From 92fd93dfa7cef38bff22ffead88c4d02ba76393a Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 3 Feb 2015 14:56:30 +0100
Subject: [PATCH] Reducing the wrapper to take bam and chrom.sizes file only
---
.../extensions/igvtools/IGVToolsCount.scala | 38 ++++++-------------
1 file changed, 12 insertions(+), 26 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index d209f9d70..2f6275176 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -16,8 +16,8 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
@Input(doc = "Bam File")
var input: File = _
- @Argument(doc = "Genome name")
- var genomeName: String = config("genomeName")
+ @Input(doc = "<genome>.chrom.sizes File")
+ var genomeChromSizes: File = _
@Output
protected var tdf: File = _
@@ -48,30 +48,14 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
this.tdf = new File(input.getAbsolutePath + ".tdf")
this.wig = new File(input.getAbsolutePath.stripSuffix(".bam") + ".wig")
-
- // check genome name or File
- val genome = new File(genomeName)
- if (!genome.exists()) {
- // check in the IGVTools genome/directory
- val genomeInDir = new File(new File(executable).getParent + File.separator + "genomes" + File.separator + genomeName + ".chrom.sizes")
- if (!genomeInDir.exists()) {
- throw new FileNotFoundException("genomeName contains a invalid filepath/genomename or not supported by IGVTools")
- } else {
- genomeName = genomeInDir.getAbsolutePath
- }
- } else {
- // redefine the genomeName.
- genomeName = genome.getAbsolutePath
- }
-
}
def cmdLine = {
required(executable) +
required("count") +
- optional("-z", maxZoom) +
- optional("-w", windowSize) +
- optional("-e", extFactor) +
+ optional("--maxZoom", maxZoom) +
+ optional("--windowSize", windowSize) +
+ optional("--extFactor", extFactor) +
optional("--preExtFactor", preExtFactor) +
optional("--postExtFactor", postExtFactor) +
optional("--windowFunctions", windowFunctions) +
@@ -83,9 +67,13 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
conditional(pairs, "--pairs") +
required(input) +
required(outputArg) +
- required(genomeName)
+ required(genomeChromSizes)
}
+ /**
+ * This part should never fail, these values are set within this wrapper
+ *
+ */
private def outputArg: String = {
(tdf.isInstanceOf[File], wig.isInstanceOf[File]) match {
case (false, false) => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
@@ -102,16 +90,14 @@ object IGVToolsCount {
* and the `genomename` (hg18,hg19,mm10)
*
* @param input Bamfile to count reads from
- * @param genomename Name of path to the genome.chrsizes.bed,
* @return a new IGVToolsCount instance
* @throws FileNotFoundException bam File is not found
* @throws IllegalArgumentException tdf or wig not supplied
*/
- def apply(root: Configurable, input: File,
- genomename: String): IGVToolsCount = {
+ def apply(root: Configurable, input: File, genomeChromSizes: File): IGVToolsCount = {
val counting = new IGVToolsCount(root)
counting.input = input
- counting.genomeName = genomename
+ counting.genomeChromSizes = genomeChromSizes
return counting
}
}
\ No newline at end of file
--
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