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Author: Ryan Wick <rrwick@gmail.com>
Last-Update: 2016-08-22
Origin: Upstream commit cd93cde1f2e4639db426e8b57b6ec5d278c0d02f
Description: Update test for recent version
--- a/tests/test_srst2.py
+++ b/tests/test_srst2.py
@@ -158,6 +158,8 @@ class TestRunBowtie(unittest.TestCase):
arg_mock.read_type = 'foo'
arg_mock.stop_after = False
arg_mock.other = False
+ arg_mock.threads = 4
+ arg_mock.use_existing_bowtie2_sam = False
actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'], arg_mock,
'db_name', 'db_path')
self.assertEqual(actual_sam, 'mapping_file.sam')
@@ -173,7 +175,8 @@ class TestRunBowtie(unittest.TestCase):
'--very-sensitive-local',
'--no-unal',
'-a',
- '-x', 'db_path'
+ '-x', 'db_path',
+ '--threads', '4'
]
run_mock.assert_called_once_with(expected_bowtie2_command)
@@ -191,6 +194,8 @@ class TestRunBowtie(unittest.TestCase):
arg_mock.read_type = 'foo'
arg_mock.stop_after = False
arg_mock.other = False
+ arg_mock.threads = 4
+ arg_mock.use_existing_bowtie2_sam = False
actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'], arg_mock,
'db_name', 'db_path')
self.assertEqual(actual_sam, 'mapping_file.sam')
@@ -206,7 +211,8 @@ class TestRunBowtie(unittest.TestCase):
'--very-sensitive-local',
'--no-unal',
'-a',
- '-x', 'db_path'
+ '-x', 'db_path',
+ '--threads', '4'
]
run_mock.assert_called_once_with(expected_bowtie2_command)
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