From 843b569ad71c1b8669ad2e8f558bf4d90e55de62 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 4 Feb 2016 15:30:32 +0100
Subject: [PATCH] remove countline and add some documentation
---
.../nl/lumc/sasc/biopet/tools/CheckFastqPairs.scala | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckFastqPairs.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckFastqPairs.scala
index bbe99cf0d..d3b45590f 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckFastqPairs.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckFastqPairs.scala
@@ -33,17 +33,21 @@ object CheckFastqPairs extends ToolCommand {
}
def main(args: Array[String]): Unit = {
+ //Start analyses of fastq files
logger.info("Start")
+ //parse all possible options into OptParser
val argsParser = new OptParser
val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+ //read in fastq file 1 and if present fastq file 2
val readFq1 = new FastqReader(cmdArgs.input)
val readFq2 = cmdArgs.input2.map(new FastqReader(_))
+ //define a counter to track the number of objects passing through the for loop
var counter = 0
- var countline = 0
+ //Iterate over the fastq file check for the length of both files if not correct, exit the tool and print error message
for (recordR1 <- readFq1.iterator()) {
if (readFq2.map(_.hasNext) == Some(false))
throw new IllegalStateException("R2 has less reads then R1")
@@ -51,6 +55,7 @@ object CheckFastqPairs extends ToolCommand {
//Getting R2 record, None if it's single end
val recordR2 = readFq2.map(_.next())
+ //Here we check if the readnames of both files are concordant
recordR2 match {
case Some(recordR2) => // Paired End
val readHeader = recordR1.getReadHeader
@@ -73,10 +78,12 @@ object CheckFastqPairs extends ToolCommand {
counter += 1
}
+ //if R2 is longer then R1 print an error code and exit the tool
if (readFq2.map(_.hasNext) == Some(true))
throw new IllegalStateException("R2 has more reads then R1")
logger.info("Done processing the Fastq file(s) no errors found")
+ //close both iterators
readFq1.close()
readFq2.foreach(_.close())
}
--
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