From 039c58a99444aaae62872f26a362709f33556696 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 19 Jul 2016 16:02:21 +0200
Subject: [PATCH] Added text to cmdArgs
---
.../nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
index 770845f78..5143c9e0c 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
@@ -29,19 +29,19 @@ object BamStats extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('R', "reference") valueName "<file>" action { (x, c) =>
c.copy(referenceFasta = Some(x))
- }
+ } text "Fasta file of reference"
opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
c.copy(outputDir = x)
- }
+ } text "Output directory"
opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
c.copy(bamFile = x)
- }
+ } text "Input bam file"
opt[Int]("binSize") valueName "<int>" action { (x, c) =>
c.copy(binSize = x)
- }
+ } text "Bin size of stats (beta)"
opt[Int]("threadBinSize") valueName "<int>" action { (x, c) =>
c.copy(threadBinSize = x)
- }
+ } text "Size of region per thread"
}
/** This is the main entry to [[BamStats]], this will do the argument parsing. */
--
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