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biopet.biopet
Commit bcc8fb10 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixing compile issues

parent aa3a03e0
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Showing with 53 additions and 53 deletions
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @ bcc8fb10
......@@ -120,16 +120,16 @@ object VcfStats extends ToolCommand {
opt[String]("genotypeTag") unbounded () valueName "<tag>" action { (x, c) =>
c.copy(genotypeTags = x :: c.genotypeTags)
} text s"Summarize these genotype tags. Default is (${defaultGenotypeFields.mkString(", ")})"
opt[Unit]("allInfoTags") unbounded () action { (x, c) =>
opt[Unit]("allInfoTags") unbounded () action { (_, c) =>
c.copy(allInfoTags = true)
} text "Summarize all info tags. Default false"
opt[Unit]("allGenotypeTags") unbounded () action { (x, c) =>
opt[Unit]("allGenotypeTags") unbounded () action { (_, c) =>
c.copy(allGenotypeTags = true)
} text "Summarize all genotype tags. Default false"
opt[Int]("binSize") unbounded () action { (x, c) =>
c.copy(binSize = x)
} text "Binsize in estimated base pairs"
opt[Unit]("writeBinStats") unbounded () action { (x, c) =>
opt[Unit]("writeBinStats") unbounded () action { (_, c) =>
c.copy(writeBinStats = true)
} text "Write bin statistics. Default False"
opt[String]("generalWiggle") unbounded () action { (x, c) =>
......@@ -205,12 +205,12 @@ object VcfStats extends ToolCommand {
}).toList ::: defaultGenotypeFields
val bedRecords = (cmdArgs.intervals match {
case Some(intervals) =>
BedRecordList.fromFile(intervals).validateContigs(cmdArgs.referenceFile)
case Some(i) =>
BedRecordList.fromFile(i).validateContigs(cmdArgs.referenceFile)
case _ => BedRecordList.fromReference(cmdArgs.referenceFile)
}).combineOverlap.scatter(cmdArgs.binSize)
val intervals: List[Interval] = bedRecords.toSamIntervals.toList
val intervals: List[Interval] = BedRecordList.fromList(bedRecords.flatten).toSamIntervals.toList
val totalBases = bedRecords.length
......@@ -242,9 +242,7 @@ object VcfStats extends ToolCommand {
// Triple for loop to not keep all bins in memory
val statsFutures = for (intervals <- Random
.shuffle(intervals)
.grouped(intervals.size / (if (intervals.size > 10) 4 else 1))
.toList)
.shuffle(bedRecords))
yield
Future {
val chunkStats = for (intervals <- intervals.grouped(25)) yield {
......@@ -254,7 +252,9 @@ object VcfStats extends ToolCommand {
val stats = createStats
logger.info("Starting on: " + interval)
val query = reader.query(interval.getContig, interval.getStart, interval.getEnd)
val samInterval = interval.toSamInterval
val query = reader.query(samInterval.getContig, samInterval.getStart, samInterval.getEnd)
if (!query.hasNext) {
Stats.mergeNestedStatsMap(stats.generalStats, fillGeneral(adInfoTags))
for (sample <- samples) yield {
......@@ -264,7 +264,7 @@ object VcfStats extends ToolCommand {
chunkCounter += 1
}
for (record <- query if record.getStart <= interval.getEnd) {
for (record <- query if record.getStart <= samInterval.getEnd) {
Stats.mergeNestedStatsMap(stats.generalStats, checkGeneral(record, adInfoTags))
for (sample1 <- samples) yield {
val genotype = record.getGenotype(sample1)
......@@ -284,19 +284,19 @@ object VcfStats extends ToolCommand {
if (cmdArgs.writeBinStats) {
val binOutputDir =
new File(cmdArgs.outputDir, "bins" + File.separator + interval.getContig)
new File(cmdArgs.outputDir, "bins" + File.separator + samInterval.getContig)
stats.writeGenotypeField(
samples,
"general",
binOutputDir,
prefix = "genotype-" + interval.getStart + "-" + interval.getEnd)
prefix = "genotype-" + samInterval.getStart + "-" + samInterval.getEnd)
stats.writeField("general",
binOutputDir,
prefix = interval.getStart + "-" + interval.getEnd)
prefix = samInterval.getStart + "-" + samInterval.getEnd)
}
status(chunkCounter, interval)
status(chunkCounter, samInterval)
stats
}
binStats.toList.fold(createStats)(_ += _)
......@@ -404,7 +404,7 @@ object VcfStats extends ToolCommand {
else buffer += key -> (map + (value -> map.getOrElse(value, 0)))
}
addToBuffer("QUAL", "not set", false)
addToBuffer("QUAL", "not set", found = false)
addToBuffer("SampleDistribution-Het", "not set", found = false)
addToBuffer("SampleDistribution-HetNonRef", "not set", found = false)
......@@ -419,25 +419,25 @@ object VcfStats extends ToolCommand {
