feat: add tags related to optical duplicates. #813
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Picard has long been able to add Sam Tags that provide information about duplicate templates: Their type (Library or Sequencing), the size of the sets they are part of, and the queryname of the representative template within the set that is _not_ a duplicate. As I look to use these tags in another repository (fgbio) I wanted to make sure that the tags are generally accepted and well defined.
|
I guess these are the tags that are described in MarkDuplicates.java: This does seem like a worthwhile addition, not least because the Git history suggests they've been in Picard for 8 or 10 years. DI and DT would need entries in §1.1 too, and they and the DS entry would want to explain what this is about a bit more. |
|
I wasn't sure if the 1.1 section was required for all tags or only for those for which there's something interesting to say....but OK... :-) |
jmarshall
reviewed
Feb 17, 2025
| Use SQ if the duplication occurred during sequencing (e.g., due to imaging error, aka "optical duplicates", or due to | ||
| over-aggressive bridge-amp). | ||
|
|
||
| \item[GL:f:\tagvalue{score}] |
There was a problem hiding this comment.
What is GL? Was this line accidentally committed?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
feat: add tags related to optical duplicates.
Picard has long been able to add Sam Tags that provide information about duplicate templates: their type (Library or Sequencing), the size of the sets they belong to, and the query name of the representative template within the set that is not a duplicate. As I look to use these tags in another repository (fgbio), I want to ensure they are generally accepted and well-defined.