bcftools
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Strict mode to fail on truncated bgzip input
Currently, bcftools issues a warning on truncated bgzip input. However, we've found that this "feature" allows upstream failures to pass silently in our pipeline. It would be valuable to have a 'strict' mode that causes bcftools to fail loudly on truncated bgzip input (likewise for samtools).
This "feature" still exists. It seemly very unlikely that a data processor would want to continue in the case of a truncated input so it would be great if it this was changed to result in a hard fail.