From 0c2b2242d7fa992f411270352dceb05c32d4c733 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 10:13:59 +0100
Subject: [PATCH] Switch to case classes
---
.../nl/lumc/sasc/biopet/tools/VcfStats.scala | 49 +++++++++----------
1 file changed, 24 insertions(+), 25 deletions(-)
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 6dd074621..11d930d59 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
@@ -61,14 +61,13 @@ object VcfStats extends ToolCommand {
*/
}
- /** Class to store sample to sample compare stats */
- class SampleToSampleStats {
- /** Number of genotypes match with other sample */
- var genotypeOverlap: Int = 0
-
- /** Number of alleles also found in other sample */
- var alleleOverlap: Int = 0
-
+ /**
+ * Class to store sample to sample compare stats
+ * @param genotypeOverlap Number of genotypes match with other sample
+ * @param alleleOverlap Number of alleles also found in other sample
+ */
+ case class SampleToSampleStats(var genotypeOverlap: Int = 0,
+ var alleleOverlap: Int = 0) {
/** Add an other class */
def +=(other: SampleToSampleStats) {
this.genotypeOverlap += other.genotypeOverlap
@@ -76,14 +75,13 @@ object VcfStats extends ToolCommand {
}
}
- /** class to store all sample relative stats */
- class SampleStats {
- /** Stores all genotype relative stats */
- val genotypeStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map()
-
- /** Stores sample to sample compare stats */
- val sampleToSample: mutable.Map[String, SampleToSampleStats] = mutable.Map()
-
+ /**
+ * class to store all sample relative stats
+ * @param genotypeStats Stores all genotype relative stats
+ * @param sampleToSample Stores sample to sample compare stats
+ */
+ case class SampleStats(val genotypeStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map(),
+ val sampleToSample: mutable.Map[String, SampleToSampleStats] = mutable.Map()) {
/** Add an other class */
def +=(other: SampleStats): Unit = {
for ((key, value) <- other.sampleToSample) {
@@ -98,13 +96,13 @@ object VcfStats extends ToolCommand {
}
}
- class Stats {
- /** Stores are general stats */
- val generalStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map()
-
- /** Stores all sample/genotype specific stats */
- val samplesStats: mutable.Map[String, SampleStats] = mutable.Map()
-
+ /**
+ * General stats class to store vcf stats
+ * @param generalStats Stores are general stats
+ * @param samplesStats Stores all sample/genotype specific stats
+ */
+ case class Stats(val generalStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map(),
+ val samplesStats: mutable.Map[String, SampleStats] = mutable.Map()) {
/** Add an other class */
def +=(other: Stats): Stats = {
for ((key, value) <- other.samplesStats) {
@@ -207,8 +205,9 @@ 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)
--
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