Improve synced reader error checking#2024
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As enum bcf_sr_error didn't explicitly set an values, the first entry (open_failed) got the value zero. As a check against zero is suggested in example code (and also used frequently in bcftools) to test for errors, it was not possible to distinguish open_failed from no error. Fix by deprecating open_failed and replacing it by a new non-zero value `bcf_sr_open_failed` to cover the case. A new entry bcf_sr_ok is added to make the OK case explicit. New entries bcf_sr_seek_error, bcf_sr_regions_error, and bcf_sr_samples_error are added for use by later updates. Signed-off-by: Rob Davies <rmd+git@sanger.ac.uk>
Mainly adds tests to ensure that memory allocations worked, along with places where hts_getline() failure may have been missed before. Ensures that errors propagate up to callers, and that bcf_srs_t::errnum is set consistently. Where possible, structures are left in a consistent state when recovering from an allocation failure. For example, fields recording how much memory was allocated are only updated after realloc() succeeds, so it does not appear that more space is available than is really the case. Fixes a couple of places where the synced reader would call exit(1) rather than return an error code to the caller. This does mean callers may have to become better at checking return values. Signed-off-by: Rob Davies <rmd+git@sanger.ac.uk>
Ensure return values are documented. Convert markup to better match doxygen format. Signed-off-by: Rob Davies <rmd+git@sanger.ac.uk>
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Mainly adds tests to ensure that memory allocations worked, along with places where
hts_getline()failure may have been missed before. Ensures that errors propagate up to callers, and thatbcf_srs_t::errnumis set consistently.The
bcf_sr_errorenumerated type used forbcf_srs_t::errnumgets two new entriesbcf_sr_seek_errorandbcf_sr_regions_errorfor cases not really covered by the existing values. As the oldopen_failedentry unfortunately had the value zero, which meant it looked like "no error" in the recommended way of checkingbcf_srs_t::errnum, it has been deprecated and replaced bybcf_sr_open_failed. Abcf_sr_okentry is also added with value zero to make the "no errors" case explicit.Where possible, structures are left in a consistent state when recovering from an allocation failure. For example, fields recording how much memory was allocated are only updated after
realloc()succeeds, so it does not appear that more space is available than is really the case.Fixes a couple of places where the synced reader would call
exit(1)rather than return an error code to the caller. This does mean callers may have to become better at checking return values.The synced reader documentation also gets some updates to make it more compatible with doxygen, and to update descriptions of the values returned by some functions.