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clintval
Parse Illumina sample sheets with Python
For illumina sample sheets with 10X multiplex libraries we often have multiple samples with the sample indexes. This obviously does not work with the package right now. Another option would...
Dear @clintval , thanks for your great work! May I know does sample-sheet support `pairend-end` reads and `multi index`? For example, I have a excel file, it record `sample_id`, `set`,...
I wanted to gauge your appetite for being able to lookup samples by `Sample_ID`. 1. `get_sample(id: str) -> Optional[Sample]` In the simple case where no lane is defined, it will...
I _think_ read structures like `10M19S+T` are supported, so why not just `+T`? I am happy to be assigned to make a PR.
- Allow samplesheet to accept a file handle or a Path like object - [replace exceptions with warnings](https://github.com/clintval/sample-sheet/commit/989298cfdabba60d4abea3e0c9ba41c4f260338f)
Due to the use of 'utf-8' encoding, sample_sheet that has special characters like ã or Ü won't be acceptable by SampleSheet class. We need a way to let the user...
Running the test suite on the master branch fails on MacOS. I am running MacOS Monterey 12.2.1 on a INTEL mac with python 3.7. pytest Error: ``` E AssertionError: 'BARC[68...
If the file passed to the SampleSheet constructor contains data but no sections the error produced is: ``` 'SampleSheet' object has no attribute '' ``` Should output an invalid formatted...
We have a sample sheet where we've added a custom section which is a headered table (along the lines of the [Data] section. It would be handy to be able...
Hey just came across this repo -- I'm not sure if you're still developing this, but just wanted to alert you to our work on [PEP](pep.databio.org/), and more specifically, [peppy](https://github.com/pepkit/peppy/)....
