Add faidx_seq_len64(), fai_adjust_region() interfaces and faidx tests #1519
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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.
whitwham
reviewed
Nov 9, 2022
test/faidx/test-faidx.sh
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| #!/bin/sh | |||
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| # Copyright (C) 2017-2018 Genome Research Ltd. | |||
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What? You mean it's not 2018? What happened?
(Now fixed).
The faidx interfaces were only being tested as side-effects of other tests. This adds dedicated tests for them.
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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.