sam_internal.h: code2base[512 -> 513] because the byte for end-of-string is missing.

[lindenb]

when compiling with g++ and including sam_internal.h (I need nibble2base) there is an error

../../htslib/sam_internal.h: In function ‘void nibble2base(uint8_t*, char*, int)’:
../../htslib/sam_internal.h:73:9: error: initializer-string for ‘const char [512]’ is too long [-fpermissive]

because code2base[512] is missing one byte for the end-of-string character.

this PR just set code2base[513].

[daviesrob]

Looking at the C99 specification, I don't think this is necessary because it explicitly mentiones the case t[3] = "abc" as valid. Also, sam_internal.h is not intended to be used outside HTSlib, and particularly not with a c++ compiler. The only supported public interfaces are those in the htslib/*.h files.

There is however an argument to be made that it would be useful to expose something like nibble2base() in our public API. If we do that, it would probably be best done by adding an exported function that can be called using an interface in htslib/sam.h.

[jkbonfield]

For an assignment, I believe it copies as many as are needed. By the sounds of it Rob's looked into the specification text which makes this more explicit.

However it wouldn't be a detrimental change so I'm amenable to changing it if it's tripping up some code sanity checking tool (with a suitable comment). How did you spot this? Was it something automated, or just eye-balling things?

[lindenb]

@jkbonfield I was creating a C++ class wrapping the sequence of a read and I wanted to use nibble2base to get the read string

https://gitlab.univ-nantes.fr/pierre.lindenbaum/htsplusplus/-/blob/master/src/AbstractSamRecord.cpp?ref_type=heads#L166

g++ complained with the error

 initializer-string for ‘const char [512]’ is too long

Jut after this PR (there must be a Murphy's law for this) I just found that I can just use

return seq_nt16_str[bam_seqi(s, pos)];

So feel free to close this PR if you think that this '512' is safe for C code.

[daviesrob]

Yes, that should work.