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sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
MIT License
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DO NOT MERGE - For comparison purposes only #134

Closed cgpu closed 3 years ago

cgpu commented 3 years ago

PR incentive

This PR enables a patch for removing from Git history a large file introduced in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/commit/3fd1aebcb314b205b53492ca4e5ede9798995c91.

To be able to view the collective changes added one commit before the large file was introduced until the current state of main, a new branch was created from this one commit prior to the introduction of the file.

This commit that was the last that didn't contain the file gencode.v35.pc_transcripts.fa.gz is https://github.com/sheynkman-lab/Long-Read-Proteogenomics/commit/96ed41e9b2e39d892ddf9780c27236da86c64506.

The branch that was created from that commit is named state-96ed41e-small-bug-in-arg.

How to review:

This PR will not be merged, and will only serve to highlight the collective changes introduced after Ben's commit https://github.com/sheynkman-lab/Long-Read-Proteogenomics/commit/96ed41e9b2e39d892ddf9780c27236da86c64506 until the current latest commit which is the latest from main as of now, https://github.com/sheynkman-lab/Long-Read-Proteogenomics/commit/e10e06a0293eff5a81e14e683965e3bfc4a4d3eb.

After @gsheynkman @bj8th confirm that these are indeed all the changes, we can apply them to a branch named cgpu-patch-for-large-file-del.

Subsequently, the main branch will change. We will remove all of the commits up until Ben's last commit to erase the existence of the file from the git history to clean up and make the repo lighter.

Lastly, all of the changes that we retained in the branch cgpu-patch-for-large-file-del will be added onto main via a PR.