Possible bug: chrX coverage suppressed after update to include chrY

[AyalYakobe]

Describe the bug

After updating dryclean to include chrY support, chromosome X coverage appears to collapse after denoising.

• Raw foreground coverage shows signal on chrX.
• After denoising, chrX coverage is abnormally low, unlike other chromosomes.
• This suggests that chrX processing may have been broken by the recent changes.

To Reproduce

Steps to reproduce the behavior:

1. Run dryclean on tumor sample data.
2. Generate coverage files (cov.rds).
3. Inspect foreground.log vs. signal.
4. Compare chrX coverage before vs. after denoising.

Expected behavior

Chromosome X should retain comparable coverage signal after denoising (relative to raw foreground), similar to other chromosomes.

Screenshots:

These are split by bins and not chromosomes but rest assured that the tail end of the graph is actually the X chromosome.

Desktop:

• OS: Red Hat Enterprise Linux 8.6 (Ootpa)
• Kernel: Linux iscb011.mskcc.org 4.18.0-425.19.2.el8_7.x86_64
• Platform: x86_64 (HPC cluster)
• R version: 4.4.3 (2025-02-28) -- "Trophy Case"
• Environment: conda (dryclean_env)
• BLAS/LAPACK: OpenBLAS 0.3.30, LAPACK 3.12.0
• Timezone: America/New_York
• Browser: N/A
• Version: N/A