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Possible regression in ambiguity reporting #93

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wasade opened this issue Feb 21, 2020 · 0 comments
Closed

Possible regression in ambiguity reporting #93

wasade opened this issue Feb 21, 2020 · 0 comments

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@wasade
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wasade commented Feb 21, 2020

Previously, we only reported ambiguities when they occurred. The output right now seems to always report an ambiguity even if there isn't one.

(qiime2-2019.10) 08:52:08 (dtmcdonald@here):sequence-search@master$ echo "10317.000004216" | redbiom fetch samples --output blhablah.biom --context $ctx
1 sample ambiguities observed. Writing ambiguity mappings to: blhablah.biom.ambiguities
(qiime2-2019.10) 08:55:04 (dtmcdonald@here):sequence-search@master$ biom summarize-table -i blhablah.biom
Num samples: 1
Num observations: 335
Total count: 11,798
Table density (fraction of non-zero values): 1.000

Counts/sample summary:
 Min: 11,798.000
 Max: 11,798.000
 Median: 11,798.000
 Mean: 11,798.000
 Std. dev.: 0.000
 Sample Metadata Categories: None provided
 Observation Metadata Categories: None provided

Counts/sample detail:
10317.000004216.58152: 11,798.000
@wasade wasade closed this as completed in c18205b Oct 1, 2021
wasade added a commit to wasade/redbiom that referenced this issue Oct 21, 2021
antgonza added a commit that referenced this issue Oct 21, 2021
* TST: bulk get index test

* Batch index requests

* A little cleanup on debug items

* Additional comments

* sty

* Update redbiom/admin.py

Co-authored-by: Antonio Gonzalez <[email protected]>

* BUG: fixes #108, thanks @cotillau!

* VER: actually bump it, partially resolves #107, thanks @BenKaehler

* tentative py3738 support

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* update actions

* BUG: fixes #93

* BUG: fixes #92

* remove unhelpful print

* Bump version

* Force json (#113)

* TST: sample id content type bug

* MAINT: fix issue where samples with .raw as a suffix were triggering unexpected returns

* Don't suffix twice

* Adjsut to account for force of json

* Address @antgonza's comments

* use the right variable name

* Verify data appear count

* Verify data appear count

Co-authored-by: Antonio Gonzalez <[email protected]>
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