Add MPC to the samtools stats man page#1963
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pd3
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Thinking if it's worth explaining what "cycle number" is. It happens that people occasionally don't know what it is
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Possibly, but I used it because cycle is already in use elsewhere in the man page (about 20 times). It felt like an easy fix. If we want to replace cycle, then it ought to be its own PR as it affects the entire document rather than one field. I'm not really sure what the right phrase is anyway, as every technology differs a little bit, and sometimes it doesn't even make sense. Eg 454 (and now Ultima Genomics) use flows. A flow may give any number of bases (including zero). It just doesn't have cycle at all. ONT and PacBio are unclocked, so streaming signal and determining the base boundaries. Cycle doesn't really make snese there either. I think when stats was written Illumina was the only option and so cycles became synonymous with base positions. I guess "Nth base from 5' end" is what it means, but it's a mouthful. I'd say do it as a separate PR, if we can work out a better term to use. |
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I meant it as a small addition, e.g. |
This is a bit convoluted when it comes to what is a match and what is not. For example N in seq and N in reference is added to the "N" column. "R" in the reference is not counted as mismatch, even if the sequence is "C" (R is A or G). Matches are case insensitive. See discussion in samtools#1954
This is a bit convoluted when it comes to what is a match and what is not. For example N in seq and N in reference is added to the "N" column, as that is all sequence Ns irrespective of reference.
Conversley "R" in the reference is not counted as mismatch, even if the sequence is "C" (R is A or G). Matches are case insensitive.
See discussion in #1954