[med-svn] [adapterremoval] 01/04: Adapt test

[Andreas Tille]

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tille pushed a commit to branch master
in repository adapterremoval.

commit 43a52e9e552b87dae8be3eb05bd5f8de7bf7c09a
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 28 16:39:12 2016 +0200

    Adapt test
---
 debian/tests/run-unit-test | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index 7d65af4..73b5491 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -14,7 +14,13 @@ AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --
 AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved
 AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename phred_64_encoded
 AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename phred_33_encoded
-AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapsed --basename collapsed_q50
+
+## The documentation has the --collapsed argument which leads to
+# AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapsed --basename collapsed_q50
+#   ERROR: Unknown argument: '--collapsed'
+# so leaving out --collapsed
+AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --basename collapsed_q50
+
 AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt
 AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq
 AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_dumux --barcode-list barcodes.txt

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