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.mosdepth.region.dist.txt missing values? #190

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adamrtalbot opened this issue Dec 6, 2022 · 0 comments
Open

.mosdepth.region.dist.txt missing values? #190

adamrtalbot opened this issue Dec 6, 2022 · 0 comments

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@adamrtalbot
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I think this is expected behaviour or there might be a setting but I can't find how to change it.

The *.mosdepth.global.region.dist.txt and *.mosdepth.region.dist.txt are missing values between the integers. Tools like MultiQC then ignore these missing values, or treat as zero etc. For example: cat sample1.mosdepth.region.dist.txt | grep -e '^total' | tail -n 302 | head -3:

total   414     1.00
total   300     1.00
total   299     1.00

The missing values between 300 and 414 cause MultiQC to give this a coverage of 0. Obviously, it can be handled, but is there a setting just to export all values? I know the output will balloon in size but I'd rather retain data where possible.

adamrtalbot pushed a commit to adamrtalbot/MultiQC that referenced this issue Dec 7, 2022
Changes:
 - Mosdepth output has missing values in *.{region,global}.dist.txt
 - This change to module fills any missing values with the next value
 - e.g., if there is 100% at 100X and 80% at 80X, the value at 90X will be recorded as 80X
 - This may underestimate coverage slightly but it's not clear from MosDepth docs how it should be handled.
 - See brentp/mosdepth#190
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