Avoid using private HTSlib headers and functions #53
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This was referenced Dec 17, 2019
Only headers in htslib/*.h are part of HTSlib's public API; cram/*.h in particular are not. Fortunately SeqLib only uses one function from cram/cram_io.h, and that is easily replaced with a public equivalent. Instead use `hts_set_fai_filename()`, which strdups the string given to it itself; `cram_set_option(fp->fp.cram, CRAM_OPT_REFERENCE, ...)` would also be an option, but it's better to avoid `fp->fp.cram` as poking into an htsFile's insides is also not supported by HTSlib.
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I see there has been some recent activity in SeqLib. @walaj It would be greatly appreciated if you would consider and merge this one too. |
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Great 👍 |
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This is completely on me for missing this for so long, saw the comment on Twitter. Thank you for this fix. |
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Thanks a lot for fixing. Would you mind tagging a new release? |
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Thanks for merging it. As @tillea suggests, it would be ideal if this appeared in a new release in due course. But certainly having this commit on master does the trick for projects that have SeqLib as a git submodule. |
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Use a public HTSlib API function to set the CRAM reference file rather than an internal CRAM-only function that is private to HTSlib.
Happily there is only one instance of a private HTSlib function being used. Fixes #21.