Change win.ia algorithm #181
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This further addresses #179 This "works" at the moment, but tests do not pass, but since I'm going to change the logic for how chromosome boundaries are set up, I will need to most likely rewrite the tests.
This addresses #179
This addresses #179 [skip ci] The current tests will not pass.
This addresses #179 [skip ci]
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This PR has been approved in #179 and will be merged. |
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The windows will now always start at position one on any given chromosome.
This will result in some windows at the beginning of chromosomes having a
value of
NAif the first variant starts beyond the first window.Windows are now calculated for each chromosome independently. The previous
version first concatenated chromosomes with at least a window-sized gap
between the chromosomes, but failed to ensure that the window always started
at the beginning of the chromosome.
(see Error using win.ia function in poppr #179).
Additionally, a penalty for users who don't define repeat lengths for Bruvo's distance is included.