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Pileup parsing deletion with . #355

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Koeng101 opened this issue Sep 21, 2023 · 4 comments
Open

Pileup parsing deletion with . #355

Koeng101 opened this issue Sep 21, 2023 · 4 comments
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@Koeng101
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enhancement New feature or request hard A major or complex undertaking medium priority The default priority for a new issue. stale
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v1.0

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@Koeng101
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I have the following read:

57      510     C       5       ..,,.   RD7HN
57      511     A       5       .-3TTG.-3TTG,-3ttg,-3ttg.-3TTG  JC7H:
57      512     T       5       *****   @?8J:
57      513     T       5       *****   @?8J:
57      514     G       5       *****   @?8J:
57      515     G       5       ..,,.   @?8J:

There must a better way of showing "deletion! oh no!" then this notation above. -3TTG along with * denormalizes the data, and since -3TTG will be a part of 511 (which is actually completely correct), this gets confusing.
@Koeng101
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(This is commenting on something that could come up when we want a "pileup.AnalyzeSequence" function)

@carreter carreter added the needs-triage An issue that needs to be triaged label Sep 23, 2023
@carreter carreter modified the milestone: v1.0 Sep 23, 2023
@carreter carreter added this to the v1.0 milestone Sep 23, 2023
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@Koeng101 reminder to triage this both here and in the roadmap!

@Koeng101 Koeng101 added enhancement New feature or request medium priority The default priority for a new issue. hard A major or complex undertaking and removed needs-triage An issue that needs to be triaged labels Sep 23, 2023
@Koeng101 Koeng101 self-assigned this Sep 23, 2023
@Koeng101
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Added labels I think, also I think generally this is gonna be "sequencing result from pileup file"

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This issue has had no activity in the past 2 months. Marking as stale.

@github-actions github-actions bot added the stale label Nov 22, 2023
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enhancement New feature or request hard A major or complex undertaking medium priority The default priority for a new issue. stale
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v1.0
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@Koeng101 @carreter