From cae64a35778ddce7c1cbeb6190899c9f1dcc49cc Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Wed, 6 Jul 2016 18:29:46 +0200
Subject: [PATCH] Add text to options parser
---
.../lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
index 68e548c12..5490de4cc 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
@@ -47,19 +47,19 @@ object CheckAllelesVcfInBam extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
- }
+ } text "VCF file"
opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputFile = x)
- }
+ } text "output VCF file name"
opt[String]('s', "sample") unbounded () minOccurs 1 action { (x, c) =>
c.copy(samples = x :: c.samples)
- }
+ } text "sample name"
opt[File]('b', "bam") unbounded () minOccurs 1 action { (x, c) =>
c.copy(bamFiles = x :: c.bamFiles)
- }
+ } text "bam file, from which the variants (VCF files) were called"
opt[Int]('m', "min_mapping_quality") maxOccurs 1 action { (x, c) =>
c.copy(minMapQual = c.minMapQual)
- }
+ } text "minimum mapping quality score for a read to be taken into account"
}
private class CountReport(
--
GitLab