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tiny-count: changes and additions to diagnostic alignment tables#309

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taimontgomery merged 3 commits intomasterfrom
issue-308
May 26, 2023
Merged

tiny-count: changes and additions to diagnostic alignment tables#309
taimontgomery merged 3 commits intomasterfrom
issue-308

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@AlexTate
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@AlexTate AlexTate commented May 25, 2023

The following columns have been added to alignment table outputs:

Column Description
Raw count The sequence's original, non-normalized count
Genomic hits The number of alignments reported for the sequence
Feature Aliases The user-defined aliases for the assigned features, if any
Mismatches The number of mismatches between the query sequence and the reference

Additionally, the Assigned Features column:

  • Has been renamed to Feature Hits for consistency
  • Has a more easily parseable string format, e.g. (feat_id_1, classifier); (feat_id_2, ); ...
  • Now shows an empty cell for alignments without feature hits rather than NONE

Note that branch issue-308's parent is issue-261. Please close PR #307 first.

Closes #308

AlexTate added 3 commits May 25, 2023 13:47
- Additional columns: raw count, genomic hits, mismatches, and feature aliases
- Renaming assigned features to feature hits
- Feature hits column is left empy if no features were assigned (rather than NONE)
- Feature hits and feature aliases are reported with formatting that should be easier to parse if the user wants to analyze the alignment table with their own scripts
@AlexTate AlexTate requested a review from taimontgomery May 25, 2023 20:58
@AlexTate AlexTate changed the base branch from master to issue-303 May 26, 2023 22:19
@AlexTate AlexTate changed the base branch from issue-303 to master May 26, 2023 22:19
@taimontgomery
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Tested on MacBook and server. Looks great!

@taimontgomery taimontgomery merged commit 1e38098 into master May 26, 2023
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tiny-count: additional fields in diagnostic alignment tables

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