Fix collapse_annotation.py KeyError on UCSC GTFs missing transcript_type

[dksenthil]

Summary

• UCSC GTFs (e.g., mm10) lack gene_type/transcript_type attributes that the GTEx pipeline's collapse_annotation.py expects, causing a KeyError in the rnaseqc2 step
• Added a local patched copy (genpipes/tools/collapse_annotation.py) that defaults missing types gracefully and warns about UCSC annotation limitations
• Updated genpipes/bfx/gtex_pipeline.py to use the local script instead of the module-provided one

Test plan

• Run rnaseq pipeline with mm10 UCSC GTF and verify collapse_gtf step completes without KeyError
• Verify warning message is printed for UCSC GTFs missing type attributes
• Confirm no regression with GENCODE/Ensembl GTFs that already have gene_type/transcript_type

[MareikeJaniak]

Thanks for doing this, Senthil. We might want to think about adding the script to c3g_tools instead of having it in the genpipes tools directory. The genpipes tools directory is more for tools that are genpipes specific, whereas script like collapse_annotation.py are usually housed under c3g_tools. What do you think, Paul?

[paulstretenowich]

I agree with Mareike.