Long term tracking issue: consistency of API

[jkbonfield]

In writing a quick bam_consensus tool I ended up with a structure like this:

typedef struct {
    // sam, bam AND hts! All the weasles in a single bag :)
    samFile *fp;
    bam_hdr_t *header;
    hts_itr_t *iter;
} pileup_cd;

It's pretty bizarre to have so many prefixes in there. Add to this the fact that the bam_hdr_t struct is read using sam_hdr_read and destroyed with bamhdr_destroy, and the index for the iterator being read using samindexload and destroyed with htsidx_destroy, we have both a mismash of sam/bam/hts format and index/idx in function names.

Most of this is due to backwards compatibility, but it would be good to make all the orthogonal API functions exist too so the code is more readable and then to document which ones are supported and which are deprecated. It may also just be an issue of fixing the existing functions. Eg hts_idx_load does exist, but it's not actually the opposite of hts_idx_destroy (load doesn't load CRAM indices, but destroy does destroy them).

It's a long term goal though and not something we have a great deal of time to do right now.

[adamspargo]

Most of this is due to backwards compatibility, but it would be good to make all the orthogonal API functions exist
too so the code is more readable and then to document which ones are supported and which are deprecated. It may also
just be an issue of fixing the existing functions. Eg hts_idx_load does exist, but it's not actually the opposite of
hts_idx_destroy (load doesn't load CRAM indices, but destroy does destroy them).

+1

Future development would be much faster once the basics are sane.

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[dlaehnemann]

I agree.

A suggestion for functions and structures dedicated to sam, bam and cram files, headers or records alike: aln_...