Re: [Samtools-devel] RFC on rationalisation of pnext/rnext fields

[James B. <jk...@sa...>]

On Tue, Nov 18, 2014 at 10:40:23AM +0800, Colin Hercus wrote:
> Hi James,
> 
> I don't know if anyone uses these tags. I know a lot use the Novoalign
> option to report multiple mappings. We do our selves but we've never had
> the need to use the HI, IH, NH, CC or CP tags.

Thinking about algorithms, the only flag I can see that is absolutely
necessary is the one that doesn't exist!

We need a way to know how many records in total have the same
identifier.  If we know that, then writing a read collation tool is
trivial.  Without it we either have to make assumptions (2 only) or do
a full name sort in order to implement algorithms such as fixmates.  A
full sort is very CPU intensive though compared to simple collation.

James

-- 
James Bonfield (jk...@sa...) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


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