On Mon, Oct 22, 2018, 7:05 AM James Bonfield <j...@sanger.ac.uk wrote: > On Fri, Oct 19, 2018 at 04:30:33PM -0600, Brent Pedersen wrote: > > I want to store a minimal representation of an alignment (more minimal > > than CRAM). > > I thought I could save the position, cigar, and MD and be able to > > reconstruct the > > read sequence, but the MD (IIUC) allows reconstructing the reference > > from the read. > > To reconstruct the sequence you'll need an analogue of MD, as you > say. This isn't something available at the moment. > > > Is there something exposed in the current htslib that would facilitate > > this? E.g. a tag that's sort of the inverse of MD? I know this must be > > used internally for CRAM. > > Internally CRAM has a number of data series to encode differences > between a sequence and a reference. These differences are called > "features" and loosely correspond to CIGAR operations. > > FN (number of features) > FP (position of feature; a delta to the last feature) > FC (feature code; type of the edit) > > Then each feature has its own associated data series. Eg FC "X" is > substitution, which stores the edit in the BS (base substitution) data > series, FC "D" (deletion) stores the deletion length (but not the > bases) in DL, and FC "I" (insertion) stores the inserted bases in IN. > > This is a rather distributed way of doing things, rather than a single > aux tag like MD. Hence we don't have any code that can easily be > used for this. > > > > > -- > James Bonfield (j...@sanger.ac.uk) > The Sanger Institute, Hinxton, Cambs, CB10 1SA > > > -- > The Wellcome Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. >
Thanks for the reply. I ended up implementing the delta encoding myself using a schema like you describe. >
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