From ee197cc65fb0b5c32eb3845a2c7d1623845f4ba8 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 11:32:39 +0100
Subject: [PATCH] Added checksum cache
---
.../biopet/core/summary/SummaryQScript.scala | 30 ++++++++++++-------
1 file changed, 20 insertions(+), 10 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index acf2727f5..f457fc278 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -11,16 +11,23 @@ import nl.lumc.sasc.biopet.extensions.Md5sum
trait SummaryQScript extends BiopetQScript {
/** Key is sample/library, None is sample or library is not applicable */
- private[summary] var summarizables: Map[(Option[String], Option[String]), List[Summarizable]] = Map()
+ private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
private[summary] var summaryQScripts: List[SummaryQScript] = Nil
def summaryFile: File
- def addSummarizable(summarizable: Summarizable,
- sampleId: Option[String] = None,
- libraryId: Option[String] = None): Unit = {
- require(libraryId.isDefined == sampleId.isDefined) // Library always require a sample
- summarizables += (sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((sampleId, libraryId), Nil))
+ def addSummarizable(summarizable: Summarizable, name: String): Unit = {
+ //TODO: Automatic sample capture
+ addSummarizable(summarizable, name, None, None)
+ }
+
+ def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String]): Unit = {
+ addSummarizable(summarizable, name, sampleId, None)
+ }
+
+ def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String], libraryId: Option[String]): Unit = {
+ if (libraryId.isDefined) require(sampleId.isDefined) // Library always require a sample
+ summarizables += (name, sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((name, sampleId, libraryId), Nil))
}
def addSummaryQScript(summaryQScript: SummaryQScript): Unit = {
@@ -31,13 +38,11 @@ trait SummaryQScript extends BiopetQScript {
val writeSummary = new WriteSummary(this)
//Automatic checksums
- val keepChecksums: Boolean = config("keep_checksums_files", default = false)
-
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) {
- if (writeSummary.md5sum) {
+ if (writeSummary.md5sum && !SummaryQScript.md5sumCache.contains(file)) {
val md5sum = Md5sum(this, file)
- md5sum.isIntermediate = !keepChecksums
writeSummary.deps :+= md5sum.output
+ SummaryQScript.md5sumCache += file -> md5sum.output
add(md5sum)
}
//TODO: add more checksums types
@@ -46,3 +51,8 @@ trait SummaryQScript extends BiopetQScript {
add(writeSummary)
}
}
+
+object SummaryQScript {
+ import scala.collection.mutable.Map
+ protected[summary] val md5sumCache: Map[File, File] = Map()
+}
\ No newline at end of file
--
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