Use an adaptive distance metric #17
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- Remove `--maxdist` and replace it with a function that is dependent on the SV size - Update the grouper to use a more sophisticated variant queue - Add a tandem repeat (TR) bed input file. Variant groups that enter a TR region are automatically extended to the end of the tandem repeat.
This file was originally downloaded from the Tandem Repeats Database for hg38, "Homo sapiens HG38 (2,5,7,50, centr. excluded) Full Genome", sorted by chromosome and position. Basic filtering was applied to remove some repeats (size < 200 or match_perc < 80.5 or score < 300). The file was then converted to BED format and overlapping regions were merged.
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Switch from a fixed distance to an adaptive distance metric for clustering variants. Fixes #5.