EGCG 9.0 and beyond

Jose R. Valverde txomsy at cnb.uam.es
Wed Mar 19 14:20:02 EST 1997

In article <5gp5q1$2ju at acebo.sdi.uam.es>,
	txomsy at cnb.uam.es (Jose R. Valverde) writes:

> 	The only caution: you need a way to convert damn %&$°"! new alignments
> /files to old dot-gaping convention. The problem arises because new GCG
> allows both, '.' and '~' to be used to represent a gap in a sequence, and
> EGCG groans at that. The symptons as they were brought up to me where that
> PRETTYBOX would refuse to load sequences aligned with PILEUP (v9). After
> much trying and misleading some of my poor users, I finally got to it, and
> a few minutes ago I wrote this small program to change '~' by '.' (which
> is pretty much untested, and maybe perhaps could change something undue 
> -hypothetically):

	As usual I was too fast in posting. I have continued having problems
and a more detailed look shew that that was not the only difference. It
seems that for some reason GCGv9 also computes check numbers differently
and that's another reason for pileup output not to be recognized properly
in EGCG8... But some sequences maintain the same checksums (!) and I can't
see where is the difference. Wait a second! The ones that keep cksum do
finish in the last column! So that may be it, that last ~ Peter was
mentioning a while back? Hum...

	Hell! I guess that'll teach me not to be so optimistic next time. I'll
need some new excuse for my suffering users.


Jose R. Valverde

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