Add notion of eligible reads to GAM comparison #4220
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I think bb379b4 will fix CI; it seems like it broke because the R we were using could no longer install the R packages we use for the plots. |
…ns of the packages the plotting scripts need
adamnovak
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This makes sure aligner is always a factor so we can do the name surgery we do on it in newer R versions.
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Changelog Entry
To be copied to the draft changelog by merger:
vg gamcomparenow keeps track of whether reads could have possibly been gotten correct, based on there being a truth position for them in the truth set, and excludes reads without a truth from plots and accuracy statistics.Description
This should help with cases where we want to simulate reads from a sample that doesn't 100% align along the reference we are using for coordinates for accuracy measurement. Reads from diverged parts of the sample that can't be given correct linear coordinates won't be used when assessing accuracy.