Is end inclusive or exclusive?

[sdelatorrep]

One may assume it's inclusive because of this sentence in the spec (description of start parameter):

• start and end:
  • special use case for exactly determined structural changes

but this assumption may be wrong. We must say it explicitly if it's inclusive or not.

[mbaudis]

The coordinate system that should be used throughout GA4GH standards is 0-based half open. So in a sequence of

ACCGTCGA

... the exact match for GTC would be

start: 3,
end: 6

... due to interbase coordinates.

I think we (...) have to fix this in the Wiki, which isn't correct for some of the positions...

(edited the error after comments by @sdelatorrep and @antbro ...)

[sdelatorrep]

mmmm I see. Then it's not clear at all in the spec.
What are interbase coordinates? Shouldn't it be start=3 as it's 0-based (so the G is at position 3) and end=6?

[antbro]

not 3-6? T

…

________________________________________ From: Michael Baudis <[email protected]> Sent: 12 July 2018 16:09 To: ga4gh-beacon/specification Cc: Subscribed Subject: Re: [ga4gh-beacon/specification] Is end inclusive or exclusive? (#202) The coordinate system that should be used throughout GA4GH standards is 0-based half open. So in a sequence of ACCGTCGA ... the exact match for GTC would be start: 4, end: 7 ... due to interbase coordinates. I think we (...) have to fix this in the Wiki, which isn't correct for some of the positions... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#202 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AI_EVCFw31xpY3Pabo6sp4jeOvwKEX1Fks5uF2angaJpZM4VMk8a>.

[mbaudis]

@sdelatorrep & @antbro O.k.; can we roll this back, please? It is, obviously, counted base -1, when talking about the positions. I had shortened an example I was using & didn't shift ...

Does the internet forget?