general stats, all info expect sample/genotype specific stats */
protected[tools] def checkGeneral(
record: VariantContext,
additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
additionalTags: List[String]): Map[String, Map[Any, Int]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
......@@ -371,11 +365,11 @@ object VcfStats extends ToolCommand {
else addToBuffer(tag, value, found = true)
}
Map(record.getContig -> buffer.toMap, "total" -> buffer.toMap)
buffer.toMap
}
protected[tools] def fillGeneral(
additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
additionalTags: List[String]): Map[String, Map[Any, Int]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
......@@ -425,11 +419,11 @@ object VcfStats extends ToolCommand {
addToBuffer(tag, "not set", found = false)
}
Map("total" -> buffer.toMap)
buffer.toMap
}
protected[tools] def fillGenotype(
additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
additionalTags: List[String]): Map[String, Map[Any, Int]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
......@@ -461,6 +455,6 @@ object VcfStats extends ToolCommand {
addToBuffer(tag, 0, found = false)
}
Map("total" -> buffer.toMap)
buffer.toMap
}
}
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @ b9a359c2
......@@ -82,19 +82,14 @@ class VcfStatsTest extends TestNGSuite with Matchers {
s1.sampleToSample("s1").alleleOverlap = 1
s2.sampleToSample("s2").alleleOverlap = 2
val bla1 = s1.genotypeStats
.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) += "1" -> mutable.Map(1 -> 1)
s1.genotypeStats += "chr" -> bla1
val bla2 = s2.genotypeStats
.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) += "2" -> mutable.Map(2 -> 2)
s2.genotypeStats += "chr" -> bla2
s1.genotypeStats += "1" -> mutable.Map(1 -> 1)
s2.genotypeStats += "2" -> mutable.Map(2 -> 2)
val ss1 = SampleToSampleStats()
val ss2 = SampleToSampleStats()
s1 += s2
s1.genotypeStats
.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map(
s1.genotypeStats shouldBe mutable.Map(
"1" -> mutable.Map(1 -> 1),
"2" -> mutable.Map(2 -> 2))
ss1.alleleOverlap = 1
......@@ -102,14 +97,12 @@ class VcfStatsTest extends TestNGSuite with Matchers {
s1.sampleToSample shouldBe mutable.Map("s1" -> ss1, "s2" -> ss2)
s1 += s2
s1.genotypeStats
.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map(
s1.genotypeStats shouldBe mutable.Map(
"1" -> mutable.Map(1 -> 1),
"2" -> mutable.Map(2 -> 4))
s1 += s1
s1.genotypeStats
.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map(
s1.genotypeStats shouldBe mutable.Map(
"1" -> mutable.Map(1 -> 2),
"2" -> mutable.Map(2 -> 8))
}
......@@ -137,50 +130,22 @@ class VcfStatsTest extends TestNGSuite with Matchers {
@Test
def testMergeNestedStatsMap(): Unit = {
val m1: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map(
"test" ->
mutable.Map("nested" -> mutable.Map("a" -> 1)))
val m2: Map[String, Map[String, Map[Any, Int]]] = Map(
"test" ->
Map("nested" -> Map("b" -> 2)))
val m1: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map("nested" -> mutable.Map("a" -> 1))
val m2: Map[String, Map[Any, Int]] = Map("nested" -> Map("b" -> 2))
Stats.mergeNestedStatsMap(m1, m2)
m1 should equal(
mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2))))
mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2)))
val m3: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map(
"test" ->
mutable.Map("nestedd" -> mutable.Map(1 -> 500)))
val m4: Map[String, Map[String, Map[Any, Int]]] = Map(
"test" ->
Map("nestedd" -> Map(6 -> 125)))
val m3: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map("nestedd" -> mutable.Map(1 -> 500))
val m4: Map[String, Map[Any, Int]] = Map("nestedd" -> Map(6 -> 125))
Stats.mergeNestedStatsMap(m3, m4)
m3 should equal(
mutable.Map("test" -> mutable.Map("nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
val m5 = m3.toMap.map(x => x._1 -> x._2.toMap.map(y => y._1 -> y._2.toMap))
Stats.mergeNestedStatsMap(m1, m5)
m1 should equal(
mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2),
"nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
m3 should equal(mutable.Map("nestedd" -> mutable.Map(1 -> 500, 6 -> 125)))
}
// @Test
// def testValueOfTsv(): Unit = {
// val i = new File(resourcePath("/sample.tsv"))
//
// valueFromTsv(i, "Sample_ID_1", "library") should be(Some("Lib_ID_1"))
// valueFromTsv(i, "Sample_ID_2", "library") should be(Some("Lib_ID_2"))
// valueFromTsv(i, "Sample_ID_1", "bam") should be(Some("MyFirst.bam"))
// valueFromTsv(i, "Sample_ID_2", "bam") should be(Some("MySecond.bam"))
// valueFromTsv(i, "Sample_ID_3", "bam") should be(empty)
// }
@Test
def testNoExistOutputDir(): Unit = {
val tmp = Files.createTempDirectory("vcfStats")
......@@ -288,26 +253,22 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val blah = checkGeneral(record, List())
blah.get("chrQ") should not be empty
blah.get("total") should not be empty
val chrq = blah("chrQ")
chrq.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
chrq.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
chrq.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
chrq.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
chrq.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
chrq.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
chrq.get("QUAL") shouldEqual Some(Map(1541 -> 1))
chrq.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
chrq.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
chrq.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
chrq.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
chrq.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
chrq.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
chrq.get("general") should not be empty
val general = chrq("general")
blah.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
blah.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
blah.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
blah.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
blah.get("QUAL") shouldEqual Some(Map(1541 -> 1))
blah.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
blah.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
blah.get("general") should not be empty
val general = blah("general")
general.get("PolymorphicInSamples") shouldEqual Some(1)
general.get("ComplexIndel") shouldEqual Some(0)
......@@ -344,8 +305,8 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
chrq.get("general") should not be empty
val totGeneral = total("general")
blah.get("general") should not be empty
val totGeneral = blah("general")
totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
totGeneral.get("ComplexIndel") shouldEqual Some(0)
......@@ -376,19 +337,15 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val blah = checkGenotype(record, genotype, List())
blah.get("chrQ") should not be empty
blah.get("total") should not be empty
val chrq = blah("chrQ")
chrq.get("GQ") shouldEqual Some(Map(99 -> 1))
chrq.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
chrq.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
chrq.get("DP") shouldEqual Some(Map(45 -> 1))
chrq.get("AD-alt") shouldEqual Some(Map(21 -> 1))
chrq.get("AD-ref") shouldEqual Some(Map(24 -> 1))
chrq.get("general") should not be empty
blah.get("GQ") shouldEqual Some(Map(99 -> 1))
blah.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
blah.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
blah.get("DP") shouldEqual Some(Map(45 -> 1))
blah.get("AD-alt") shouldEqual Some(Map(21 -> 1))
blah.get("AD-ref") shouldEqual Some(Map(24 -> 1))
blah.get("general") should not be empty
val general = chrq("general")
val general = blah("general")
general.get("Hom") shouldEqual Some(0)
general.get("NoCall") shouldEqual Some(0)
general.get("Variant") shouldEqual Some(1)
......@@ -412,7 +369,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total.get("AD-ref") shouldEqual Some(Map(24 -> 1))
total.get("general") should not be empty
val totGeneral = total("general")
val totGeneral = blah("general")
totGeneral.get("Hom") shouldEqual Some(0)
totGeneral.get("NoCall") shouldEqual Some(0)
totGeneral.get("Variant") shouldEqual Some(1)
......
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