Sfitz add mosdepth quantize #88
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…M into merge-test
| mosdepth_quantize_use_fast_algorithm: | ||
| type: 'Bool' | ||
| required: false | ||
| default: false | ||
| help: 'Use fast algorithm for quantizing coverage values' |
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question (non-blocking): Is there a downside to enabling the use of the fast algorithm by default?
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Yeah, this is a difficult decision. Not using fast mode gives more "correct" results. Fast mode ignores paired read overlaps and CIGAR strings (thus indels wrt ref). Ignoring the paired read overlap is the bigger issue, especially for samples with small insert sizes (wrt read length). This is noted in the README. The time difference isn't clear as I haven't benchmarked more than a few samples and not directly on scratch. It's enough that the mosdepth author recommends fast mode for most use-cases (I assume non-small insert cases). We currently have fast mode true by default for the regular mosdepth coverage calculation, so we should probably change one or the other to make them consistent.
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That's fair, we can gather more data as needed and then make a decision
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Test path within initial description has been updated for new test results. |
Description
Testing Results
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