Add faidx_seq_len64() as a replacement for faidx_seq_len() that can return the correct length of sequences longer than INT_MAX.
Make faidx_seq_len() clamp its output at INT_MAX, which is probably slightly less bad than overflowing.
Adds a fai_adjust_region() function that can be used to ensure that a given range does not go beyond the end of the requested sequence. The interface is designed so that the output of fai_parse_region() can be passed to it. This essentially exposes the internal faidx_adjust_position() function which is currently used to enforce the same limits in the faidx_fetch_seq64() and faidx_fetch_qual64() interfaces. The new function allows callers to get a better idea of what will be retrieved by applying the limits in advance.
While writing this, I discovered that faidx didn't really have any tests of its own, although some were run as side-effects of other tests. The second (rather bigger) commit adds some dedicated faidx tests.
Add
faidx_seq_len64()as a replacement forfaidx_seq_len()that can return the correct length of sequences longer thanINT_MAX.Make
faidx_seq_len()clamp its output atINT_MAX, which is probably slightly less bad than overflowing.Adds a
fai_adjust_region()function that can be used to ensure that a given range does not go beyond the end of the requested sequence. The interface is designed so that the output offai_parse_region()can be passed to it. This essentially exposes the internalfaidx_adjust_position()function which is currently used to enforce the same limits in thefaidx_fetch_seq64()andfaidx_fetch_qual64()interfaces. The new function allows callers to get a better idea of what will be retrieved by applying the limits in advance.While writing this, I discovered that faidx didn't really have any tests of its own, although some were run as side-effects of other tests. The second (rather bigger) commit adds some dedicated faidx tests.