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key names in branch_lengths JSON #180
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Emma and I just looked at this. the different branch length can all go. treetime internally uses the |
I think good to have If this JSON is going to have |
Notes from working on BEAST parsing (which uses
|
@emmahodcroft this commit (branch |
Is this now superseded by #316, and if so, can we close? |
The current branch lengths JSON (from
augur refine
) contains keysbranch_length
,clock_length
andmutation_length
. It's not clear thatbranch_length
is measured in units of time, and appears to be always equal toclock_length
. Can we remove the former and use the latter downstream? (Or rename the former if it's somehow different)It also refers to
numdate
andnum_date_confidence
. Can the former be madenum_date
for consistency? (I believe this JSON is only consumed byaugur export
)Separately,
raw_date
differs-by-one fromdate
(e.g.2016-04-04
vs2016-04-05
) - is this a bug?The text was updated successfully, but these errors were encountered: