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Support circular sequences #70

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reece opened this issue Sep 7, 2019 · 4 comments
Open

Support circular sequences #70

reece opened this issue Sep 7, 2019 · 4 comments
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enhancement New feature or request keep alive exempt issue from staleness checks

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@reece
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reece commented Sep 7, 2019

Seqrepo does not currently provide special support for circular sequences. It should.

The easier implementation is with a boolean that assumes the origin at interbase position 0.
An alternative is to support arbitrary origin locations by storing the origin position. For linear sequences, the value is unset. All coordinate computations would need to be modified to circularly permute based on this origin.

@reece
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reece commented Jul 17, 2023

As discussed in #113, we won't support circular sequences as a schema property.

Instead, we will add support for callers to request that a sequence is interpreted as circular.. Possible features:

  • Add circular=False to fetch method (i.e., ~fabgz.py:62). By default, no change in behavior. If circular=True, allow end < start and handle cross-origin sequence fetches.
  • Consider how/whether to implement SeqRepo class-level flag. One idea: Seqrepo(..., circular_fn=None). circular_fn maps accessions → circular flag. If None, no change to current behavior (and same as False). Could also be True(orlambda (ac): True`), then effectively end < start isn't an error and good luck. The challenge with this is that fetch is a sequence-level function, irrespective of alias. It's possible that we can implement this as part of the SequenceProxy (but I'm unsure).

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This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Sep 26, 2023
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github-actions bot commented Oct 3, 2023

This issue was closed because it has been stalled for 7 days with no activity.

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Oct 3, 2023
@reece reece added stale closed Issue was closed automatically due to inactivity and removed stale closed Issue was closed automatically due to inactivity labels Nov 27, 2023
@reece reece reopened this Dec 8, 2023
@github-actions github-actions bot removed the stale Issue is stale and subject to automatic closing label Dec 9, 2023
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github-actions bot commented Mar 9, 2024

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Mar 9, 2024
@jsstevenson jsstevenson added enhancement New feature or request keep alive exempt issue from staleness checks and removed stale Issue is stale and subject to automatic closing labels Mar 12, 2024
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Labels
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