Return value of sam.Record.End()

[ay...@grailbio.com]

Hi all,

I am looking for clarification about the return value of sam.Record.End():

// End returns the highest query-consuming coordinate end of the alignment.                                                                                                                                                                                        
// The position returned by End is not valid if r.Cigar.IsValid(r.Seq.Length)                                                                                                                                                                                      
// is false.                                                                                                                                                                                                                                                      
func (r *Record) End() int {
    pos := r.Pos
    end := pos
    for _, co := range r.Cigar {
        pos += co.Len() * co.Type().Consumes().Reference
        end = max(end, pos)
    }
    return end
}

The comment says that End() returns the highest query-consuming coordinate of the alignment.

I'm guessing that means the End() return value points to an actual base in the read (as opposed

to the position right after the last base).  I assume that Start() is also supposed to point to an

actual base.

The question is, the code adds the number of consumed characters from the cigar, so if I have a

read with Start() == 10, and the cigar is 1M, then End() will return 11.

But that seems wrong because 11 doesn't actually point go part of the read.  Is this the intended 

behavior of End()?  Or is End() supposed to return 10 in this case?

Thanks, Alex

[Dan Kortschak]

All of the biogo code uses zero-based half-open indexing. Unfortunately
many file formats (including SAM) use 1-based indexing.

Zero-based half-open has the extremely satisfying property that end-
start = length. And it matches the semantics of nearly every
programming languages slicing operations.

Maybe the docs could be improved. Please send a PR if you have better
wording.

Dan