Wrap ctype.h functions to avoid array subscript warnings#2306
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Copy HTSlib's internal wrappers for interfaces in <ctype.h> into sam_utils.h (as it's widely included already) and use them on cases where the input has `char` type. Fixes "array subscript has type 'char'" warnings on platforms that still implement them as a macro around an array look-up. The ctype interface wrappers were originally authored by John Marshall in HTSlib commit fc9aeb6
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There are a couple more, which this PR doesn't fix.
Edit: approved on the other changes though. Thanks |
Need to cast to unsigned to ensure all possible values are +ve.
This function takes data from various sources that may not have been well-filtered for unexpected character values. It therefore needs to be able to handle them, at least to the extent of not producing undefined behaviour. Rename variable `c` to `chr` to make it easier to find. Change type of `chr` and `rb` to char, to match the type of the data sources they may be set from. Use toupper_c() wrapper due to the change of type above. In case char is signed, cast `rb` to uint8_t before using it to index seq_nt16_table. Similarly, cast `chr` to uint8_t before passing the value to tv->my_mvaddch() (which takes int) to ensure the result it always positive.
Avoids sign-conversion warnings should they be enabled.
char should be cast to uint8_t, not int, to prevent sign extension.
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Copy HTSlib's internal wrappers for interfaces in
<ctype.h>intosam_utils.h(as it's widely included already) and use them on cases where the input haschartype. Fixes "array subscript has type 'char'" warnings on platforms that still implement them as a macro around an array look-up.The ctype interface wrappers were originally authored by John Marshall in HTSlib commit fc9aeb6f7.