From 8145ca779a07098b5903a6aad0fa4697e47067c6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 11:53:14 +0100
Subject: [PATCH] Add new summary to seqstat
---
.../lumc/sasc/biopet/extensions/Seqstat.scala | 31 ++++++++++++++++---
.../pipelines/flexiprep/Flexiprep.scala | 4 ++-
2 files changed, 29 insertions(+), 6 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
index d30d19fdf..c7c1a4436 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
@@ -21,16 +21,18 @@ package nl.lumc.sasc.biopet.extensions
*/
import argonaut._, Argonaut._
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
import scalaz._, Scalaz._
import scala.io.Source
-import scala.collection.mutable.Map
+import scala.collection.mutable
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
-class Seqstat(val root: Configurable) extends BiopetCommandLineFunction {
+class Seqstat(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
override val defaultVmem = "4G"
@Input(doc = "Input FastQ", required = true)
@@ -48,6 +50,25 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction {
if (json.isEmpty) return jNull
else return json.get.fieldOrEmptyObject("stats")
}
+
+ def summaryData: Map[String, Any] = {
+ val map = ConfigUtils.fileToConfigMap(output)
+
+ ConfigUtils.any2map(map.getOrElse("stats", Map()))
+ }
+
+ def summaryFiles: Map[String, File] = {
+ Map("fastq" -> input)
+ }
+
+ override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
+ (v1, v2) match {
+ case (v1: Int, v2: Int) if key == "len_min" => if (v1 < v2) v1 else v2
+ case (v1: Int, v2: Int) if key == "len_max" => if (v1 > v2) v1 else v2
+ case (v1: Int, v2: Int) => v1 + v2
+ case _ => v1
+ }
+ }
}
object Seqstat {
@@ -60,7 +81,7 @@ object Seqstat {
}
def mergeSummaries(jsons: List[Json]): Json = {
- def addJson(json: Json, total: Map[String, Long]) {
+ def addJson(json: Json, total: mutable.Map[String, Long]) {
for (key <- json.objectFieldsOrEmpty) {
if (json.field(key).get.isObject) addJson(json.field(key).get, total)
else if (json.field(key).get.isNumber) {
@@ -76,8 +97,8 @@ object Seqstat {
}
}
- var basesTotal: Map[String, Long] = Map()
- var readsTotal: Map[String, Long] = Map()
+ var basesTotal: mutable.Map[String, Long] = mutable.Map()
+ var readsTotal: mutable.Map[String, Long] = mutable.Map()
var encoding: Set[Json] = Set()
for (json <- jsons) {
encoding += json.fieldOrEmptyString("qual_encoding")
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 2d4c5c2be..9db2ab7ae 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -45,7 +45,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def summaryFiles = Map()
- def summaryData = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip)
+ def summaryData = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
var paired: Boolean = input_R2.isDefined
var R1_ext: String = _
@@ -161,12 +161,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val seqstat_R1 = Seqstat(this, R1, outDir)
seqstat_R1.isIntermediate = true
add(seqstat_R1)
+ addSummarizable(seqstat_R1, "seqstat_R1")
//summary.addSeqstat(seqstat_R1, R2 = false, after = false, chunk)
if (paired) {
val seqstat_R2 = Seqstat(this, R2, outDir)
seqstat_R2.isIntermediate = true
add(seqstat_R2)
+ addSummarizable(seqstat_R2, "seqstat_R2")
//summary.addSeqstat(seqstat_R2, R2 = true, after = false, chunk)
}
--
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