addToBuffer("SampleDistribution-Filtered", "not set", found = false)
addToBuffer("SampleDistribution-Variant", "not set", found = false)
addToBuffer("general", "Total", false)
addToBuffer("general", "Biallelic", false)
addToBuffer("general", "ComplexIndel", false)
addToBuffer("general", "Filtered", false)
addToBuffer("general", "FullyDecoded", false)
addToBuffer("general", "Indel", false)
addToBuffer("general", "Mixed", false)
addToBuffer("general", "MNP", false)
addToBuffer("general", "MonomorphicInSamples", false)
addToBuffer("general", "NotFiltered", false)
addToBuffer("general", "PointEvent", false)
addToBuffer("general", "PolymorphicInSamples", false)
addToBuffer("general", "SimpleDeletion", false)
addToBuffer("general", "SimpleInsertion", false)
addToBuffer("general", "SNP", false)
addToBuffer("general", "StructuralIndel", false)
addToBuffer("general", "Symbolic", false)
addToBuffer("general", "SymbolicOrSV", false)
addToBuffer("general", "Variant", false)
addToBuffer("general", "Total", found = false)
addToBuffer("general", "Biallelic", found = false)
addToBuffer("general", "ComplexIndel", found = false)
addToBuffer("general", "Filtered", found = false)
addToBuffer("general", "FullyDecoded", found = false)
addToBuffer("general", "Indel", found = false)
addToBuffer("general", "Mixed", found = false)
addToBuffer("general", "MNP", found = false)
addToBuffer("general", "MonomorphicInSamples", found = false)
addToBuffer("general", "NotFiltered", found = false)
addToBuffer("general", "PointEvent", found = false)
addToBuffer("general", "PolymorphicInSamples", found = false)
addToBuffer("general", "SimpleDeletion", found = false)
addToBuffer("general", "SimpleInsertion", found = false)
addToBuffer("general", "SNP", found = false)
addToBuffer("general", "StructuralIndel", found = false)
addToBuffer("general", "Symbolic", found = false)
addToBuffer("general", "SymbolicOrSV", found = false)
addToBuffer("general", "Variant", found = false)
val skipTags = List("QUAL", "general")
......@@ -460,7 +460,7 @@ object VcfStats extends ToolCommand {
else buffer += key -> (map + (value -> map.getOrElse(value, 0)))
}
addToBuffer("QUAL", Math.round(record.getPhredScaledQual), true)
addToBuffer("QUAL", Math.round(record.getPhredScaledQual), found = true)
addToBuffer("SampleDistribution-Het",
record.getGenotypes.count(genotype => genotype.isHet),
......@@ -500,7 +500,7 @@ object VcfStats extends ToolCommand {
genotype.isHetNonRef || genotype.isHet || genotype.isHomVar),
found = true)
addToBuffer("general", "Total", true)
addToBuffer("general", "Total", found = true)
addToBuffer("general", "Biallelic", record.isBiallelic)
addToBuffer("general", "ComplexIndel", record.isComplexIndel)
addToBuffer("general", "Filtered", record.isFiltered)
......@@ -541,22 +541,22 @@ object VcfStats extends ToolCommand {
else buffer += key -> (map + (value -> map.getOrElse(value, 0)))
}
addToBuffer("DP", "not set", false)
addToBuffer("GQ", "not set", false)
addToBuffer("general", "Total", false)
addToBuffer("general", "Het", false)
addToBuffer("general", "HetNonRef", false)
addToBuffer("general", "Hom", false)
addToBuffer("general", "HomRef", false)
addToBuffer("general", "HomVar", false)
addToBuffer("general", "Mixed", false)
addToBuffer("general", "NoCall", false)
addToBuffer("general", "NonInformative", false)
addToBuffer("general", "Available", false)
addToBuffer("general", "Called", false)
addToBuffer("general", "Filtered", false)
addToBuffer("general", "Variant", false)
addToBuffer("DP", "not set", found = false)
addToBuffer("GQ", "not set", found = false)
addToBuffer("general", "Total", found = false)
addToBuffer("general", "Het", found = false)
addToBuffer("general", "HetNonRef", found = false)
addToBuffer("general", "Hom", found = false)
addToBuffer("general", "HomRef", found = false)
addToBuffer("general", "HomVar", found = false)
addToBuffer("general", "Mixed", found = false)
addToBuffer("general", "NoCall", found = false)
addToBuffer("general", "NonInformative", found = false)
addToBuffer("general", "Available", found = false)
addToBuffer("general", "Called", found = false)
addToBuffer("general", "Filtered", found = false)
addToBuffer("general", "Variant", found = false)
val skipTags = List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used", "general")
......
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