From a08964e01cdae11dbf3bbd1f133fdb89a05a8074 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 30 Jan 2015 12:55:20 +0100
Subject: [PATCH] Add notes on input - output compression
---
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 382b59925..aaa2797b6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -229,9 +229,13 @@ object FastqSync extends ToolCommand {
class OptParser extends AbstractOptParser {
+ // TODO: make output format independent from input format?
head(
s"""
- |$commandName - Sync paired-end FASTQ files
+ |$commandName - Sync paired-end FASTQ files.
+ |
+ |This tool works with gzipped or non-gzipped FASTQ files. The output
+ |file will be gzipped when the input is also gzipped.
""".stripMargin)
opt[File]('r', "ref") required () valueName "<fastq>" action { (x, c) =>
--
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