Cigar interface

[magicDGS]

No description provided.

[lindenb]

@magicDGS in Cigar : shouldn't you use long instead of int for the lengths ?

[magicDGS]

@lindenb - that's a good question, as I was thinking about it for some time (also in the draft that I am preparing for reads), and I decided to use int instead of long for several reasons:

• Arrays/Lists in java are always int indexed - thus, the maximum lenght for most implementations will be Integer.MAX_VALUE (2³¹-1)
• In the SAM specs, the template length (always lower or equal than the read length unless there is only one read) is in the range [-2³¹+1, 2³¹-1], which fits into the java Integer.MAX_VALUE range
• In the BAM specs, both l_seq (int32_t) and n_cigar_op (int16_t) fit into the java Integer.MAX_VALUE range
• In the CRAM v3 specs, the read lenghts are defined as int, which is also a signed 32-bit integer. Thus, it also fits in the Integer.MAX_VALUE range

In the case of Locatable and other reference-based coordinates, I proposed the change of the API to use long as you suggest in your comment (see proposal for Locatable interface in #6).

@lindenb - are you worried of integer overflow due to the sum of the element's length? In that case, either we return long as you suggest or explicitly add to the API that the sum of each element length should not be more than Integer.MAX_VALUE to avoid the issue (we can add a check in default implementation).

What do you think, @samtools/htsjdk-next-maintainers?

[lindenb]

are you worried of integer overflow due to the sum of the element's length?

I was worried about someone who could design a 'virtual' read spanning a whole sequence :-) but I agree keeping 'int' is easier.

[magicDGS]

If there is any usage case for that kind of virtual read, we can either 1) make it possible to return long in an implementation-dependent manner; or 2) add a new interface for LongCigar extending this one, and add a method to check if it allows long sizes (e.g., with a method that throws by default in Cigar). Other solutions are welcome if this is really needed.