Small improvements

[anderdnavarro]

I have changed three things:

1. I have added the option to allow the user to change the default predictions_DeepTumour.json output name with the --outName tag
2. LiftOver chain file was prepared for chr1 prefix style chromosomes only. I have added a new file without the chr prefix.
3. In the Readme, the Local Environment section specifies Python 3.10, but we use Python 3.9 and there are some packages that are not supported for Python 3.10. I have specified Python 3.9 because it's also the one used for the Docker image.

[lstein]

Nice that you are working on this! Lincoln

…

On Wed, Sep 30, 2026 at 1:22 PM Ander ***@***.***> wrote: I have changed three things: 1. I have added the option to allow the user to change the default predictions_DeepTumour.json output name with the --outName tag 2. LiftOver chain file was prepared for *chr1* prefix style chromosomes only. I have added a new file without the *chr* prefix. 3. In the Readme, the *Local Environment* section specifies *Python 3.10*, but we use *Python 3.9* and there are some packages that are not supported for Python 3.10. I have specified Python 3.9 because it's also the one used for the Docker image. ------------------------------ You can view, comment on, or merge this pull request online at: #11 Commit Summary - a2028d2 <a2028d2> Allow user to change output file name - a895471 <a895471> Fix a liftover issue when reference and vcf don't have the same chrom prefix - b5e72ca <b5e72ca> Update requirements in the readme File Changes (4 files <https://github.com/LincolnSteinLab/DeepTumour/pull/11/files>) - *M* README.md <https://github.com/LincolnSteinLab/DeepTumour/pull/11/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5> (2) - *A* requirements/hg38ToHg19_nochr.over.chain.gz <https://github.com/LincolnSteinLab/DeepTumour/pull/11/files#diff-159c8f870fb6c0f92685e3cf0e2b9b9290074c8b51cb198f75d19b641a477370> (0) - *M* src/DeepTumour.py <https://github.com/LincolnSteinLab/DeepTumour/pull/11/files#diff-76b99144f6e732743b38e81d9da27602bc23ceb5edf43b5771f34224642c4356> (8) - *M* src/utils.py <https://github.com/LincolnSteinLab/DeepTumour/pull/11/files#diff-51246e53255db77c9edad496f074aa1bdbf8dbdc11f89a02040115c9ab4fa7f0> (10) Patch Links: - https://github.com/LincolnSteinLab/DeepTumour/pull/11.patch - https://github.com/LincolnSteinLab/DeepTumour/pull/11.diff — Reply to this email directly, view it on GitHub <#11?email_source=notifications&email_token=AAA3EVMBO4KFXVDBPXZQPJD5RU6ORA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF42DMOJTG43DGNBZGOTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVRTG633UMVZF6Y3MNFRWW>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAA3EVM7SL7L6YRFDFDZMC35RU6ORAVCNFSNUABFKJSXA33TNF2G64TZHM4TMNZWGQZDAMZXHNEXG43VMU5TKNRVGAZTKNRZGI32C5QC> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[anderdnavarro]

With the last two commits, I have:

1. Added debugging files to build a Dev Container in VS Code and use its default debugpy engine for faster and easier debugging.
2. Fixed an error while filtering the VCF that caused DeepTumour v3.0.5 to always predict "CNS-PiloAstro".

In more detail, the last two DeepTumour updates used an extra filtering step to keep only "PASS" mutations. However, the allel.vcf_to_dataframe() function we use to read the VCF considers the field FILTER == '.' as FAIL. Having FILTER == '.' is common in many VCFs, and OncoGAN produces VCFs in this format. Therefore, I have added a step to update the FILTER field from . to PASS before using the allel.vcf_to_dataframe() function, avoiding the removal of all mutations in these cases.

[anderdnavarro]

I have checked that this version works and have nothing else to add. If everybody agrees, I think this pull request is ready to be merged.