From b91de09952112a99ff67fc9f1c617ae7e53aef3f Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 27 Oct 2014 17:07:59 +0100
Subject: [PATCH] Update input and output FASTQs argument flag names
---
.../nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index c8c212246..98f0c704c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -181,20 +181,20 @@ object ExtractAlignedFastq extends ToolCommand {
// yes, we are appending and yes it's O(n) ~ preserving order is more important than speed here
c.copy(intervals = c.intervals :+ x) } text "Interval strings"
- opt[File]("f1") required() valueName "<fastq>" action { (x, c) =>
+ opt[File]('i', "in1") required() valueName "<fastq>" action { (x, c) =>
c.copy(inputFastq1 = x) } validate {
x => if (x.exists) success else failure("Input FASTQ file 1 not found")
} text "Input FASTQ file 1"
- opt[File]("f2") optional() valueName "<fastq>" action { (x, c) =>
+ opt[File]('j', "in2") optional() valueName "<fastq>" action { (x, c) =>
c.copy(inputFastq1 = x) } validate {
x => if (x.exists) success else failure("Input FASTQ file 2 not found")
} text "Input FASTQ file 2 (default: none)"
- opt[File]("o1") required() valueName "<fastq>" action { (x, c) =>
+ opt[File]('o', "out1") required() valueName "<fastq>" action { (x, c) =>
c.copy(outputFastq1 = x) } text "Output FASTQ file 1"
- opt[File]("o2") optional() valueName "<fastq>" action { (x, c) =>
+ opt[File]('p', "out2") optional() valueName "<fastq>" action { (x, c) =>
c.copy(outputFastq1 = x) } text "Output FASTQ file 2 (default: none)"
opt[Int]('Q', "min_mapq") optional() action { (x, c) =>
--
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