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This in regard to _Sequence Alignment/Map Format Specification_ (2022-08-22) § 1.4 "The alignment section: mandatory fields".
In the following SAM record, the quality scores field (`QUAL`) is ambig…
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## The problem
Some properties have limited support for [intrinsic functions](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/intrinsic-function-reference.html) (e.g. `Ref`, `Fn::Get…
hoffa updated
3 weeks ago
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I have been trying to use [iRep](https://github.com/christophertbrown/iRep) which seems to use the function`ctbBio.mapped.get_reads()` and `ctbBio.mapped.reads_from_mapping()` from this package to par…
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Continuation of this email thread with keilbeck&genetics.utah.edu & evan.christensen&utah.edu, from tfallon&ucsd.edu. That thread resolved to give a shot at SO sponsored submission of bioinformatics f…
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Is it possible to start supporting the [Serverless Application Model](https://github.com/awslabs/serverless-application-model) transform in the linter?
Currently, I get a bunch of errors like this …
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Last bit of https://github.com/galaxyproject/tools-devteam/issues/92 which was mostly dealt with.
The problem with tophat is that it does not allow arbitrary read groups or at least all of the valid …
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### Describe your idea/feature/enhancement
I wish SAM CLI would accept a local path to an image archive (the kind of thing which can be loaded by `docker image load`) for the value of `ImageUri…
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(SAM specification)
Not only does it need to be documented, but we need to codify all the various constraints. The code already disallows B going beyond the bounds of the sequence (1M2B1M) but what a…
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Following [x.com/@fiamh](https://x.com/fiamh/status/1782261875876692322) I was made aware of the proposal for how to store modified base information in VCF files.
A quick search and I could not fin…
cjw85 updated
2 weeks ago
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> What application are you using?
Signs & Markings Operations
> Describe the problem.
We published a good chunk of SAM data during #2817, this will get the rest taken care of.
We are …