Add cigar X/=

[armintoepfer]

This is the patch I'm applying to convert M to X/=. It does not yet include the command-line toggle and ignores the python/js stack. It is also not well tested. Feel free to implement it your style or if it looks good, I can add the CLI toggle.

See this PR as a base for discussions and not ready to merge.

Also cheers to @nlhepler who did the main work, long time ago.

[1pakch]

Obviously not for me to decide, but I would keep the cigar opcodes exactly the same as in the SAM/BAM spec.

[1pakch]

I think defining the opcodes in the header (e.g. #define CIGAR_M 0) and not hardcoding them would be very beneficial. If this is done consistently one can easily (and reliably) locate all the places where opcodes are used.

[1pakch]

@lh3
BTW, I am wondering what was the reason for not defining cigar pairs as

typedef struct {
        uint32_t op : 4;
        uint32_t count : 28;
} cigar_t;

which would obviate the need of explicit masking and shifting.

[nlhepler]

@armintoepfer thanks for posting this and for taking it across the finish line!

I figure at a minimum this behavior needs to be toggle-able via a command-line switch?

And @ilya-kolpakov, I agree it should probably use the numerical conventions from the BAM spec ([MIDNSHPX=] is [012345678]).

Please let me know if there are any suggestions on what needs to be done.

[lh3]

Thanks a lot for this PR. Very straightforward and better than my initial plan.

Merged via 154d2ca. I have only made some tiny changes. Option --eqx enables the feature. Thanks again.

[lh3]

PS: I haven't carefully tested the feature, though.