Number=1 and concat/uniq separators

[Brent Pedersen]

I'm thinking of making a backwards incompatible change for version 0.11.0.

The background is in this issue: https://github.com/brentp/vcfanno/issues/16

Currently, vcfanno uses Number=1 for everything. This actually works for a suprisingly large number of cases.

In the commit referenced from that issue, I have changed it so that when op="self", the Number will be pulled from

the annotation header.

I propose that for ops concat, uniq, we use Number=. and continue to use Number=1 for all other ops.

This would require changing the concat/uniq separators from "|" to ",". I think this is sensible but want to get any

feedback.

Also if there are any other issues related to the Number stuff, please let me know.

-Brent

[daniel...@deaddriftbio.com]

I think its a good idea myself.

[Brent Pedersen]

Thanks for the feedback. I've pushed these changes to master so that:

• when op=self, pull Number from the annotation file (previously Number was always 1)
• when op=concat or op=uniq user Number=.

this will be in the next release. Meanwhile there's a linux binary here:

http://home.chpc.utah.edu/~u6000771/vcfanno_0.11a_linux