[Samtools-devel] Meaning of PNEXT on unmapped mates

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

Consider the following example

Seq	73	chr3	100	0	10M	=	100	0	...
Seq	133	chr3	100	0	*	=	100	0	...

The mate is unmapped, but in the traditional manner it is placed at
the same location as the mapped read.  However RNEXT and PNEXT is
filled out for both entries.  I saw this in real data, but it got me
wondering whether it is permitted.

It sounds incorrect and destroys some of the benefit of RNEXT/PNEXT if
it includes unmapped reads too.  However the specification isn't
clear.  It uses phrases like "PNEXT: Position of the primary alignment
of the NEXT read in the template".  I guess "primary alignment"
doesn't exist as it's not aligned, merely located adjacent to another
read, which then puts it into the category of "the information is
unavailable".  However that's trying to read between the lines and
it's not explicitly stated.

Is it categorically the case that RNEXT/PNEXT/TLEN should never have
values when the mate is unmapped?  If so I'll consider it a bug that
this data was produced in such a manner.

Thanks,

James

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


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