Remove trailing tab in VariantsToTable output header #7559
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droazen
approved these changes
Nov 10, 2021
| @@ -63,6 +64,7 @@ public IntegrationTestSpec(String args, List<String> expectedFileNames) { | |||
| this.compareBamFilesSorted = false; | |||
| this.validationStringency = ValidationStringency.DEFAULT_STRINGENCY; | |||
| this.tempExtension = DEFAULT_TEMP_EXTENSION; | |||
| this.trimWhiteSpace = true; | |||
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Was IntegrationTestSpec previously defaulting to trimming whitespace before doing the comparison vs the expected output(s), or is this PR introducing a change in default behavior?
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@droazen previously (and still after this pr) IntegrationTestSpec defaulted to trimming whitespace. Which is how this bug was never caught by tests before.
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Ah, I see...in that case I think I'll open a separate ticket to see if we can change the default for IntegrationTestSpec to not ignore leading/trailing whitespace. Go ahead and merge once tests pass 👍
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If VariantsToTable is run without any genotype field outputs (or on a vcf with no sample data), the header line contains an extra trailing tab, which is not included in the table rows. This confuses many tsv parsers, which see the header as having an extra (blank) field, and so complain that the rows of the table do not contain enough fields.
This pr fixes this so that there is no longer a trailing tab in this case.