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max-depth and high-depth options #643

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@SchwarzMarek

Could you please clarify how exactly:
--max-depth and --high-depth options now (v0.6.4) work in modkit pileup?

In the documentations for 0.6.4 in section Migrating to Modkit v0.6.0+ pileup states:

"--max-depth removed. Modkit v0.6.0 has a new algorithm that doesn’t use max-depth. If you have a modBAM with very high depth and you don’t want to tabulate counts for this depth it is currently recommended to subsample the modBAM before using Modkit."

Since v0.6.4 has "--max-depth", does the "new algorithm" apply only to v0.6.0?

"In Modkit versions v0.6.0 and v0.6.1 pileup will saturate depth at 65,535 (maximum for a unsigned 16-bit integer). If your modBAM has a depth greater than this value, it is recommended to use the --high-depth flag so that 65,535 reads will be used at each genomic position."

Does it mean that the coverage is hard-set to "65,535" if --high-depth is used? And which has precedence if --high-depth and --max-depth are used concurrently?

Thank you for clarification
Marek

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