From 6ae2579ac93dababdfea8d09b99051c5dbb13490 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Tue, 3 Feb 2015 12:22:26 +0100
Subject: [PATCH] Refactor FastQC encoding retrieval
---
.../biopet/pipelines/flexiprep/Fastqc.scala | 17 ++++++++++++++---
.../biopet/pipelines/flexiprep/SeqtkSeq.scala | 2 +-
2 files changed, 15 insertions(+), 4 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index e9569f7e6..0dd72a620 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -66,9 +66,20 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
else fqModules
}
- protected case class Sequence(name: String, seq: String)
- def getFoundAdapters: List[Sequence] = {
- def getSeqs(file: File) = {
+ /**
+ * Retrieves the FASTQ file encoding as computed by FastQC.
+ *
+ * @return encoding name
+ * @throws NoSuchElementException when the "Basic Statistics" key does not exist in the mapping or
+ * when a line starting with "Encoding" does not exist.
+ */
+ @throws(classOf[NoSuchElementException])
+ lazy val encoding: String =
+ qcModules("Basic Statistics")
+ .dropWhile(!_.startsWith("Encoding"))
+ .head
+ .stripPrefix("Encoding\t")
+
if (file != null) {
(for (
line <- Source.fromFile(file).getLines(); if line.startsWith("#");
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index f6d6ac9d7..0fdeee289 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -25,7 +25,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
override def beforeCmd {
super.beforeCmd
if (fastqc != null && Q == None) {
- val encoding = fastqc.getEncoding
+ val encoding = fastqc.encoding
Q = encoding match {
case null => None
case s if (s.contains("Sanger / Illumina 1.9")) => None
--
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