FilterSamReads has a bug and can't filter read by read name. #1055
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- fixed this bug - added positive and negative tests
gbggrant
approved these changes
Jan 10, 2018
| } | ||
| } | ||
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| final File reads = File.createTempFile(TEST_DIR.getAbsolutePath(),"reads"); |
| String.format("%s=%s", fileArgument, dummyFile), | ||
| }; | ||
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| // make sure results is successful |
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update comment 'make sure program invocation failed - inputs validation error'
| @Test(dataProvider = "badArgumentCombinationsdata") | ||
| public void testBadArgumentCombinations(final FilterSamReads.Filter filter, final String fileArgument) throws IOException { | ||
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| final File dummyFile = File.createTempFile(TEST_DIR.getAbsolutePath(),"dummy"); |
| program.READ_LIST_FILE = inputFile; | ||
| break; | ||
| default: | ||
| throw new IllegalArgumentException("not configured for filter==" + filter); |
| "INPUT=testdata/picard/sam/aligned.sam", | ||
| String.format("OUTPUT=%s", temp.getAbsolutePath()), | ||
| String.format("FILTER=%s", filter.toString()), | ||
| String.format("%s=%s", fileArgument, dummyFile), |
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dummyFile.getAbsolutePath()
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fixes #1070
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