From 105185025d85f2ca3f19c000a7e432ec194a3b19 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 4 Dec 2014 09:50:49 +0100
Subject: [PATCH] Documentation updates
---
.../biopet/tools/ExtractAlignedFastq.scala | 22 ++++++++++++++++++-
.../nl/lumc/sasc/biopet/tools/WipeReads.scala | 17 +++++---------
2 files changed, 26 insertions(+), 13 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index e56202dfa..b05591cbf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -19,9 +19,10 @@ import nl.lumc.sasc.biopet.core.ToolCommand
object ExtractAlignedFastq extends ToolCommand {
+ /** type alias for Fastq input (may or may not be paired) */
type FastqInput = (FastqRecord, Option[FastqRecord])
- /** function to get FastqRecord ID */
+ /** Get the FastqRecord ID */
def fastqId(rec: FastqRecord) = rec.getReadHeader.split(" ")(0)
/**
@@ -125,6 +126,13 @@ object ExtractAlignedFastq extends ToolCommand {
}
}
+ /**
+ * Extracts reads from the given input Fastq file and writes to a new output Fastq file
+ *
+ * @param memFunc Predicate for extracting reads. If evaluates to true, the read is extracted.
+ * @param inputFastq1 Input [[FastqReader]] object.
+ * @param outputFastq1 Output [[BasicFastqWriter]] object.
+ */
def extractReads(memFunc: FastqInput => Boolean,
inputFastq1: FastqReader, outputFastq1: BasicFastqWriter): Unit =
inputFastq1.iterator.asScala
@@ -132,6 +140,15 @@ object ExtractAlignedFastq extends ToolCommand {
.filter(rec => memFunc(rec._1, rec._2))
.foreach(rec => outputFastq1.write(rec._1))
+ /**
+ * Extracts reads from the given input Fastq pairs and writes to new output Fastq pair files
+ *
+ * @param memFunc Predicate for extracting reads. If evaluates to true, the read is extracted.
+ * @param inputFastq1 Input [[FastqReader]] object for pair 1.
+ * @param outputFastq1 Input [[FastqReader]] object for pair 2.
+ * @param inputFastq2 Output [[BasicFastqWriter]] object for pair 1.
+ * @param outputFastq2 Output [[BasicFastqWriter]] object for pair 2.
+ */
def extractReads(memFunc: FastqInput => Boolean,
inputFastq1: FastqReader, outputFastq1: BasicFastqWriter,
inputFastq2: FastqReader, outputFastq2: BasicFastqWriter): Unit =
@@ -143,6 +160,7 @@ object ExtractAlignedFastq extends ToolCommand {
outputFastq2.write(rec._2)
})
+ /** Default arguments */
case class Args(inputBam: File = new File(""),
intervals: List[String] = List.empty[String],
inputFastq1: File = new File(""),
@@ -152,6 +170,7 @@ object ExtractAlignedFastq extends ToolCommand {
minMapQ: Int = 0,
commonSuffixLength: Int = 0) extends AbstractArgs
+ /** Command line argument parser */
class OptParser extends AbstractOptParser {
head(
@@ -213,6 +232,7 @@ object ExtractAlignedFastq extends ToolCommand {
}
}
+ /** Parses the command line argument */
def parseArgs(args: Array[String]): Args =
new OptParser()
.parse(args, Args())
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index 9bfb15686..82014b589 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -47,12 +47,7 @@ class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
object WipeReads extends ToolCommand {
- /**
- * Creates a SamReader object from an input BAM file, ensuring it is indexed
- *
- * @param inBam input BAM file
- * @return
- */
+ /** Creates a SamReader object from an input BAM file, ensuring it is indexed */
private def prepInBam(inBam: File): SamReader = {
val bam = SamReaderFactory
.make()
@@ -62,6 +57,7 @@ object WipeReads extends ToolCommand {
bam
}
+ /** Creates a [[SAMFileWriter]] object for writing, indexed */
private def prepOutBam(outBam: File, templateBam: File,
writeIndex: Boolean = true, async: Boolean = true): SAMFileWriter =
new SAMFileWriterFactory()
@@ -336,6 +332,7 @@ object WipeReads extends ToolCommand {
}
}
+ /** Default arguments */
case class Args(inputBam: File = new File(""),
targetRegions: File = new File(""),
outputBam: File = new File(""),
@@ -348,6 +345,7 @@ object WipeReads extends ToolCommand {
bloomSize: Long = 70000000,
bloomFp: Double = 4e-7) extends AbstractArgs
+ /** Command line argument parser */
class OptParser extends AbstractOptParser {
head(
@@ -418,12 +416,7 @@ object WipeReads extends ToolCommand {
}
- /**
- * Parses the command line argument
- *
- * @param args Array of arguments
- * @return
- */
+ /** Parses the command line argument */
def parseArgs(args: Array[String]): Args = new OptParser()
.parse(args, Args())
.getOrElse(sys.exit(1))
--
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