From 198fc86c328ea18e00d3b28632cf2870f66260ce Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 19 Aug 2015 15:37:11 +0200
Subject: [PATCH] Added logging
---
.../sasc/biopet/tools/RegionAfCount.scala | 23 +++++++++++++++----
1 file changed, 18 insertions(+), 5 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index 2052b7a56..f7c4324d2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -55,6 +55,8 @@ object RegionAfCount extends ToolCommand {
val argsParser = new OptParser
val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+ logger.info("Start")
+
val regions = (for (line <- Source.fromFile(cmdArgs.bedFile).getLines()) yield {
val values = line.split("\t")
require(values.length >= 3, "to less columns in bed file")
@@ -63,8 +65,10 @@ object RegionAfCount extends ToolCommand {
new Interval(values(0), values(1).toInt, values(2).toInt, true, name)
}).toList
- val counts = (for (region <- regions) yield region.getName -> {
- (for (vcfFile <- cmdArgs.vcfFiles) yield vcfFile -> {
+ var c = 0
+
+ val afCounts = (for (region <- regions.par) yield region.getName -> {
+ val sum = (for (vcfFile <- cmdArgs.vcfFiles.par) yield vcfFile -> {
val reader = new VCFFileReader(vcfFile, true)
val it = reader.query(region.getContig, region.getStart, region.getEnd)
val sum = (for (v <- it) yield {
@@ -77,14 +81,23 @@ object RegionAfCount extends ToolCommand {
reader.close()
sum
}).toMap
+
+ c += 1
+ if (c % 100 == 0) logger.info(s"$c regions done")
+
+ sum
}).toMap
+ logger.info(s"Done reading, $c regions")
+
val writer = new PrintWriter(cmdArgs.outputFile)
writer.println("\t" + cmdArgs.vcfFiles.map(_.getName).mkString("\t"))
- for (c <- counts) {
- writer.print(c._1 + "\t")
- writer.println(cmdArgs.vcfFiles.map(c._2(_)).mkString("\t"))
+ for (r <- regions) {
+ writer.print(r.getName + "\t")
+ writer.println(cmdArgs.vcfFiles.map(afCounts(r.getName)(_)).mkString("\t"))
}
writer.close()
+
+ logger.info("Done")
}
}
\ No newline at end of file
--
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