Commit 11a6c2db authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added general stats

parent 612be8f7
......@@ -114,15 +114,17 @@ object VcfStats extends ToolCommand {
val samples = header.getSampleNamesInOrder.toList
val intervals: List[Interval] = (
for (seq <- header.getSequenceDictionary.getSequences;
for (
seq <- header.getSequenceDictionary.getSequences;
chunks = seq.getSequenceLength / 10000000;
i <- 1 until chunks) yield {
i <- 1 until chunks
) yield {
val size = seq.getSequenceLength / chunks
val begin = size * (i-1) + 1
val begin = size * (i - 1) + 1
val end = if (i >= chunks) seq.getSequenceLength else size * i
new Interval(seq.getSequenceName, begin, end)
}
).toList
).toList
val totalBases = intervals.foldRight(0L)(_.length() + _)
......@@ -144,7 +146,7 @@ object VcfStats extends ToolCommand {
var variantCounter = 0L
var baseCounter = 0L
def status(count: Int, interval:Interval): Unit = {
def status(count: Int, interval: Interval): Unit = {
variantCounter += count
baseCounter += interval.length()
val fraction = baseCounter.toFloat / totalBases * 100
......@@ -158,8 +160,9 @@ object VcfStats extends ToolCommand {
val stats = createStats
logger.info("Starting on: " + interval)
for (record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd)
if record.getStart <= interval.getEnd) {
for (
record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd) if record.getStart <= interval.getEnd
) {
mergeNestedStatsMap(stats.generalStats, checkGeneral(record))
for (sample1 <- samples) yield {
val genotype = record.getGenotype(sample1)
......@@ -201,13 +204,25 @@ object VcfStats extends ToolCommand {
buffer += "DP" -> Map((if (genotype.hasDP) genotype.getDP else "not set") -> 1)
buffer += "GQ" -> Map((if (genotype.hasGQ) genotype.getGQ else "not set") -> 1)
def addToBuffer(key:String, value:Any): Unit = {
def addToBuffer(key: String, value: Any): Unit = {
val map = buffer.getOrElse(key, Map())
buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
}
val usedAlleles = (for (allele <- genotype.getAlleles) yield record.getAlleleIndex(allele)).toList
if (genotype.isHet) addToBuffer("general", "Het")
if (genotype.isHetNonRef) addToBuffer("general", "HetNonRef")
if (genotype.isHom) addToBuffer("general", "Hom")
if (genotype.isHomRef) addToBuffer("general", "HomRef")
if (genotype.isHomVar) addToBuffer("general", "HomVar")
if (genotype.isMixed) addToBuffer("general", "Mixed")
if (genotype.isNoCall) addToBuffer("general", "NoCall")
if (genotype.isNonInformative) addToBuffer("general", "NonInformative")
if (genotype.isAvailable) addToBuffer("general", "Available")
if (genotype.isCalled) addToBuffer("general", "Called")
if (genotype.isFiltered) addToBuffer("general", "Filtered")
if (genotype.hasAD) {
val ad = genotype.getAD
for (i <- 0 until ad.size if ad(i) > 0) {
......@@ -218,21 +233,20 @@ object VcfStats extends ToolCommand {
else addToBuffer("AD-not_used", ad(i))
}
}
buffer.toMap
}
def writeGenotypeFields(stats: Stats, prefix: String, samples: List[String]) {
val fields = List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used")
val fields = List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used", "general")
for (field <- fields) {
val file = new File(prefix + field + ".tsv")
file.getParentFile.mkdirs()
val writer = new PrintWriter(file)
writer.println(samples.mkString("\t", "\t", ""))
val keySet = (for (sample <- samples) yield
stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any,Int]()).keySet).fold(Set[Any]())(_ ++ _)
val keySet = (for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any, Int]()).keySet).fold(Set[Any]())(_ ++ _)
for (key <- keySet.toList.sortWith(sortAnyAny(_, _))) {
val values = for (sample <- samples) yield
stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any,Int]()).getOrElse(key, 0)
val values = for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any, Int]()).getOrElse(key, 0)
writer.println(values.mkString(key + "\t", "\t", ""))
}
writer.close()
......@@ -315,9 +329,9 @@ object VcfStats extends ToolCommand {
logger.info("Starting: " + command)
val process = Process(command).run(ProcessLogger(x => logger.debug(x), x => logger.debug(x)))
if (process.exitValue() == 0) logger.info("Done: " + command)
if (process.exitValue() == 0) logger.info("Done: " + command)
else {
logger.warn("Failed: " + command)
logger.warn("Failed: " + command)
if (!logger.isDebugEnabled) logger.warn("Use -l debug for more info")
}
}
......
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