immunedb

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Bump numpy from 1.19.5 to 1.22.0

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Bumps [numpy](https://github.com/numpy/numpy) from 1.19.5 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

Bump bottle from 0.12.16 to 0.12.20

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Bumps [bottle](https://github.com/bottlepy/bottle) from 0.12.16 to 0.12.20. Commits a2b0ee6 Release of 0.12.20 04b27f1 Merge branch 'release-0.12+cheroot' of https://github.com/juergh/bottle into ... e140e1b Gracefully handle errors during early request binding. 6e9c55a Added depr...

dependabot[bot]

I am still quite new to bioinformatics, but I am attempting to run the immuneDB docker pipeline via Singularity. I was able to use Docker on my local machine to...

Liamck

hi, Thank you very much for your software that can support igblast outputs, but I noted that this tools only support TRA/TRB in TCR analysis. Also the document says you...

haoqing12

new file added

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areensh

Error when running igblast.sh with IGL and IGK options (human)

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Hi, Thanks for this tool. It works perfectly with VH sequences, but when I wanted to try it on kappa and lambda locus, I had the following error: BLAST Database...

Elyes88

Bumps [eventlet](https://github.com/eventlet/eventlet) from 0.24.1 to 0.31.0. Changelog Sourced from eventlet's changelog. 0.31.0 IMPORTANT: websocket: Limit maximum uncompressed frame length to 8MiB https://github.com/eventlet/eventlet/security/advisories/GHSA-9p9m-jm8w-94p2 0.30.3 wsgi: websocket ALREADY_HANDLED flag on corolocal green.ssl:...

dependabot[bot]

When collapsing similar clones with the same copy number, V-identity should be used to break the tie. https://github.com/arosenfeld/immunedb/blob/24d34edbc6b732fdc2848d05d5c6919ba39fe1df/immunedb/aggregation/clones.py#L91-92

arosenfeld

MemoryError when identifying large fasta(q) files (>6GB)

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I am trying to run immunedb on a quite large dataset, with fastq file >10GB in a docker container, and memory error was shown after several minutes of waiting. I...

azuretimm

https://github.com/arosenfeld/immunedb/blob/0cfc896d7cdacfa38b7a7516b7d20cce16dfa043/immunedb/common/modify.py#L38 When swapping sample names, this duplication check doesn't avoid an integrity error.

arosenfeld