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5' mismatch trimmer `trim_5p_mismatch.py` works with hisat2 output and bowtie output but not with default STAR output, because of differences in flags in the SAM file.
Currently, `trim_5p_mismatch.…
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§ 4.2 "The BAM format" (2022-08-22) describes the layout of a reference information section (`n_ref`...`l_ref`). However, there is no explanation on what this is used for or how it should be used, con…
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One problem I have with the BAM/SAM format is that the reference is not kept with the read file. You allude to this in your paper. Keeping old references around, especially for poorly characterized…
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## Problem
## Steps to reproduce the issue
It seems like VSCode/AWS-Toolkit can't access my OS's path because it always complains that delve can't be found (even though I can access it via VSC…
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**Describe the bug**
The plugin validation and code code insight do no recognize ES6-type exports in javascipt files.
**To reproduce**
1. Create an `index.js` file with this content
```javascr…
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(A) Convert FASTQ to uBAM and add read group information using FastqToSam
Picard's FastqToSam transforms a FASTQ file to an unmapped BAM, requires two read group fields and makes optional specificati…
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The specifications for tabix and csi are incomplete, currently being variously only essentially a struct layout with no semantic explanation or restrictions, or a description of the underlying storage…
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### Description:
Got this error when trying to test my lambda authorizer locally with `sam build` and `sam local start-api`: `Unable to parse the Lambda ARN for Authorizer 'LambdaAuthorizer', s…
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### Is this related to a new or existing Amplify category?
function
### Is this related to another service?
Lambda function
### Describe the feature you'd like to request
Cloudformation has https…
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```bash
vsearch \
--usearch_global