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Remove reference to secondary coordinates #150

Merged
merged 2 commits into from
Oct 8, 2024
Merged

Remove reference to secondary coordinates #150

merged 2 commits into from
Oct 8, 2024

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susannasiebert
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Secondary coordinates no longer exists on gene variants in the new, formalized coordinate system and since we are currently only pulling gene variants, references to those attributes cause errors.

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@acoffman acoffman left a comment

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+1

chr = getattr(c, 'chromosome2', None)
if all([start, stop, chr]):
variant_records.append([chr, start, stop, None, None, hash(v)])
#start = getattr(c, 'start2', None)
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Is there a reason to comment this out rather than just deleting?

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It's a reminder to myself to put something similar back in its place once we have fusion support added.

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Makes sense, good to leave it in then!

@susannasiebert susannasiebert merged commit eb7ccc4 into master Oct 8, 2024
5 of 6 checks passed
@acoffman acoffman deleted the fusions branch October 8, 2024 15:52
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2 participants