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…NSE and fix NAMESPACE.
…n get_allele_counts
…al (#24) * Fix: corrected parameter in get_allele_counts() in preprocess_rrbs_normal() * Fix: corrected parameter in preprocess_rrbs_normal() * Added messages for each step
… Selects OT/OB and overlapping paired end reads with reduced dependency on exact BAM flags from Bismark.
Lesky47
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Feb 24, 2026
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Lesky47
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I reviewed the modified functions from main branch for RRBS and modified functions from WGBS branch in R/ directory. I skipped a line-by-line review of the WGBS additions like tests and vignettes since that branch is already verified. I tested CAMDAC v0.2.0 with 4 RRBS and 4 WGBS samples and fixed some bugs in PR28. Everything else looks good to go.
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Be sure to mention that for RRBS data min_mapq should be set to 0 instead of 1. |
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pipeline()function to enable WGBS and RRBS from one entrypoint..count..) was deprecated in ggplot2 3.4.0. #13