Add peak calling for FIRE into ft #94
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…ng, also need to turn that into a real peak file
…ng, also need to turn that into a real peak file
Co-authored-by: Mitchell R. Vollger <mvollger@gmai.com>
…ng, also need to turn that into a real peak file
…ng, also need to turn that into a real peak file
…s and incoperating the underlying FIRE elements so I can find the natural peak start and end
Add new `mock-fire` CLI subcommand that generates mock BAM files with FIRE elements from a BED file. Each interval becomes a FIRE element, with the 4th column grouping intervals into the same mock read. Bug fixes: - Fix score calculation overflow when quality=255 by capping at 253 and limiting max score to 100 - Fix peak merging to select representative peak by highest score instead of lowest FDR, ensuring the peak_max reflects the position with most FIRE coverage - Add hidden --min-fire-coverage parameter to call-peaks for testing with low-coverage data New files: - src/cli/mock_fire_opts.rs - src/subcommands/mock_fire.rs
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